Mercurial > repos > bgruening > bismark
changeset 13:f211753166bd draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d
author | bgruening |
---|---|
date | Tue, 30 Jul 2019 06:30:36 -0400 |
parents | 78c791a11b4c |
children | b6aa3b6ba129 |
files | bismark2report_wrapper.xml bismark_bowtie2_wrapper.xml bismark_deduplicate_wrapper.xml bismark_methylation_extractor.xml test-data/dedup_reads.bam test-data/input1.fq test-data/input1.fq.gz test-data/input1.fq.gzip test-data/mapped_reads.bam test-data/mapped_reads_short.bam test-data/mapping_report.txt test-data/mapping_report_short.txt test-data/output_html_report.html test-data/output_splitting_report.txt test-data/summary.txt test-data/summary_short.txt |
diffstat | 16 files changed, 4699 insertions(+), 79 deletions(-) [+] |
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--- a/bismark2report_wrapper.xml Wed Jun 05 07:44:26 2019 -0400 +++ b/bismark2report_wrapper.xml Tue Jul 30 06:30:36 2019 -0400 @@ -1,9 +1,9 @@ -<tool id="bismark_pretty_report" name="Bismark Pretty Report" version="0.20.0" profile="17.01"> +<tool id="bismark_pretty_report" name="Bismark Pretty Report" version="0.22.1" profile="17.01"> <description>Generates a graphical HTML report page from report outputs of Bismark</description> <requirements> - <requirement type="package" version="0.20.0">bismark</requirement> + <requirement type="package" version="0.22.1">bismark</requirement> <requirement type="package" version="1.8">samtools</requirement> - <requirement type="package" version="2.3.4.2">bowtie2</requirement> + <requirement type="package" version="2.3.5">bowtie2</requirement> </requirements> <command><![CDATA[ python '$__tool_directory__/bismark2report_wrapper.py'
--- a/bismark_bowtie2_wrapper.xml Wed Jun 05 07:44:26 2019 -0400 +++ b/bismark_bowtie2_wrapper.xml Tue Jul 30 06:30:36 2019 -0400 @@ -1,11 +1,47 @@ -<tool id="bismark_bowtie2" name="Bismark Mapper" version="0.20.0.3" profile="18.01"> +<tool id="bismark_bowtie2" name="Bismark Mapper" version="0.22.1" profile="18.01"> <description>Bisulfite reads mapper</description> <requirements> - <requirement type="package" version="0.20.0">bismark</requirement> + <requirement type="package" version="0.22.1">bismark</requirement> <requirement type="package" version="1.8">samtools</requirement> - <requirement type="package" version="2.3.4.2">bowtie2</requirement> + <requirement type="package" version="2.3.5">bowtie2</requirement> </requirements> <command><![CDATA[ + #if $singlePaired.sPaired == "single": + #if $singlePaired.input_singles.ext == "fasta": + #set read1 = 'input_1.fa' + #elif $singlePaired.input_singles.ext in ["fastq.gz", "fastqsanger.gz"]: + #set read1 = 'input_1.fq.gz' + #else + #set read1 = 'input_1.fq' + #end if + ln -s '${singlePaired.input_singles}' ${read1} && + #else: + #set $mate1 = list() + #set $mate2 = list() + #for $mate_pair in $singlePaired.mate_list + $mate1.append( str($mate_pair.input_mate1) ) + $mate2.append( str($mate_pair.input_mate2) ) + + #if $mate_pair.input_mate1.ext == "fasta": + #set read1 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1)) + '_1.fa' + #elif $mate_pair.input_mate1.ext in ["fastq.gz", "fastqsanger.gz"]: + #set read1 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1)) + '_1.fq.gz' + #else + #set read1 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1)) + '_1.fq' + #end if + ln -s '${mate_pair.input_mate1}' ${read1} && + + #if $mate_pair.input_mate2.ext == "fasta": + #set read2 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1)) + '_2.fa' + #elif $mate_pair.input_mate2.ext in ["fastq.gz", "fastqsanger.gz"]: + #set read2 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1)) + '_2.fq.gz' + #else + #set read2 = re.sub('[^\s\w\-]', '_', str($mate_pair.input_mate1)) + '_2.fq' + #end if + ln -s '${mate_pair.input_mate2}' ${read2} && + #end for + #end if + python '$__tool_directory__/bismark_wrapper.py' ## Change this to accommodate the number of threads you have available. @@ -29,7 +65,7 @@ ## #if $singlePaired.sPaired == "single": - --single-paired '$singlePaired.input_singles' + --single-paired '${read1}' #if $singlePaired.input_singles.ext in ["fastq", "fastq.gz", "fastqillumina"]: --phred64-quals @@ -41,12 +77,6 @@ #end if #else: --mate-paired - #set $mate1 = list() - #set $mate2 = list() - #for $mate_pair in $singlePaired.mate_list - $mate1.append( str($mate_pair.input_mate1) ) - $mate2.append( str($mate_pair.input_mate2) ) - #end for --mate1 #echo ','.join($mate1) --mate2 #echo ','.join($mate2) @@ -407,7 +437,7 @@ <param name="genomeSource" value="history"/> <param name="own_file" value="mm10.tiny.fa.gz" /> <param name="sPaired" value="single"/> - <param name="input_singles" value="input1.fq.gz" ftype="fastqsanger"/> + <param name="input_singles" value="input1.fq.gzip" ftype="fastqsanger.gz"/> <param name="sort_bam" value="false"/> <param name="settingsType" value="custom"/> <param name="suppressed_read_file" value="true"/> @@ -427,6 +457,30 @@ <output name="report_file" file="mapping_report.txt" ftype="txt" lines_diff="6"/> <output name="output" file="mapped_reads.bam" ftype="qname_input_sorted.bam" lines_diff="14"/> </test> + <test> + <param name="genomeSource" value="history"/> + <param name="own_file" value="mm10.tiny.fa.gz" /> + <param name="sPaired" value="single"/> + <param name="input_singles" value="input1.fq" ftype="fastqsanger"/> + <param name="sort_bam" value="false"/> + <param name="settingsType" value="custom"/> + <param name="suppressed_read_file" value="true"/> + <param name="unmapped_read_file" value="true"/> + <param name="bismark_stdout" value="true"/> + <param name="isReportOutput" value="true"/> + + <output name="output_stdout" file="summary_short.txt" ftype="txt" lines_diff="80"> + <assert_contents> + <has_text text="Sequences analysed in total:" /> + <has_text text="1000" /> + <has_text text="Mapping efficiency:" /> + <has_text text="0.8%" /> + <has_text text="Bismark run complete" /> + </assert_contents> + </output> + <output name="report_file" file="mapping_report_short.txt" ftype="txt" lines_diff="6"/> + <output name="output" file="mapped_reads_short.bam" ftype="qname_input_sorted.bam" lines_diff="14"/> + </test> </tests> <help>
--- a/bismark_deduplicate_wrapper.xml Wed Jun 05 07:44:26 2019 -0400 +++ b/bismark_deduplicate_wrapper.xml Tue Jul 30 06:30:36 2019 -0400 @@ -1,9 +1,9 @@ -<tool id="bismark_deduplicate" name="Bismark Deduplicate" version="0.20.0" profile="18.01"> +<tool id="bismark_deduplicate" name="Bismark Deduplicate" version="0.22.1" profile="18.01"> <description>Deduplicates reads mapped by Bismark</description> <requirements> - <requirement type="package" version="0.20.0">bismark</requirement> + <requirement type="package" version="0.22.1">bismark</requirement> <requirement type="package" version="1.8">samtools</requirement> - <requirement type="package" version="2.3.4.2">bowtie2</requirement> + <requirement type="package" version="2.3.5">bowtie2</requirement> </requirements> <command><![CDATA[ python '$__tool_directory__/bismark_deduplicate_wrapper.py'
--- a/bismark_methylation_extractor.xml Wed Jun 05 07:44:26 2019 -0400 +++ b/bismark_methylation_extractor.xml Tue Jul 30 06:30:36 2019 -0400 @@ -1,9 +1,9 @@ -<tool id="bismark_methylation_extractor" name="Bismark Meth. Extractor" version="0.20.0" profile="18.01"> +<tool id="bismark_methylation_extractor" name="Bismark Meth. Extractor" version="0.22.1" profile="18.01"> <description>Reports on methylation status of reads mapped by Bismark</description> <requirements> - <requirement type="package" version="0.20.0">bismark</requirement> + <requirement type="package" version="0.22.1">bismark</requirement> <requirement type="package" version="1.8">samtools</requirement> - <requirement type="package" version="2.3.4.2">bowtie2</requirement> + <requirement type="package" version="2.3.5">bowtie2</requirement> </requirements> <command><![CDATA[ python '$__tool_directory__/bismark_methylation_extractor.py'
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input1.fq Tue Jul 30 06:30:36 2019 -0400 @@ -0,0 +1,4000 @@ +@1_1 +TTGTATATATTAGATAAATTAATTTTTTTTGTTTGTATGTTAAATTTTTTAATTAATTTATTAATATTTTGTGAATTTTTAGATA ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEE +@1_2 +TAATTTTGAATTTTGGTTGGGTAGTTTGTTTTAGAATTATTATGGTTATATAGTTTTTTAGTAAGATTGTTATTTATTATTTGAT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEAEAEEEAEEAE +@1_3 +TTGGTGGGGGTGTGGAAATTTGTATTGTGTGGATTTTTATTGAATATGGATAAAGAGTTAAGAGTTGGGTTGTAAAGTTAAGGAT ++ +AAAAAEEEEEAEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEAEEEEEE/EEEEEEEEEEEEEAA<EEEEEE +@1_4 +AAGTGGTTTTAAATGGTTTAAGGTTAAATTAGATAGATAAGGTTTGGCGTGGATTATATATTATTGTAGAATTATTTTTTGTGTA ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEAEEEEEEEEEEEEEAEEEEEEEEEEEEE/EAAEEEE<E +@1_5 +TGAGGAATTGAATTTAGTTTTAGAATTTTATAGGGATTTATTTGTTTTTTTTTTGGTTGAGTTATTGATTTTTAATTTTGTAAAT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAE<E6//AE/AEA<6EEAEAE/EEA/E<EE6 +@1_6 +TGTGGTTAATTGGAAGTGATTGAAATTATAGAAGTGAATTTTTGGATAATGGGTATTAGTGTATTTAGAGTTATGTATGAGAGAT ++ +AAAAAEEEEAEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<E<EEEEEEEEEAEAEEEEEEE +@1_7 +GATGATGGAGAAGGATTTAGTTTATTGTTGGTGGGGTTATTGTTAGGATGGTATTTTTGAGTTTAATAAGAAAGTAATTTTAAGT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEE/EEEE +@1_8 +GTGTGGGGTTTTGGGGTGAATTTTAGTTTATAGGTTATTTTAGTGTTTAAAAAATGAGTTTTTTATTTAAATAGTGGGAGGAGAT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEE6/EEEEEEEEEEEAEEEEEEAEEEAEEEEEEEEEEEEE +@1_9 +ATTAAGGGGAGATATCGGATTTTTGTTATGTAGGGATTTTATTGTTTTAATGTTATTTATAGTTTTAAAGTTAATGGGTGGGTAT ++ +AAAAAEEEAEEEEEEE/EEEAEEE6EEEEEEEEEEEEEEEEEEEAEEEEEEE/EEEEEEEE<EEEAEEEE/EEE/AAAEAAE/E/ +@1_10 +AGGTGTGAAAGGTAGTTGTGGATGTTTTTGTTTTTGGTTTATTTTATTAGGTTGAAGGGGTGGGGGAAGGGGTGGGGTGGGGGAA ++ +6AAAAEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE +@1_11 +GACAGGTTATGAATATTAATATGGTTTTAGCAATAGTAGGGATTACGGATATTAGTATGGTTTTCTGTAATAGTACAGATTATTG ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEE/EE<6EEEEEEE/EEEAEAEEEA/EEAE +@1_12 +CAGGACGTGAAATATGGCGAGGAAAATTTAAAAAGGTGGAAAATTTAGAAATGTTTATTGTAGGAGGTGGAGCTCGGAAGCGAAC ++ +AAAAAEEEE/EEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEAEEEEE/<6EEEEEEEEE/EEEEE<///EE/A/E//EA +@1_13 +CCCCGTATGTATGTTATAAATAATGGGAATTTTTTTTTAAATATAGGGATTAGATATATTTAATTAATAAATATTTATTATAAAA ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE +@1_14 +TACAGTCTTTGGTTAATTAGTTTAAATAAGATTAATTTGGAGGGAAGAAGAGTGTAGTAGTTTGATGGTATTTATAGGTTTATAG ++ +AAAAAEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEE +@1_15 +ATGTAGCGGGATTTGGTAATGTGTAAGGGTTATTTAGGTGGTATTGGTTTTGAAGGTATGAAGGGGTTACGTAGAGCAGTTGAGG ++ +AAAAAEEEEEE6EEAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEE<EEEEEEEEAEEEEEEEAAEEEAEAEEAEAEEEEEEEE +@1_16 +TGATAGGATGTATGGGACAATTTTAATATTTTTGTATTTGTTGAGGTTTGTTTTGTGATTAATTATATGTTTAGTTTTGGAGAAG ++ +AAAAAEEEEEEEEEEEEEEEEEAEEEEEEAEEEE/EE/AEEEEEAEA/EEAEEEEEEEE/EEEEE<EEEAEEEAAA/EEEEEEAA +@1_17 +GAAAGTAGATTGGAGATTTTGTAGTTTGGTAGGTGTTTTAGGGTATTTATTATTAAAATAAAAGATAGTTTTTGTTTATAGAAGG ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEE +@1_18 +GGTTTTAAAGAGATTTGTTTATTTGTTTATTGAGGTTAAAAAAAGTTTTGTAAATATAGATAAGTATTGGAGTAGTTAGGAAAGT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEAEEEE/EEE +@1_19 +TATGTAGATTAAGGTTGTTAGTGTATTTGTTTAGTTTGGGAATATTTTTATTGGTTTTTTTAGGGATATATTAATGAGTAGTGTA ++ +AAAAAEEE/EEEEEAEAEEEEEEEEEEEEEEEEE/EEAE/EEEEE//E/EEEEE<<A<A<EEE6EE/EEEEAEEEAEAAEE/EEE +@1_20 +TGTGGGGTATAGTATAAATAACGTTTTATTGGGTGTTGGTTTGGTGTTGTTATGTTTTTAAATATTGGTTTTTAAGTTTTGGTTG ++ +AAAAAEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE6EEEEEEAEEEEEEEEEE/EEEAAEEEEEEAE<EEEAA +@1_21 +CTACAGGATGGGAGAAGATTTTTATAGTTATATTTTAGGAAATGGGTTAATATTTAGAATATGTAAAATTTTATTAAATATTTTA ++ +AAAAAEEEEEEEEEAEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEA<EE<EEEAEEEEAE +@1_22 +AAGGGTTTTTTGTTTTTATAAGAGTTGAGTTATGGTTATATTTTTTGTTTTTTATGAATAATTGGATAAAATTATGTGAAAGTTT ++ +AAAAAEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEAE +@1_23 +AGTTAGCTTGGATTTTATACATTTTTGGAATTAGTTAGTTATAGGTAAGTTTTTATTGAGTTAGAAATGGTAGAGGTATTATGGG ++ +A6AAAA6A//EE/E/E6AA/EAEEE6A/EEE/E///E/E/AAEEEEEE/E//6AE/EEEEE/E/EAE/<E<EEEEE/EE////AE +@1_24 +AGTAGTTTTTTTTGTAGTAGTATTCGGGTTTATGGGTAAGGGAATGTGAATTAAATTAAGGAATTTTGTGAAATATGAATTGTTT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEAEEEAAE +@1_25 +TGGGTCATAGAGATTGTGGAGGTTTTAGAGTTTATTCGTAGATAGGTATATGGTGAGGTTAAGTTTGTTTTTTAGTTTTTTAATT ++ +AAAAAEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEAEEEE +@1_26 +AGATGATTTAGTGGTTAAGAGTATTGATTGTTTTTTTAGAGGTTTTGAGTTTAAATTTTAGTAATTATATGGTGGTTTATAATTA ++ +/AAAA//EA/EEEE6EEEEEEEA/EAE/EEAE<//AEEEEEEEE//E/<AEAEEE66AEEEEEEEEEEE<6E6EA<A</EAAE</ +@1_27 +GTAAATATAAAAATAATTTAGATTTTTATTTATGAGTTTTTTGTTAATTATTTTTTTTTTTCAATAAACACAAACACAAATTCAA ++ +AAA///6A/AE/EA//AAE/EEE66E6EEEA/EE/EA//</<EAA/E6//////////////EA//AE//<EEEAE/EEE///A/ +@1_28 +GGTTTGTTTTGGGAATGTTGATTTATTTGTTTGAAAGATAAAATTTTGAAAGATAGTGAGAAAGATCGGAAGAGCACACGTCTGA ++ +/AAAAEEE/AAEEEAE/EEAEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEA/AEEEEAE/E<A/E//<AA +@1_29 +GTACTATTTCAGGTTTTTTAGTGTTTATTTTTTATTTTTTACGTTTTTGTGATTTCTCTATTTTTTAAGAGCTGCCGAGCCCCCC ++ +AAAAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE6/E///EA////E/EEEA/////<A/////E/EEEE/ +@1_30 +ATATATATAGTTATATTAGTAGAAGTAGTTATTTTTTAGTTTTTTTGGTGTTGATATTTTATAATTTTGTTTAGAGTTAATATTT ++ 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+AAAAAEEAEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEE/EAEEEE/EAEEEEAEEEAEEEAAE<EA<EEEE6 +@1_36 +TATAAATACGGATTAAATAAATATAAGGGAGTTAGGTGAAAGGTTTTTTTTTAGGAAGTTTAATAGTATATTTATGAAGTGTAGT ++ +AAAAAEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEAEEEEEAEEEEEEAEEEEEE +@1_37 +GCTATCACCTGTATCTTATTCTCACACATACCAACCATAACATATATACATTTAATAAATTATTTTTGTTATTACGTATTTTTAA ++ +AAAAAEEE/EEEEEEAEEEEEEAAEEEEE/EEA/AAEEEEEEEEAEEEAEEEEEEEEEEEEEEAEEAEEEAEEE<EEEE</<AEE +@1_38 +ATGGAGGAAATTTGGGTATAAGTTTTTTAGTGATAGTTTGTTTGATTAGCGGTATAAGTTTTTTGATTTGTTAATAAGTTAAAAG ++ +6AAAAEEEEE/AEEEEEEEEEEEEEEEEEEEEEAEEE/EAEEEEEEEEEEEEEEEEEEEA/6/EEE/EAE/AEE<EEEE<EEEEE +@1_39 +TGAAAAGTATAGTATGGTGTAAATGGGAGGGATATTATAATAGTTAATTAATTTTGTGGTATTGATTTTTTTTTTATTTGATTGA ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEAAEEEEE +@1_40 +AGGTAATGATAAAAAGAAGAAAAAAGTTTTTTTAGAAGATTTTATTAATTATTTATGTAATGTGAAATGATTAGTTTTGAAAGAT ++ 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+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEA +@1_506 +GTGTATAGATGGTAAGGTATTTAGATATTATTTATTTAGTTATTTTAGAATATGTTATGGGAGGTTAGAAAGATTTTAATGTTAG ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEAEEE/EEA//AEE/AEEAE/EEEAE//E +@1_507 +TAGTAATTGTAATAAAAGATTATATGGGAAAGAGGTAATATTTGTGTTTAAAGTAGATTTGGTGGTTGGTTTTGGGTGTGTGGGG ++ +AAAAAEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE/<EEEEEEEEEEEEEA +@1_508 +GATTGATAAAGGTGTTTAGTTCGTATTTTTTGTTTTGAGAGAAGTGAGGGAGTGGGGGAGAAAATGATTTATTATGATGTGGATG ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEA +@1_509 +AAGGGGTAAGTTAGGCGTGGTGGTATATTTTTTTAATTTTAGTATTCGGGAGGTAGAGGTAGGCGGATTTTTGAGTTTGAGGTTA ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEA +@1_510 +AAGATAGGATTCGGGTTATATTATTTATTATTAAGGATATTTTTTTATTTGATTATTTTATTGGGCGATTGAGGTTATTGTTCGT ++ 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+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEE/EEE<EEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEE/E/EE +@1_961 +ATTAGTGAATATATTTAGTTTGAGGTATGTTTATTTTTTTGTGGGTGTAATGAGATTAAAGTTTAAAGAAATTTTTTTGTTTGGT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEAEAAEEEEAEEEEEAE/AEEAAEEE<EEEEE +@1_962 +GTAGGAGTTGAAAAGAATTTAGATGTTGTTTAAAAGAGGAATGGATATAGAAAGCATTTTTAATGTTTTTTTGAAGTTATTTTTT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEE<E<EAEEAEEEEAEAEEEEEEEEEEEEAEEE +@1_963 +AGCAGGTAGGAGGTTGTGTAGATATTGAGAAATAATTGTTATAAGTTATTTGAGTAGTTTGGTAATTAGAGGTTGGGTTATAAAG ++ +6AAAAEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAE/EEEEEAE6E<EEEEEAAEEEEEAAEEEEE<EEEEE +@1_964 +GGTGTGTAGGGTATTTACGTAGAGATTGGGGTAGTTAGTTGCGGGAGGGTGTGTGAAATTATTTGGTTATTTGAGAATATGAATA ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEEEEEEEEEEE +@1_965 +TTTAGGAGTAGGTGTGTTATTGTGGGTGTGGATTTAAGATTTTTATTTTGGTTATTTGGAAGTTAGTTTTTTTATTAGTAGTTTT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEAEEEEEEAEEEEEEEEEEEAEEEEEAEEEEEEEEEEEAEEEEE/EEEEEEEEEEE<EEE +@1_966 +CTATGGTTGAGAAGATAAAGTTAAAGTTAGAAGTTTATTTTATAGTTATAAAGAAATGGAAAATATGAGTAGAATAGTTAAGAAA ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE +@1_967 +TGGTGTTTGTGGTTTTTTAGTTTTTGCGGTAGAGGTTTTTGTTAGTATTATGAATTGTGTTTGTAGTAGATATTTTAAGTTTTTA ++ +AAAAAAEEEEEEEEEEEEEEEAEEEEEEEEEEEEEAEEEEEE/AEEEEEEEEEEEEEEEAAEA<EEEEEEAAAEE/EEEEEAEEE +@1_968 +ACGGGGATATTTGTATTTTGGTATTTAGGGGTTTTATGGAGAGTTGGTCGTATAAGTGAGGTTGATTTTAGATTTTAGTTTTTTT ++ +6AAAAEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEAAEEAEEAEAEAE/E/EEEEAEAEEEE +@1_969 +GTGGTGTTTATATTGTGATGGGTTGTTTTTTCGAATTATGTGTAAAAGTAAGTATTTTTAAAGTGTTGTTTAGTGGTTATTTGGT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEEEEEEEEEEE +@1_970 +ATGGTAGATTGTTTTTATGATTTGATATGTTTTTTTAATTTTATTTATTTTATTTAGTTTTAAATGTTTGAATTTGAGGTTGTAT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEE +@1_971 +ATTAGTGGTATGTTTATTTTGGTTTTTTTGTATTAAGAGTAGTTTTTATTAGTATTTTAATGTTTATATTAGATAGGGATTGAAT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEAEEEEEEEEEEEEEEE +@1_972 +CCATATCGGTTTTTTTGTTTTTTATTTGTTTTTTGTAGTTTTGGGGATTGAGTTTAGGGAGTTGTGTGTTAGGTAAGTATTTGAT ++ +AAAAAAAEEEAEEEEEEEAEEEEEEEE<EEEEEEAEEEEEEEEEAEEEEEEEAEEEEEEEEEEAEEAEEEEEEEEEEEEEEEEE/ +@1_973 +AGTTAGTTTTTATTTTAGTGGAGTAAGTTGTTGTGTATTTTGTAAAATGAAATATTAAGTTTGATATTTTTGTAGAGTTATAAAA ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEAEAEEAEEEEAEEEEEEE +@1_974 +TGGTATAAAGAAAAAGATAAATTTTGTGTATGTTGTTTTAGTTTATTTATTTAATAATTTTTTAATATTTTTGAAAAAAAATGTT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAEEEEEEEEEEEEE +@1_975 +GGGGAAGATGGAGGTTTAGATAAATATTTATTGTTAGTAAACGAAGTTTTTAGTTTTAGTATTGGGTTATAATTTTTCGAATTGT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEAEAAEAEEEEA +@1_976 +TGGTAGATGGGTTAAAGTTTTTTTTTTATTTTAGATATATGAATTGAGTATTTAATGATTTGTTTTTTTTTTATTTTTTTTATCT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEE</EEEA//<E</<AAEEEA//E6E<EEEEE/</E +@1_977 +ATGTGAGTTTTGGGTTAGGTTTGTATTTTATTTAATAGGGTTGACGTGATAGTATGTTGGATGTGGGAGATCGGAAGAGCACACG ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEE<E6A<E/E +@1_978 +TGGGATTTGAAATGTATTGATATATGAATGTAGATTTATGTATGGTATTTAATATATAATTTAGGGATGGGTAAATGATATTTTA ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEAEEEEEEE +@1_979 +GAATATGTAGTTAGAGTTAAGAGTTTAGGGGTATTGGTTAGTTTATAATGTTGTTTCATTTATAGGGTTGAAGATTTTTTTAGTT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEEEEEEE6EEEE/EEEEEEEEEAEAEE6AAEE<EAAAAE<EAEEEAE +@1_980 +CAGATGATCGAGATTTGTAAGGATGGATTTTAGAAGGGAATATAAGTTAAAATTAATATAATTTAGGAATAGAATTGTAAAATTT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEAEEEAAEEEAEEEEEEE +@1_981 +TGTAAGTTTTGGATATGGAATTTATATTATTATTTATGTGTTAGAATTTTATGTTTTTAAATTATAGTTGAAAAAATAGTTGGTT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE +@1_982 +AATGTGGTGGTTTGGTGGTATATGTTTCGAGTTTTAGTATTTAGGGTAGATATAGGTAAATTTTTTTGAGTTTGAGGTTTGTTTT ++ +AAAAAEEEAEEEEEE6EEEEEEEEE/EEAAAEEEEEAEEEEEEEE6EEEEEEEEEE/EEEEEAAEA/AAE<E<EE/EAAE/EEEE +@1_983 +ATGGAAGAGTGGGTAGAAAGATTATAATAGGTAGAAATAGTATGTATTTGTAAAAATAATTTTTGAGTATGATATGGTTATTGTA ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE< +@1_984 +GTGGTTACATGTATTGGGTTTTTGAGGTGAAGGTAGGAATAGTAAGGGAGGAAATGGTAAGAGAAGAAAGGAGATTAAGATAGAT ++ +AAAAAEEEEEEEEAEEEEEEAEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEE/AEEE/AEEE/ +@1_985 +TGATAGGTTGTTATTTTTTAAAAGAATATTTGTGATTAATTTTATTTTAGACTCTTATTTTTATGTTATTTTTTCTATTACTTAT ++ +AA/AA//EE/EEEEEEE/E///A//EA6E6E/E/E////EE///AEEE//E<E/EE/E<</E//EEA//6/E/A/A/E/E//E/E +@1_986 +TTGTAGGTTAGAATAGTAGGTTTGAGTAAGGTTACGTTAAAGGTTTGAATGGGTATTTATATTTAAAGTATAAGTAAGAATTTTT ++ +AAAAAEEEEEEEEEEEEEEEEEEAEEEEEEAEEEAEEEEEEEEEEEEEE<EEEEEAEEEEEEEEEEEEEEEEE<EEEEEEEEEAE +@1_987 +AGAACAGTTAGTTTTTCATTATTAATTTTTTTCATTTTTTTAGAATTTAAGTTGATTTTTAAGTTTTTTGATGTAAGAGGAAAAG ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEE +@1_988 +GTAATATCAGTATTTAGAAATTTGAGGTTGAAAGATTATGAATTTAAGATTATTTTGAGTTATATAGTAAGATTTTGTTTAAAAA ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAEEEEAEEEAEE<EEEEEEEEEEEEEEEEE +@1_989 +AGGTGAGATGGGTTTTATTTTTTTTTGTTTTTGATGTTTTAATTTTTTTTTTTTTTTTATAATTTCTTTTTGTTCTGCTATTTTT ++ +AAAAAEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEAE/E///////AE//////<///<6//E +@1_990 +ATCTCTCTCTATCTATCTCTATCTATATAAATATATATATATATATATATATATATCTTTATATATATATATATCTTTATCTAGA ++ +AAAAAEEEEEEEAEEEEEE//EEEEEEEE6EEEEEE6E/EEEEE/A6EEE/E/E///E/////EAE/AE//A/E/</E/////</ +@1_991 +TCTGTTGGAGGTAGATGGGAAGATAGGAGGGATTTGATAGGTTAGGGTAGAGGTATGAGAGGTGGTGTTGAGGATGGGAGAGAAG ++ +AAAAAE/EEEAEEEEEEEEEE6EEE6EEEEEE/EE<EAEEEEEEAEEEEAEEEEE<AEE/EEEEAAA<E<EEEE/EEE/E<EEE/ +@1_992 +AAAGGATGGTAGTTTTTATTTTTTAGGTGGAATTATTTATTTTTTATTTTGATTAGTTTTTTTTTATAATTATTGTTTATTTTTG ++ +AAAAAEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEAEEEEEEEEEEEEE6 +@1_993 +GGTGATATTAGAGTAAGAATTATTGTGAGGAATTAGAGATAGATATGAAAAAGAATATTGTTTATTTTGTAGATTATATAGAGTG ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAE<EEEEEE<EEEEEAEEEEEEEEEEE +@1_994 +GTTGGGGGTAGGGGGAGGATTATGCGTTATTAATAAAATATTTTTTAAGTTGGATTGAGGATAGGAAATTTTTTTTTTTGATAAT ++ +AAAAAEEEAAEEEEEEEEEEEEEAEEEEEEEE6EEEEEEEEEEEEEEEEEEEEE<EE<EEEEEEEEAEEE<EEEEEEEEEEAEEE +@1_995 +GCAGAATTGTTTATTAAGATTTTTGATATTTAATTTTTGTTTTTTTTAGTATTTTGATTAATTATTTAAGTTACATTTTGTTTAT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEEAEEEEAEAEEEE/EEEAEA +@1_996 +ATGCATATTATTATAGTGTAATGGCGTAAAATAGAAATAATTTTGTTAGTTTTAGATTTAGGTATAATGGAGTGAATATATTTTT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE +@1_997 +CAAGTTAAGAGATAGATTAGAAAAGAGAAAATGAGATTAAGAAGTATAGATCGGATGGTTTGAAGGACGTTAATAAATTTTTTTG ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEE<EEEEEEEEEEEAAEAAEEEEEEE<EEAEE< +@1_998 +TTGTAGGTTCGTGGGTATTTAGATGTATTTATTATTATTATTATTATTATTATTATTATTATTATTATTTTAGACTTGGGATTTT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEE/AEEEEE<AEA +@1_999 +AAGTTTTAAGGAGTTATTTATAGATGGTATTTGTTTTGTTTTTTAGAATATTTAAAGGATTTTTGGATAGTATTTTATTAGTTTA ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEA +@1_1000 +AGAATAGTAGTAGTAGGTAGTCTTTTTGTTTTATAATATATTTAGTTTTAGATGTAAGGTTATTTTAGTAGTGTTATATTTGGTT ++ +AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEAEAEEEEEEEEAEE
--- a/test-data/mapping_report.txt Wed Jun 05 07:44:26 2019 -0400 +++ b/test-data/mapping_report.txt Tue Jul 30 06:30:36 2019 -0400 @@ -1,6 +1,6 @@ -Bismark report for: /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmpywNSSM/files/000/dataset_2.dat (version: v0.20.0) +Bismark report for: input_1.fq.gz (version: v0.22.1) Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed) -Bismark was run with Bowtie 2 against the bisulfite genome of /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp4_4hiluf/ with the specified options: -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --quiet +Bismark was run with Bowtie 2 against the bisulfite genome of /tmp/tmpProAS5/ with the specified options: -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --quiet Final Alignment report ======================
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mapping_report_short.txt Tue Jul 30 06:30:36 2019 -0400 @@ -0,0 +1,42 @@ +Bismark report for: input_1.fq (version: v0.22.1) +Option '--directional' specified (default mode): alignments to complementary strands (CTOT, CTOB) were ignored (i.e. not performed) +Bismark was run with Bowtie 2 against the bisulfite genome of /tmp/tmpVM2AEy/ with the specified options: -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --quiet + +Final Alignment report +====================== +Sequences analysed in total: 1000 +Number of alignments with a unique best hit from the different alignments: 8 +Mapping efficiency: 0.8% +Sequences with no alignments under any condition: 983 +Sequences did not map uniquely: 9 +Sequences which were discarded because genomic sequence could not be extracted: 0 + +Number of sequences with unique best (first) alignment came from the bowtie output: +CT/CT: 6 ((converted) top strand) +CT/GA: 2 ((converted) bottom strand) +GA/CT: 0 (complementary to (converted) top strand) +GA/GA: 0 (complementary to (converted) bottom strand) + +Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 + +Final Cytosine Methylation Report +================================= +Total number of C's analysed: 143 + +Total methylated C's in CpG context: 3 +Total methylated C's in CHG context: 2 +Total methylated C's in CHH context: 3 +Total methylated C's in Unknown context: 0 + +Total unmethylated C's in CpG context: 1 +Total unmethylated C's in CHG context: 36 +Total unmethylated C's in CHH context: 98 +Total unmethylated C's in Unknown context: 0 + +C methylated in CpG context: 75.0% +C methylated in CHG context: 5.3% +C methylated in CHH context: 3.0% +Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0 + + +Bismark completed in 0d 0h 0m 5s
--- a/test-data/output_html_report.html Wed Jun 05 07:44:26 2019 -0400 +++ b/test-data/output_html_report.html Tue Jul 30 06:30:36 2019 -0400 @@ -4,7 +4,7 @@ <head> <meta http-equiv="content-type" content="text/html; charset=UTF-8"> - <title>Bismark Processing Report - /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmpDiq_J8/files/000/dataset_2.dat</title> + <title>Bismark Processing Report - input_1.fq.gz</title> <style> body { @@ -148,8 +148,8 @@ <h1>Bismark Processing Report</h1> <div class="subtitle"> - <h3>/private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmpDiq_J8/files/000/dataset_2.dat</h3> - <p>Data processed at 14:27 on 2018-08-21</p> + <h3>input_1.fq.gz</h3> + <p>Data processed at 10:50 on 2019-07-30</p> </div> </div> @@ -923,13 +923,27 @@ }, }; - Plotly.newPlot('mbias1_plot', data, layout,{displaylogo: false}, {modeBarButtonsToRemove: ['toImage', - 'sendDataToCloud', - 'resetScale2d', - 'hoverClosestCartesian', - 'hoverCompareCartesian', - 'toggleZoom', - 'toggleSpikelines']}); + var options = { + displaylogo: false, + modeBarButtonsToRemove: + ['zoom2d', + 'sendDataToCloud', + 'pan', + 'pan2d', + 'resetScale2d', + 'hoverClosestCartesian', + 'hoverCompareCartesian', + 'toggleSpikelines'] + , + toImageButtonOptions: { + filename: 'Bismark M-bias Read 1', + width: 1600, + height: 600, + format: 'png' + } + }; + + Plotly.newPlot('mbias1_plot', data, layout, options); </script> <!-- M-bias Plot 2--> @@ -1045,7 +1059,7 @@ }, }, xaxis: { - title: 'Position in read [bp]', + title: 'Position in Read [bp]', showline: true, titlefont: { size: 18, @@ -1059,13 +1073,28 @@ }, }; - Plotly.newPlot('mbias2_plot', data, layout, {displaylogo: false}, {modeBarButtonsToRemove: ['toImage', - 'sendDataToCloud', - 'resetScale2d', - 'hoverClosestCartesian', - 'hoverCompareCartesian', - 'toggleZoom', - 'toggleSpikelines']}); + + var options2 = { + displaylogo: false, + modeBarButtonsToRemove: + ['zoom2d', + 'sendDataToCloud', + 'pan', + 'pan2d', + 'resetScale2d', + 'hoverClosestCartesian', + 'hoverCompareCartesian', + 'toggleSpikelines'] + , + toImageButtonOptions: { + filename: 'Bismark M-bias Read 2', + width: 1600, + height: 600, + format: 'png' + } + }; + + Plotly.newPlot('mbias2_plot', data, layout, options2); </script> @@ -1075,7 +1104,7 @@ </a> - <p>Analysis produced by <a href="https://github.com/FelixKrueger/Bismark"><strong>Bismark</strong></a> (version v0.19.1) - a tool to map bisulfite converted sequence reads and determine cytosine methylation states</p> + <p>Analysis produced by <a href="https://github.com/FelixKrueger/Bismark"><strong>Bismark</strong></a> (version v0.22.1) - a tool to map bisulfite converted sequence reads and determine cytosine methylation states</p> <p>Report graphs rendered using <a href="https://plot.ly/">plot.ly</a>, design last changed 07 Aug 2018</p> </footer>
--- a/test-data/output_splitting_report.txt Wed Jun 05 07:44:26 2019 -0400 +++ b/test-data/output_splitting_report.txt Tue Jul 30 06:30:36 2019 -0400 @@ -1,7 +1,7 @@ -dataset_11.dat +dataset_76c1988f-01b0-427e-9dbe-bfb5eee1c664.dat Parameters used to extract methylation information: -Bismark Extractor Version: v0.20.0 +Bismark Extractor Version: v0.22.1 Bismark result file: single-end (SAM format) Output specified: comprehensive
--- a/test-data/summary.txt Wed Jun 05 07:44:26 2019 -0400 +++ b/test-data/summary.txt Tue Jul 30 06:30:36 2019 -0400 @@ -1,8 +1,8 @@ Create a temporary index with the offered files from the user. Utilizing the script: bismark_genome_preparation -Generating index with: 'bismark_genome_preparation --bowtie2 /var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp4_4hiluf' +Generating index with: 'bismark_genome_preparation --bowtie2 /tmp/tmpProAS5' Writing bisulfite genomes out into a single MFA (multi FastA) file -Bisulfite Genome Indexer version v0.20.0 (last modified 26 April 2018) +Bisulfite Genome Indexer version v0.22.1 (last modified: 14 April 2019) Step I - Prepare genome folders - completed @@ -79,7 +79,7 @@ No samples; assembling all-inclusive block Sorting block of length 756159 for bucket 1 (Using difference cover) - Sorting block time: 00:00:01 + Sorting block time: 00:00:00 Returning block of 756160 for bucket 1 Exited Ebwt loop fchr[A]: 0 @@ -118,7 +118,7 @@ ebwtTotSz: 252096 color: 0 reverse: 0 -Total time for call to driver() for forward index: 00:00:01 +Total time for call to driver() for forward index: 00:00:00 Reading reference sizes Time reading reference sizes: 00:00:00 Calculating joined length @@ -162,7 +162,7 @@ No samples; assembling all-inclusive block Sorting block of length 756159 for bucket 1 (Using difference cover) - Sorting block time: 00:00:00 + Sorting block time: 00:00:01 Returning block of 756160 for bucket 1 Exited Ebwt loop fchr[A]: 0 @@ -201,7 +201,7 @@ ebwtTotSz: 252096 color: 0 reverse: 1 -Total time for backward call to driver() for mirror index: 00:00:00 +Total time for backward call to driver() for mirror index: 00:00:01 Settings: Output files: "BS_GA.*.bt2" Line rate: 6 (line is 64 bytes) @@ -264,7 +264,7 @@ No samples; assembling all-inclusive block Sorting block of length 756159 for bucket 1 (Using difference cover) - Sorting block time: 00:00:01 + Sorting block time: 00:00:00 Returning block of 756160 for bucket 1 Exited Ebwt loop fchr[A]: 0 @@ -303,7 +303,7 @@ ebwtTotSz: 252096 color: 0 reverse: 0 -Total time for call to driver() for forward index: 00:00:01 +Total time for call to driver() for forward index: 00:00:00 Reading reference sizes Time reading reference sizes: 00:00:00 Calculating joined length @@ -347,7 +347,7 @@ No samples; assembling all-inclusive block Sorting block of length 756159 for bucket 1 (Using difference cover) - Sorting block time: 00:00:00 + Sorting block time: 00:00:01 Returning block of 756160 for bucket 1 Exited Ebwt loop fchr[A]: 0 @@ -386,29 +386,29 @@ ebwtTotSz: 252096 color: 0 reverse: 1 -Total time for backward call to driver() for mirror index: 00:00:00 -Running bismark with: 'bismark --bam --gzip --temp_dir /var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmprjiux3me -o /var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmprjiux3me/results --quiet --fastq -L 20 -D 15 -R 2 --un --ambiguous /var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp4_4hiluf /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmpywNSSM/files/000/dataset_2.dat' -Path to Bowtie 2 specified as: bowtie2 -Bowtie seems to be working fine (tested command 'bowtie2 --version' [2.3.4]) +Total time for backward call to driver() for mirror index: 00:00:01 +Running bismark with: 'bismark --bam --gzip --temp_dir /tmp/tmpvcY9eC -o /tmp/tmpvcY9eC/results --quiet --fastq -L 20 -D 15 -R 2 --un --ambiguous /tmp/tmpProAS5 input_1.fq.gz' +Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.3.5]) Output format is BAM (default) -Alignments will be written out in BAM format. Samtools found here: '/Users/scholtalbers/miniconda3/envs/mulled-v1-7f230b3d24f9f00e91e72af479ffae49907f4592b1a7a4b05436e0a99567150a/bin/samtools' -Reference genome folder provided is /var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp4_4hiluf/ (absolute path is '/private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp4_4hiluf/)' +Alignments will be written out in BAM format. Samtools found here: '/home/abretaud/miniconda3/envs/mulled-v1-9f2317dbfb405ed6926c55752e5c11678eee3256a6ea680d1c0f912251153030/bin/samtools' +Reference genome folder provided is /tmp/tmpProAS5/ (absolute path is '/tmp/tmpProAS5/)' FastQ format specified -Input files to be analysed (in current folder '/private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmpywNSSM/job_working_directory/000/3/working'): -/private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmpywNSSM/files/000/dataset_2.dat +Input files to be analysed (in current folder '/tmp/tmpq6T4hb/job_working_directory/000/4/working'): +input_1.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) -Created output directory /var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmprjiux3me/results/! +Created output directory /tmp/tmpvcY9eC/results/! -Output will be written into the directory: /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmprjiux3me/results/ +Output will be written into the directory: /tmp/tmpvcY9eC/results/ -Using temp directory: /var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmprjiux3me -Temporary files will be written into the directory: /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmprjiux3me/ +Using temp directory: /tmp/tmpvcY9eC +Temporary files will be written into the directory: /tmp/tmpvcY9eC/ Setting parallelization to single-threaded (default) -Current working directory is: /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmpywNSSM/job_working_directory/000/3/working +Summary of all aligner options: -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --quiet +Current working directory is: /tmp/tmpq6T4hb/job_working_directory/000/4/working -Now reading in and storing sequence information of the genome specified in: /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp4_4hiluf/ +Now reading in and storing sequence information of the genome specified in: /tmp/tmpProAS5/ chr chrY_JH584300_random (182347 bp) chr chrY_JH584301_random (259875 bp) @@ -421,33 +421,33 @@ ======================================= Input file is in FastQ format -Writing a C -> T converted version of the input file dataset_2.dat to /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmprjiux3me/dataset_2.dat_C_to_T.fastq.gz +Writing a C -> T converted version of the input file input_1.fq.gz to /tmp/tmpvcY9eC/input_1.fq.gz_C_to_T.fastq.gz -Created C -> T converted version of the FastQ file dataset_2.dat (44115 sequences in total) +Created C -> T converted version of the FastQ file input_1.fq.gz (44115 sequences in total) -Input file is dataset_2.dat_C_to_T.fastq.gz (FastQ) +Input file is input_1.fq.gz_C_to_T.fastq.gz (FastQ) -Now running 2 instances of Bowtie 2 against the bisulfite genome of /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp4_4hiluf/ with the specified options: -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --quiet +Now running 2 instances of Bowtie 2 against the bisulfite genome of /tmp/tmpProAS5/ with the specified options: -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --quiet -Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmprjiux3me/dataset_2.dat_C_to_T.fastq.gz with options -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --quiet --norc) -Using Bowtie 2 index: /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp4_4hiluf/Bisulfite_Genome/CT_conversion/BS_CT +Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from /tmp/tmpvcY9eC/input_1.fq.gz_C_to_T.fastq.gz with options -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --quiet --norc) +Using Bowtie 2 index: /tmp/tmpProAS5/Bisulfite_Genome/CT_conversion/BS_CT Found first alignment: 1_1 4 * 0 0 * * 0 0 TTGTATATATTAGATAAATTAATTTTTTTTGTTTGTATGTTAAATTTTTTAATTAATTTATTAATATTTTGTGAATTTTTAGATA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEE YT:Z:UU -Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmprjiux3me/dataset_2.dat_C_to_T.fastq.gz with options -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --quiet --nofw) -Using Bowtie 2 index: /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp4_4hiluf/Bisulfite_Genome/GA_conversion/BS_GA +Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from /tmp/tmpvcY9eC/input_1.fq.gz_C_to_T.fastq.gz with options -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --quiet --nofw) +Using Bowtie 2 index: /tmp/tmpProAS5/Bisulfite_Genome/GA_conversion/BS_GA Found first alignment: 1_1 4 * 0 0 * * 0 0 TTGTATATATTAGATAAATTAATTTTTTTTGTTTGTATGTTAAATTTTTTAATTAATTTATTAATATTTTGTGAATTTTTAGATA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEE YT:Z:UU ->>> Writing bisulfite mapping results to /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmprjiux3me/results/dataset_2.dat_bismark_bt2.bam <<< +>>> Writing bisulfite mapping results to /tmp/tmpvcY9eC/results/input_1_bismark_bt2.bam <<< -Unmapped sequences will be written to /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmprjiux3me/results/dataset_2.dat_unmapped_reads.fq.gz -Ambiguously mapping sequences will be written to /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmprjiux3me/results/dataset_2.dat_ambiguous_reads.fq.gz +Unmapped sequences will be written to /tmp/tmpvcY9eC/results/input_1.fq.gz_unmapped_reads.fq.gz +Ambiguously mapping sequences will be written to /tmp/tmpvcY9eC/results/input_1.fq.gz_ambiguous_reads.fq.gz -Reading in the sequence file /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmpywNSSM/files/000/dataset_2.dat +Reading in the sequence file input_1.fq.gz Processed 44115 sequences in total -Successfully deleted the temporary file /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmprjiux3me/dataset_2.dat_C_to_T.fastq.gz +Successfully deleted the temporary file /tmp/tmpvcY9eC/input_1.fq.gz_C_to_T.fastq.gz Final Alignment report ======================
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary_short.txt Tue Jul 30 06:30:36 2019 -0400 @@ -0,0 +1,495 @@ +Create a temporary index with the offered files from the user. Utilizing the script: bismark_genome_preparation +Generating index with: 'bismark_genome_preparation --bowtie2 /tmp/tmpVM2AEy' +Writing bisulfite genomes out into a single MFA (multi FastA) file + +Bisulfite Genome Indexer version v0.22.1 (last modified: 14 April 2019) + +Step I - Prepare genome folders - completed + + + +Total number of conversions performed: +C->T: 146875 +G->A: 150504 + +Step II - Genome bisulfite conversions - completed + + +Bismark Genome Preparation - Step III: Launching the Bowtie 2 indexer +Please be aware that this process can - depending on genome size - take several hours! +Settings: + Output files: "BS_CT.*.bt2" + Line rate: 6 (line is 64 bytes) + Lines per side: 1 (side is 64 bytes) + Offset rate: 4 (one in 16) + FTable chars: 10 + Strings: unpacked + Max bucket size: default + Max bucket size, sqrt multiplier: default + Max bucket size, len divisor: 4 + Difference-cover sample period: 1024 + Endianness: little + Actual local endianness: little + Sanity checking: disabled + Assertions: disabled + Random seed: 0 + Sizeofs: void*:8, int:4, long:8, size_t:8 +Input files DNA, FASTA: + genome_mfa.CT_conversion.fa +Building a SMALL index +Reading reference sizes + Time reading reference sizes: 00:00:00 +Calculating joined length +Writing header +Reserving space for joined string +Joining reference sequences + Time to join reference sequences: 00:00:00 +bmax according to bmaxDivN setting: 189039 +Using parameters --bmax 141780 --dcv 1024 + Doing ahead-of-time memory usage test + Passed! Constructing with these parameters: --bmax 141780 --dcv 1024 +Constructing suffix-array element generator +Building DifferenceCoverSample + Building sPrime + Building sPrimeOrder + V-Sorting samples + V-Sorting samples time: 00:00:00 + Allocating rank array + Ranking v-sort output + Ranking v-sort output time: 00:00:00 + Invoking Larsson-Sadakane on ranks + Invoking Larsson-Sadakane on ranks time: 00:00:00 + Sanity-checking and returning +Building samples +Reserving space for 12 sample suffixes +Generating random suffixes +QSorting 12 sample offsets, eliminating duplicates +QSorting sample offsets, eliminating duplicates time: 00:00:00 +Multikey QSorting 12 samples + (Using difference cover) + Multikey QSorting samples time: 00:00:00 +Calculating bucket sizes +Splitting and merging + Splitting and merging time: 00:00:00 +Avg bucket size: 756159 (target: 141779) +Converting suffix-array elements to index image +Allocating ftab, absorbFtab +Entering Ebwt loop +Getting block 1 of 1 + No samples; assembling all-inclusive block + Sorting block of length 756159 for bucket 1 + (Using difference cover) + Sorting block time: 00:00:00 +Returning block of 756160 for bucket 1 +Exited Ebwt loop +fchr[A]: 0 +fchr[C]: 235897 +fchr[G]: 235897 +fchr[T]: 386401 +fchr[$]: 756159 +Exiting Ebwt::buildToDisk() +Returning from initFromVector +Wrote 4446745 bytes to primary EBWT file: BS_CT.1.bt2 +Wrote 189044 bytes to secondary EBWT file: BS_CT.2.bt2 +Re-opening _in1 and _in2 as input streams +Returning from Ebwt constructor +Headers: + len: 756159 + bwtLen: 756160 + sz: 189040 + bwtSz: 189040 + lineRate: 6 + offRate: 4 + offMask: 0xfffffff0 + ftabChars: 10 + eftabLen: 20 + eftabSz: 80 + ftabLen: 1048577 + ftabSz: 4194308 + offsLen: 47260 + offsSz: 189040 + lineSz: 64 + sideSz: 64 + sideBwtSz: 48 + sideBwtLen: 192 + numSides: 3939 + numLines: 3939 + ebwtTotLen: 252096 + ebwtTotSz: 252096 + color: 0 + reverse: 0 +Total time for call to driver() for forward index: 00:00:00 +Reading reference sizes + Time reading reference sizes: 00:00:00 +Calculating joined length +Writing header +Reserving space for joined string +Joining reference sequences + Time to join reference sequences: 00:00:00 + Time to reverse reference sequence: 00:00:00 +bmax according to bmaxDivN setting: 189039 +Using parameters --bmax 141780 --dcv 1024 + Doing ahead-of-time memory usage test + Passed! Constructing with these parameters: --bmax 141780 --dcv 1024 +Constructing suffix-array element generator +Building DifferenceCoverSample + Building sPrime + Building sPrimeOrder + V-Sorting samples + V-Sorting samples time: 00:00:00 + Allocating rank array + Ranking v-sort output + Ranking v-sort output time: 00:00:00 + Invoking Larsson-Sadakane on ranks + Invoking Larsson-Sadakane on ranks time: 00:00:00 + Sanity-checking and returning +Building samples +Reserving space for 12 sample suffixes +Generating random suffixes +QSorting 12 sample offsets, eliminating duplicates +QSorting sample offsets, eliminating duplicates time: 00:00:00 +Multikey QSorting 12 samples + (Using difference cover) + Multikey QSorting samples time: 00:00:00 +Calculating bucket sizes +Splitting and merging + Splitting and merging time: 00:00:00 +Avg bucket size: 756159 (target: 141779) +Converting suffix-array elements to index image +Allocating ftab, absorbFtab +Entering Ebwt loop +Getting block 1 of 1 + No samples; assembling all-inclusive block + Sorting block of length 756159 for bucket 1 + (Using difference cover) + Sorting block time: 00:00:00 +Returning block of 756160 for bucket 1 +Exited Ebwt loop +fchr[A]: 0 +fchr[C]: 235897 +fchr[G]: 235897 +fchr[T]: 386401 +fchr[$]: 756159 +Exiting Ebwt::buildToDisk() +Returning from initFromVector +Wrote 4446745 bytes to primary EBWT file: BS_CT.rev.1.bt2 +Wrote 189044 bytes to secondary EBWT file: BS_CT.rev.2.bt2 +Re-opening _in1 and _in2 as input streams +Returning from Ebwt constructor +Headers: + len: 756159 + bwtLen: 756160 + sz: 189040 + bwtSz: 189040 + lineRate: 6 + offRate: 4 + offMask: 0xfffffff0 + ftabChars: 10 + eftabLen: 20 + eftabSz: 80 + ftabLen: 1048577 + ftabSz: 4194308 + offsLen: 47260 + offsSz: 189040 + lineSz: 64 + sideSz: 64 + sideBwtSz: 48 + sideBwtLen: 192 + numSides: 3939 + numLines: 3939 + ebwtTotLen: 252096 + ebwtTotSz: 252096 + color: 0 + reverse: 1 +Total time for backward call to driver() for mirror index: 00:00:00 +Settings: + Output files: "BS_GA.*.bt2" + Line rate: 6 (line is 64 bytes) + Lines per side: 1 (side is 64 bytes) + Offset rate: 4 (one in 16) + FTable chars: 10 + Strings: unpacked + Max bucket size: default + Max bucket size, sqrt multiplier: default + Max bucket size, len divisor: 4 + Difference-cover sample period: 1024 + Endianness: little + Actual local endianness: little + Sanity checking: disabled + Assertions: disabled + Random seed: 0 + Sizeofs: void*:8, int:4, long:8, size_t:8 +Input files DNA, FASTA: + genome_mfa.GA_conversion.fa +Building a SMALL index +Reading reference sizes + Time reading reference sizes: 00:00:00 +Calculating joined length +Writing header +Reserving space for joined string +Joining reference sequences + Time to join reference sequences: 00:00:00 +bmax according to bmaxDivN setting: 189039 +Using parameters --bmax 141780 --dcv 1024 + Doing ahead-of-time memory usage test + Passed! Constructing with these parameters: --bmax 141780 --dcv 1024 +Constructing suffix-array element generator +Building DifferenceCoverSample + Building sPrime + Building sPrimeOrder + V-Sorting samples + V-Sorting samples time: 00:00:00 + Allocating rank array + Ranking v-sort output + Ranking v-sort output time: 00:00:00 + Invoking Larsson-Sadakane on ranks + Invoking Larsson-Sadakane on ranks time: 00:00:00 + Sanity-checking and returning +Building samples +Reserving space for 12 sample suffixes +Generating random suffixes +QSorting 12 sample offsets, eliminating duplicates +QSorting sample offsets, eliminating duplicates time: 00:00:00 +Multikey QSorting 12 samples + (Using difference cover) + Multikey QSorting samples time: 00:00:00 +Calculating bucket sizes +Splitting and merging + Splitting and merging time: 00:00:00 +Avg bucket size: 756159 (target: 141779) +Converting suffix-array elements to index image +Allocating ftab, absorbFtab +Entering Ebwt loop +Getting block 1 of 1 + No samples; assembling all-inclusive block + Sorting block of length 756159 for bucket 1 + (Using difference cover) + Sorting block time: 00:00:00 +Returning block of 756160 for bucket 1 +Exited Ebwt loop +fchr[A]: 0 +fchr[C]: 386401 +fchr[G]: 533276 +fchr[T]: 533276 +fchr[$]: 756159 +Exiting Ebwt::buildToDisk() +Returning from initFromVector +Wrote 4446745 bytes to primary EBWT file: BS_GA.1.bt2 +Wrote 189044 bytes to secondary EBWT file: BS_GA.2.bt2 +Re-opening _in1 and _in2 as input streams +Returning from Ebwt constructor +Headers: + len: 756159 + bwtLen: 756160 + sz: 189040 + bwtSz: 189040 + lineRate: 6 + offRate: 4 + offMask: 0xfffffff0 + ftabChars: 10 + eftabLen: 20 + eftabSz: 80 + ftabLen: 1048577 + ftabSz: 4194308 + offsLen: 47260 + offsSz: 189040 + lineSz: 64 + sideSz: 64 + sideBwtSz: 48 + sideBwtLen: 192 + numSides: 3939 + numLines: 3939 + ebwtTotLen: 252096 + ebwtTotSz: 252096 + color: 0 + reverse: 0 +Total time for call to driver() for forward index: 00:00:00 +Reading reference sizes + Time reading reference sizes: 00:00:00 +Calculating joined length +Writing header +Reserving space for joined string +Joining reference sequences + Time to join reference sequences: 00:00:00 + Time to reverse reference sequence: 00:00:00 +bmax according to bmaxDivN setting: 189039 +Using parameters --bmax 141780 --dcv 1024 + Doing ahead-of-time memory usage test + Passed! Constructing with these parameters: --bmax 141780 --dcv 1024 +Constructing suffix-array element generator +Building DifferenceCoverSample + Building sPrime + Building sPrimeOrder + V-Sorting samples + V-Sorting samples time: 00:00:00 + Allocating rank array + Ranking v-sort output + Ranking v-sort output time: 00:00:00 + Invoking Larsson-Sadakane on ranks + Invoking Larsson-Sadakane on ranks time: 00:00:00 + Sanity-checking and returning +Building samples +Reserving space for 12 sample suffixes +Generating random suffixes +QSorting 12 sample offsets, eliminating duplicates +QSorting sample offsets, eliminating duplicates time: 00:00:00 +Multikey QSorting 12 samples + (Using difference cover) + Multikey QSorting samples time: 00:00:00 +Calculating bucket sizes +Splitting and merging + Splitting and merging time: 00:00:00 +Avg bucket size: 756159 (target: 141779) +Converting suffix-array elements to index image +Allocating ftab, absorbFtab +Entering Ebwt loop +Getting block 1 of 1 + No samples; assembling all-inclusive block + Sorting block of length 756159 for bucket 1 + (Using difference cover) + Sorting block time: 00:00:00 +Returning block of 756160 for bucket 1 +Exited Ebwt loop +fchr[A]: 0 +fchr[C]: 386401 +fchr[G]: 533276 +fchr[T]: 533276 +fchr[$]: 756159 +Exiting Ebwt::buildToDisk() +Returning from initFromVector +Wrote 4446745 bytes to primary EBWT file: BS_GA.rev.1.bt2 +Wrote 189044 bytes to secondary EBWT file: BS_GA.rev.2.bt2 +Re-opening _in1 and _in2 as input streams +Returning from Ebwt constructor +Headers: + len: 756159 + bwtLen: 756160 + sz: 189040 + bwtSz: 189040 + lineRate: 6 + offRate: 4 + offMask: 0xfffffff0 + ftabChars: 10 + eftabLen: 20 + eftabSz: 80 + ftabLen: 1048577 + ftabSz: 4194308 + offsLen: 47260 + offsSz: 189040 + lineSz: 64 + sideSz: 64 + sideBwtSz: 48 + sideBwtLen: 192 + numSides: 3939 + numLines: 3939 + ebwtTotLen: 252096 + ebwtTotSz: 252096 + color: 0 + reverse: 1 +Total time for backward call to driver() for mirror index: 00:00:01 +Running bismark with: 'bismark --bam --gzip --temp_dir /tmp/tmpHOWuwJ -o /tmp/tmpHOWuwJ/results --quiet --fastq -L 20 -D 15 -R 2 --un --ambiguous /tmp/tmpVM2AEy input_1.fq' +Bowtie 2 seems to be working fine (tested command 'bowtie2 --version' [2.3.5]) +Output format is BAM (default) +Alignments will be written out in BAM format. Samtools found here: '/home/abretaud/miniconda3/envs/mulled-v1-9f2317dbfb405ed6926c55752e5c11678eee3256a6ea680d1c0f912251153030/bin/samtools' +Reference genome folder provided is /tmp/tmpVM2AEy/ (absolute path is '/tmp/tmpVM2AEy/)' +FastQ format specified + +Input files to be analysed (in current folder '/tmp/tmpq6T4hb/job_working_directory/000/8/working'): +input_1.fq +Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) +Created output directory /tmp/tmpHOWuwJ/results/! + +Output will be written into the directory: /tmp/tmpHOWuwJ/results/ + +Using temp directory: /tmp/tmpHOWuwJ +Temporary files will be written into the directory: /tmp/tmpHOWuwJ/ +Setting parallelization to single-threaded (default) + +Summary of all aligner options: -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --quiet +Current working directory is: /tmp/tmpq6T4hb/job_working_directory/000/8/working + +Now reading in and storing sequence information of the genome specified in: /tmp/tmpVM2AEy/ + +chr chrY_JH584300_random (182347 bp) +chr chrY_JH584301_random (259875 bp) +chr chrY_JH584302_random (155838 bp) +chr chrY_JH584303_random (158099 bp) + +Single-core mode: setting pid to 1 + +Single-end alignments will be performed +======================================= + +Input file is in FastQ format +Writing a C -> T converted version of the input file input_1.fq to /tmp/tmpHOWuwJ/input_1.fq_C_to_T.fastq.gz + +Created C -> T converted version of the FastQ file input_1.fq (1000 sequences in total) + +Input file is input_1.fq_C_to_T.fastq.gz (FastQ) + +Now running 2 instances of Bowtie 2 against the bisulfite genome of /tmp/tmpVM2AEy/ with the specified options: -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --quiet + +Now starting the Bowtie 2 aligner for CTreadCTgenome (reading in sequences from /tmp/tmpHOWuwJ/input_1.fq_C_to_T.fastq.gz with options -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --quiet --norc) +Using Bowtie 2 index: /tmp/tmpVM2AEy/Bisulfite_Genome/CT_conversion/BS_CT + +Found first alignment: 1_1 4 * 0 0 * * 0 0 TTGTATATATTAGATAAATTAATTTTTTTTGTTTGTATGTTAAATTTTTTAATTAATTTATTAATATTTTGTGAATTTTTAGATA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEE YT:Z:UU +Now starting the Bowtie 2 aligner for CTreadGAgenome (reading in sequences from /tmp/tmpHOWuwJ/input_1.fq_C_to_T.fastq.gz with options -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --quiet --nofw) +Using Bowtie 2 index: /tmp/tmpVM2AEy/Bisulfite_Genome/GA_conversion/BS_GA + +Found first alignment: 1_1 4 * 0 0 * * 0 0 TTGTATATATTAGATAAATTAATTTTTTTTGTTTGTATGTTAAATTTTTTAATTAATTTATTAATATTTTGTGAATTTTTAGATA AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEE YT:Z:UU + +>>> Writing bisulfite mapping results to /tmp/tmpHOWuwJ/results/input_1_bismark_bt2.bam <<< + +Unmapped sequences will be written to /tmp/tmpHOWuwJ/results/input_1.fq_unmapped_reads.fq.gz +Ambiguously mapping sequences will be written to /tmp/tmpHOWuwJ/results/input_1.fq_ambiguous_reads.fq.gz + +Reading in the sequence file input_1.fq +Processed 1000 sequences in total + + +Successfully deleted the temporary file /tmp/tmpHOWuwJ/input_1.fq_C_to_T.fastq.gz + +Final Alignment report +====================== +Sequences analysed in total: 1000 +Number of alignments with a unique best hit from the different alignments: 8 +Mapping efficiency: 0.8% + +Sequences with no alignments under any condition: 983 +Sequences did not map uniquely: 9 +Sequences which were discarded because genomic sequence could not be extracted: 0 + +Number of sequences with unique best (first) alignment came from the bowtie output: +CT/CT: 6 ((converted) top strand) +CT/GA: 2 ((converted) bottom strand) +GA/CT: 0 (complementary to (converted) top strand) +GA/GA: 0 (complementary to (converted) bottom strand) + +Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 + +Final Cytosine Methylation Report +================================= +Total number of C's analysed: 143 + +Total methylated C's in CpG context: 3 +Total methylated C's in CHG context: 2 +Total methylated C's in CHH context: 3 +Total methylated C's in Unknown context: 0 + +Total unmethylated C's in CpG context: 1 +Total unmethylated C's in CHG context: 36 +Total unmethylated C's in CHH context: 98 +Total unmethylated C's in Unknown context: 0 + +C methylated in CpG context: 75.0% +C methylated in CHG context: 5.3% +C methylated in CHH context: 3.0% +Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0 + + +Bismark completed in 0d 0h 0m 5s + +==================== +Bismark run complete +==================== +