| Previous changeset 12:78c791a11b4c (2019-06-05) Next changeset 14:b6aa3b6ba129 (2019-07-30) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b9780e368b2e46dc541a846519ccc9593226ee0d |
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modified:
bismark2report_wrapper.xml bismark_bowtie2_wrapper.xml bismark_deduplicate_wrapper.xml bismark_methylation_extractor.xml test-data/dedup_reads.bam test-data/mapped_reads.bam test-data/mapping_report.txt test-data/output_html_report.html test-data/output_splitting_report.txt test-data/summary.txt |
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added:
test-data/input1.fq test-data/input1.fq.gzip test-data/mapped_reads_short.bam test-data/mapping_report_short.txt test-data/summary_short.txt |
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removed:
test-data/input1.fq.gz |
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| diff -r 78c791a11b4c -r f211753166bd bismark2report_wrapper.xml --- 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' |
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| diff -r 78c791a11b4c -r f211753166bd bismark_bowtie2_wrapper.xml --- 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 |
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| @@ -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> |
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| diff -r 78c791a11b4c -r f211753166bd bismark_deduplicate_wrapper.xml --- 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 |
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| @@ -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 '$__tool_directory__/bismark_deduplicate_wrapper.py' |
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| diff -r 78c791a11b4c -r f211753166bd bismark_methylation_extractor.xml --- a/bismark_methylation_extractor.xml Wed Jun 05 07:44:26 2019 -0400 +++ b/bismark_methylation_extractor.xml Tue Jul 30 06:30:36 2019 -0400 |
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| @@ -1,9 +1,9 @@ -<tool id="bismark_methylation_extractor" name="Bismark Meth. Extractor" version="0.20.0" profile="18.01"> +<tool id="bismark_methylation_extractor" name="Bismark Meth. Extractor" version="0.22.1" profile="18.01"> <description>Reports on methylation status of reads mapped by Bismark</description> <requirements> - <requirement type="package" version="0.20.0">bismark</requirement> + <requirement type="package" version="0.22.1">bismark</requirement> <requirement type="package" version="1.8">samtools</requirement> - <requirement type="package" version="2.3.4.2">bowtie2</requirement> + <requirement type="package" version="2.3.5">bowtie2</requirement> </requirements> <command><![CDATA[ python '$__tool_directory__/bismark_methylation_extractor.py' |
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| diff -r 78c791a11b4c -r f211753166bd test-data/dedup_reads.bam |
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| Binary file test-data/dedup_reads.bam has changed |
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| diff -r 78c791a11b4c -r f211753166bd test-data/input1.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input1.fq Tue Jul 30 06:30:36 2019 -0400 |
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| b'@@ -0,0 +1,4000 @@\n+@1_1\n+TTGTATATATTAGATAAATTAATTTTTTTTGTTTGTATGTTAAATTTTTTAATTAATTTATTAATATTTTGTGAATTTTTAGATA\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEE\n+@1_2\n+TAATTTTGAATTTTGGTTGGGTAGTTTGTTTTAGAATTATTATGGTTATATAGTTTTTTAGTAAGATTGTTATTTATTATTTGAT\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<EEEEEEEEEEEEEEEEEEEAEAEEEAEEAE\n+@1_3\n+TTGGTGGGGGTGTGGAAATTTGTATTGTGTGGATTTTTATTGAATATGGATAAAGAGTTAAGAGTTGGGTTGTAAAGTTAAGGAT\n++\n+AAAAAEEEEEAEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEAEEEEEE/EEEEEEEEEEEEEAA<EEEEEE\n+@1_4\n+AAGTGGTTTTAAATGGTTTAAGGTTAAATTAGATAGATAAGGTTTGGCGTGGATTATATATTATTGTAGAATTATTTTTTGTGTA\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEAEEEEEEEEEEEEEAEEEEEEEEEEEEE/EAAEEEE<E\n+@1_5\n+TGAGGAATTGAATTTAGTTTTAGAATTTTATAGGGATTTATTTGTTTTTTTTTTGGTTGAGTTATTGATTTTTAATTTTGTAAAT\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAE<E6//AE/AEA<6EEAEAE/EEA/E<EE6\n+@1_6\n+TGTGGTTAATTGGAAGTGATTGAAATTATAGAAGTGAATTTTTGGATAATGGGTATTAGTGTATTTAGAGTTATGTATGAGAGAT\n++\n+AAAAAEEEEAEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<E<EEEEEEEEEAEAEEEEEEE\n+@1_7\n+GATGATGGAGAAGGATTTAGTTTATTGTTGGTGGGGTTATTGTTAGGATGGTATTTTTGAGTTTAATAAGAAAGTAATTTTAAGT\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEE/EEEE\n+@1_8\n+GTGTGGGGTTTTGGGGTGAATTTTAGTTTATAGGTTATTTTAGTGTTTAAAAAATGAGTTTTTTATTTAAATAGTGGGAGGAGAT\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEE6/EEEEEEEEEEEAEEEEEEAEEEAEEEEEEEEEEEEE\n+@1_9\n+ATTAAGGGGAGATATCGGATTTTTGTTATGTAGGGATTTTATTGTTTTAATGTTATTTATAGTTTTAAAGTTAATGGGTGGGTAT\n++\n+AAAAAEEEAEEEEEEE/EEEAEEE6EEEEEEEEEEEEEEEEEEEAEEEEEEE/EEEEEEEE<EEEAEEEE/EEE/AAAEAAE/E/\n+@1_10\n+AGGTGTGAAAGGTAGTTGTGGATGTTTTTGTTTTTGGTTTATTTTATTAGGTTGAAGGGGTGGGGGAAGGGGTGGGGTGGGGGAA\n++\n+6AAAAEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\n+@1_11\n+GACAGGTTATGAATATTAATATGGTTTTAGCAATAGTAGGGATTACGGATATTAGTATGGTTTTCTGTAATAGTACAGATTATTG\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEE/EE<6EEEEEEE/EEEAEAEEEA/EEAE\n+@1_12\n+CAGGACGTGAAATATGGCGAGGAAAATTTAAAAAGGTGGAAAATTTAGAAATGTTTATTGTAGGAGGTGGAGCTCGGAAGCGAAC\n++\n+AAAAAEEEE/EEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEAEEEEE/<6EEEEEEEEE/EEEEE<///EE/A/E//EA\n+@1_13\n+CCCCGTATGTATGTTATAAATAATGGGAATTTTTTTTTAAATATAGGGATTAGATATATTTAATTAATAAATATTTATTATAAAA\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\n+@1_14\n+TACAGTCTTTGGTTAATTAGTTTAAATAAGATTAATTTGGAGGGAAGAAGAGTGTAGTAGTTTGATGGTATTTATAGGTTTATAG\n++\n+AAAAAEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEE\n+@1_15\n+ATGTAGCGGGATTTGGTAATGTGTAAGGGTTATTTAGGTGGTATTGGTTTTGAAGGTATGAAGGGGTTACGTAGAGCAGTTGAGG\n++\n+AAAAAEEEEEE6EEAEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEE<EEEEEEEEAEEEEEEEAAEEEAEAEEAEAEEEEEEEE\n+@1_16\n+TGATAGGATGTATGGGACAATTTTAATATTTTTGTATTTGTTGAGGTTTGTTTTGTGATTAATTATATGTTTAGTTTTGGAGAAG\n++\n+AAAAAEEEEEEEEEEEEEEEEEAEEEEEEAEEEE/EE/AEEEEEAEA/EEAEEEEEEEE/EEEEE<EEEAEEEAAA/EEEEEEAA\n+@1_17\n+GAAAGTAGATTGGAGATTTTGTAGTTTGGTAGGTGTTTTAGGGTATTTATTATTAAAATAAAAGATAGTTTTTGTTTATAGAAGG\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEE\n+@1_18\n+GGTTTTAAAGAGATTTGTTTATTTGTTTATTGAGGTTAAAAAAAGTTTTGTAAATATAGATAAGTATTGGAGTAGTTAGGAAAGT\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEAEEEE/EEE\n+@1_19\n+TATGTAGATTAAGGTTGTTAGTGTATTTGTTTAGTTTGGGAATATTTTTATTGGTTTTTTTAGGGATATATTAATGAGTAGTGTA\n++\n+AAAAAEEE/EEEEEAEAEEEEEEEEEEEEEEEEE/EEAE/EEEEE//E/EEEEE<<A<A<EEE6EE/EEEEAEEEAEAAEE/EEE\n+@1_20\n+TGTGGGGTATAGTATAAATAACGTTTTATTGGGTGTTGGTTTGGTGTTGTTATGTTTTTAAATATTGGTTTTTAAGTTTTGGTTG\n++\n+AAAAAEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE6EEEEEEAEEEEEEEEEE/EEEAAEEEEEEAE<EEEAA\n+@1_21\n+CTACAGGATGGGAGAAGATTTTTATAGTTATATTTTAGGAAATGGGTTAATATTTAGAATATGTAAAATTTTATTAAATATTTTA\n++\n+AAAAAEEEEEEEEEAEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEA<EE<EEEAEEEEAE\n+@1_22\n+AAGGGTTTTTTGTTTTTATAAGAGTTGAGTTATGGTTATATTTTTTGTTTTTTATGAATAATTGGATAAAATTATGTGAAAGTTT\n++\n+AAAAAEEEAEEEEEEEEEEEEEEEEEE'..b'AGGGTTGAAGATTTTTTTAGTT\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEEEEEEE6EEEE/EEEEEEEEEAEAEE6AAEE<EAAAAE<EAEEEAE\n+@1_980\n+CAGATGATCGAGATTTGTAAGGATGGATTTTAGAAGGGAATATAAGTTAAAATTAATATAATTTAGGAATAGAATTGTAAAATTT\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEAEEEAAEEEAEEEEEEE\n+@1_981\n+TGTAAGTTTTGGATATGGAATTTATATTATTATTTATGTGTTAGAATTTTATGTTTTTAAATTATAGTTGAAAAAATAGTTGGTT\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\n+@1_982\n+AATGTGGTGGTTTGGTGGTATATGTTTCGAGTTTTAGTATTTAGGGTAGATATAGGTAAATTTTTTTGAGTTTGAGGTTTGTTTT\n++\n+AAAAAEEEAEEEEEE6EEEEEEEEE/EEAAAEEEEEAEEEEEEEE6EEEEEEEEEE/EEEEEAAEA/AAE<E<EE/EAAE/EEEE\n+@1_983\n+ATGGAAGAGTGGGTAGAAAGATTATAATAGGTAGAAATAGTATGTATTTGTAAAAATAATTTTTGAGTATGATATGGTTATTGTA\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE<\n+@1_984\n+GTGGTTACATGTATTGGGTTTTTGAGGTGAAGGTAGGAATAGTAAGGGAGGAAATGGTAAGAGAAGAAAGGAGATTAAGATAGAT\n++\n+AAAAAEEEEEEEEAEEEEEEAEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEE/AEEE/AEEE/\n+@1_985\n+TGATAGGTTGTTATTTTTTAAAAGAATATTTGTGATTAATTTTATTTTAGACTCTTATTTTTATGTTATTTTTTCTATTACTTAT\n++\n+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\n+@1_986\n+TTGTAGGTTAGAATAGTAGGTTTGAGTAAGGTTACGTTAAAGGTTTGAATGGGTATTTATATTTAAAGTATAAGTAAGAATTTTT\n++\n+AAAAAEEEEEEEEEEEEEEEEEEAEEEEEEAEEEAEEEEEEEEEEEEEE<EEEEEAEEEEEEEEEEEEEEEEE<EEEEEEEEEAE\n+@1_987\n+AGAACAGTTAGTTTTTCATTATTAATTTTTTTCATTTTTTTAGAATTTAAGTTGATTTTTAAGTTTTTTGATGTAAGAGGAAAAG\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEEEEE\n+@1_988\n+GTAATATCAGTATTTAGAAATTTGAGGTTGAAAGATTATGAATTTAAGATTATTTTGAGTTATATAGTAAGATTTTGTTTAAAAA\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAEEEEAEEEAEE<EEEEEEEEEEEEEEEEE\n+@1_989\n+AGGTGAGATGGGTTTTATTTTTTTTTGTTTTTGATGTTTTAATTTTTTTTTTTTTTTTATAATTTCTTTTTGTTCTGCTATTTTT\n++\n+AAAAAEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEAE/E///////AE//////<///<6//E\n+@1_990\n+ATCTCTCTCTATCTATCTCTATCTATATAAATATATATATATATATATATATATATCTTTATATATATATATATCTTTATCTAGA\n++\n+AAAAAEEEEEEEAEEEEEE//EEEEEEEE6EEEEEE6E/EEEEE/A6EEE/E/E///E/////EAE/AE//A/E/</E/////</\n+@1_991\n+TCTGTTGGAGGTAGATGGGAAGATAGGAGGGATTTGATAGGTTAGGGTAGAGGTATGAGAGGTGGTGTTGAGGATGGGAGAGAAG\n++\n+AAAAAE/EEEAEEEEEEEEEE6EEE6EEEEEE/EE<EAEEEEEEAEEEEAEEEEE<AEE/EEEEAAA<E<EEEE/EEE/E<EEE/\n+@1_992\n+AAAGGATGGTAGTTTTTATTTTTTAGGTGGAATTATTTATTTTTTATTTTGATTAGTTTTTTTTTATAATTATTGTTTATTTTTG\n++\n+AAAAAEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEAEEEEEEEEEEEEE6\n+@1_993\n+GGTGATATTAGAGTAAGAATTATTGTGAGGAATTAGAGATAGATATGAAAAAGAATATTGTTTATTTTGTAGATTATATAGAGTG\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAE<EEEEEE<EEEEEAEEEEEEEEEEE\n+@1_994\n+GTTGGGGGTAGGGGGAGGATTATGCGTTATTAATAAAATATTTTTTAAGTTGGATTGAGGATAGGAAATTTTTTTTTTTGATAAT\n++\n+AAAAAEEEAAEEEEEEEEEEEEEAEEEEEEEE6EEEEEEEEEEEEEEEEEEEEE<EE<EEEEEEEEAEEE<EEEEEEEEEEAEEE\n+@1_995\n+GCAGAATTGTTTATTAAGATTTTTGATATTTAATTTTTGTTTTTTTTAGTATTTTGATTAATTATTTAAGTTACATTTTGTTTAT\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEEAEEEEAEAEEEE/EEEAEA\n+@1_996\n+ATGCATATTATTATAGTGTAATGGCGTAAAATAGAAATAATTTTGTTAGTTTTAGATTTAGGTATAATGGAGTGAATATATTTTT\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE\n+@1_997\n+CAAGTTAAGAGATAGATTAGAAAAGAGAAAATGAGATTAAGAAGTATAGATCGGATGGTTTGAAGGACGTTAATAAATTTTTTTG\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEE<EEEEEEEEEEEAAEAAEEEEEEE<EEAEE<\n+@1_998\n+TTGTAGGTTCGTGGGTATTTAGATGTATTTATTATTATTATTATTATTATTATTATTATTATTATTATTTTAGACTTGGGATTTT\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEEAEEEEAEEEEEEEE/AEEEEE<AEA\n+@1_999\n+AAGTTTTAAGGAGTTATTTATAGATGGTATTTGTTTTGTTTTTTAGAATATTTAAAGGATTTTTGGATAGTATTTTATTAGTTTA\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEA\n+@1_1000\n+AGAATAGTAGTAGTAGGTAGTCTTTTTGTTTTATAATATATTTAGTTTTAGATGTAAGGTTATTTTAGTAGTGTTATATTTGGTT\n++\n+AAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEEEEEEEEAEAEEEEEEEEAEE\n' 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| diff -r 78c791a11b4c -r f211753166bd test-data/input1.fq.gz |
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| Binary file test-data/input1.fq.gz has changed |
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| diff -r 78c791a11b4c -r f211753166bd test-data/input1.fq.gzip |
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| Binary file test-data/input1.fq.gzip has changed |
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| diff -r 78c791a11b4c -r f211753166bd test-data/mapped_reads.bam |
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| Binary file test-data/mapped_reads.bam has changed |
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| diff -r 78c791a11b4c -r f211753166bd test-data/mapped_reads_short.bam |
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| Binary file test-data/mapped_reads_short.bam has changed |
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| diff -r 78c791a11b4c -r f211753166bd test-data/mapping_report.txt --- 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 |
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| @@ -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 ====================== |
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| diff -r 78c791a11b4c -r f211753166bd test-data/mapping_report_short.txt --- /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 |
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| @@ -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 |
| b |
| diff -r 78c791a11b4c -r f211753166bd test-data/output_html_report.html --- 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> |
| b |
| diff -r 78c791a11b4c -r f211753166bd test-data/output_splitting_report.txt --- 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 |
| b |
| @@ -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 |
| b |
| diff -r 78c791a11b4c -r f211753166bd test-data/summary.txt --- 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 |
| [ |
| b'@@ -1,8 +1,8 @@\n Create a temporary index with the offered files from the user. Utilizing the script: bismark_genome_preparation\n-Generating index with: \'bismark_genome_preparation --bowtie2 /var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp4_4hiluf\'\n+Generating index with: \'bismark_genome_preparation --bowtie2 /tmp/tmpProAS5\'\n Writing bisulfite genomes out into a single MFA (multi FastA) file\n \n-Bisulfite Genome Indexer version v0.20.0 (last modified 26 April 2018)\n+Bisulfite Genome Indexer version v0.22.1 (last modified: 14 April 2019)\n \n Step I - Prepare genome folders - completed\n \n@@ -79,7 +79,7 @@\n No samples; assembling all-inclusive block\n Sorting block of length 756159 for bucket 1\n (Using difference cover)\n- Sorting block time: 00:00:01\n+ Sorting block time: 00:00:00\n Returning block of 756160 for bucket 1\n Exited Ebwt loop\n fchr[A]: 0\n@@ -118,7 +118,7 @@\n ebwtTotSz: 252096\n color: 0\n reverse: 0\n-Total time for call to driver() for forward index: 00:00:01\n+Total time for call to driver() for forward index: 00:00:00\n Reading reference sizes\n Time reading reference sizes: 00:00:00\n Calculating joined length\n@@ -162,7 +162,7 @@\n No samples; assembling all-inclusive block\n Sorting block of length 756159 for bucket 1\n (Using difference cover)\n- Sorting block time: 00:00:00\n+ Sorting block time: 00:00:01\n Returning block of 756160 for bucket 1\n Exited Ebwt loop\n fchr[A]: 0\n@@ -201,7 +201,7 @@\n ebwtTotSz: 252096\n color: 0\n reverse: 1\n-Total time for backward call to driver() for mirror index: 00:00:00\n+Total time for backward call to driver() for mirror index: 00:00:01\n Settings:\n Output files: "BS_GA.*.bt2"\n Line rate: 6 (line is 64 bytes)\n@@ -264,7 +264,7 @@\n No samples; assembling all-inclusive block\n Sorting block of length 756159 for bucket 1\n (Using difference cover)\n- Sorting block time: 00:00:01\n+ Sorting block time: 00:00:00\n Returning block of 756160 for bucket 1\n Exited Ebwt loop\n fchr[A]: 0\n@@ -303,7 +303,7 @@\n ebwtTotSz: 252096\n color: 0\n reverse: 0\n-Total time for call to driver() for forward index: 00:00:01\n+Total time for call to driver() for forward index: 00:00:00\n Reading reference sizes\n Time reading reference sizes: 00:00:00\n Calculating joined length\n@@ -347,7 +347,7 @@\n No samples; assembling all-inclusive block\n Sorting block of length 756159 for bucket 1\n (Using difference cover)\n- Sorting block time: 00:00:00\n+ Sorting block time: 00:00:01\n Returning block of 756160 for bucket 1\n Exited Ebwt loop\n fchr[A]: 0\n@@ -386,29 +386,29 @@\n ebwtTotSz: 252096\n color: 0\n reverse: 1\n-Total time for backward call to driver() for mirror index: 00:00:00\n-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\'\n-Path to Bowtie 2 specified as: bowtie2\n-Bowtie seems to be working fine (tested command \'bowtie2 --version\' [2.3.4])\n+Total time for backward call to driver() for mirror index: 00:00:01\n+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\'\n+Bowtie 2 seems to be working fine (tested command \'bowtie2 --version\' [2.3.5])\n Output format is BAM (default)\n-Alignments will be written out in BAM format. Samtools found here: \'/Users/scholtalbers/miniconda3/envs/mulled-v1-7f230b3d24f9f00e91e72af479ffae49907f4592b1a7a4b05436e0a99567150a/bin/samtools\'\n-Reference genome folder provided is /var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp4_4hiluf/\t(absolute path is \'/private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp4_4hiluf/)\'\n+Alignments will be written out in BAM forma'..b't_2.dat to /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmprjiux3me/dataset_2.dat_C_to_T.fastq.gz\n+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\n \n-Created C -> T converted version of the FastQ file dataset_2.dat (44115 sequences in total)\n+Created C -> T converted version of the FastQ file input_1.fq.gz (44115 sequences in total)\n \n-Input file is dataset_2.dat_C_to_T.fastq.gz (FastQ)\n+Input file is input_1.fq.gz_C_to_T.fastq.gz (FastQ)\n \n-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\n+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\n \n-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)\n-Using Bowtie 2 index: /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp4_4hiluf/Bisulfite_Genome/CT_conversion/BS_CT\n+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)\n+Using Bowtie 2 index: /tmp/tmpProAS5/Bisulfite_Genome/CT_conversion/BS_CT\n \n Found first alignment:\t1_1\t4\t*\t0\t0\t*\t*\t0\t0\tTTGTATATATTAGATAAATTAATTTTTTTTGTTTGTATGTTAAATTTTTTAATTAATTTATTAATATTTTGTGAATTTTTAGATA\tAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEE\tYT:Z:UU\n-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)\n-Using Bowtie 2 index: /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp4_4hiluf/Bisulfite_Genome/GA_conversion/BS_GA\n+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)\n+Using Bowtie 2 index: /tmp/tmpProAS5/Bisulfite_Genome/GA_conversion/BS_GA\n \n Found first alignment:\t1_1\t4\t*\t0\t0\t*\t*\t0\t0\tTTGTATATATTAGATAAATTAATTTTTTTTGTTTGTATGTTAAATTTTTTAATTAATTTATTAATATTTTGTGAATTTTTAGATA\tAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEE\tYT:Z:UU\n \n->>> Writing bisulfite mapping results to /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmprjiux3me/results/dataset_2.dat_bismark_bt2.bam <<<\n+>>> Writing bisulfite mapping results to /tmp/tmpvcY9eC/results/input_1_bismark_bt2.bam <<<\n \n-Unmapped sequences will be written to /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmprjiux3me/results/dataset_2.dat_unmapped_reads.fq.gz\n-Ambiguously mapping sequences will be written to /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmprjiux3me/results/dataset_2.dat_ambiguous_reads.fq.gz\n+Unmapped sequences will be written to /tmp/tmpvcY9eC/results/input_1.fq.gz_unmapped_reads.fq.gz\n+Ambiguously mapping sequences will be written to /tmp/tmpvcY9eC/results/input_1.fq.gz_ambiguous_reads.fq.gz\n \n-Reading in the sequence file /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmpywNSSM/files/000/dataset_2.dat\n+Reading in the sequence file input_1.fq.gz\n Processed 44115 sequences in total\n \n \n-Successfully deleted the temporary file /private/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmprjiux3me/dataset_2.dat_C_to_T.fastq.gz\n+Successfully deleted the temporary file /tmp/tmpvcY9eC/input_1.fq.gz_C_to_T.fastq.gz\n \n Final Alignment report\n ======================\n' |
| b |
| diff -r 78c791a11b4c -r f211753166bd test-data/summary_short.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/summary_short.txt Tue Jul 30 06:30:36 2019 -0400 |
| [ |
| b'@@ -0,0 +1,495 @@\n+Create a temporary index with the offered files from the user. Utilizing the script: bismark_genome_preparation\n+Generating index with: \'bismark_genome_preparation --bowtie2 /tmp/tmpVM2AEy\'\n+Writing bisulfite genomes out into a single MFA (multi FastA) file\n+\n+Bisulfite Genome Indexer version v0.22.1 (last modified: 14 April 2019)\n+\n+Step I - Prepare genome folders - completed\n+\n+\n+\n+Total number of conversions performed:\n+C->T:\t146875\n+G->A:\t150504\n+\n+Step II - Genome bisulfite conversions - completed\n+\n+\n+Bismark Genome Preparation - Step III: Launching the Bowtie 2 indexer\n+Please be aware that this process can - depending on genome size - take several hours!\n+Settings:\n+ Output files: "BS_CT.*.bt2"\n+ Line rate: 6 (line is 64 bytes)\n+ Lines per side: 1 (side is 64 bytes)\n+ Offset rate: 4 (one in 16)\n+ FTable chars: 10\n+ Strings: unpacked\n+ Max bucket size: default\n+ Max bucket size, sqrt multiplier: default\n+ Max bucket size, len divisor: 4\n+ Difference-cover sample period: 1024\n+ Endianness: little\n+ Actual local endianness: little\n+ Sanity checking: disabled\n+ Assertions: disabled\n+ Random seed: 0\n+ Sizeofs: void*:8, int:4, long:8, size_t:8\n+Input files DNA, FASTA:\n+ genome_mfa.CT_conversion.fa\n+Building a SMALL index\n+Reading reference sizes\n+ Time reading reference sizes: 00:00:00\n+Calculating joined length\n+Writing header\n+Reserving space for joined string\n+Joining reference sequences\n+ Time to join reference sequences: 00:00:00\n+bmax according to bmaxDivN setting: 189039\n+Using parameters --bmax 141780 --dcv 1024\n+ Doing ahead-of-time memory usage test\n+ Passed! Constructing with these parameters: --bmax 141780 --dcv 1024\n+Constructing suffix-array element generator\n+Building DifferenceCoverSample\n+ Building sPrime\n+ Building sPrimeOrder\n+ V-Sorting samples\n+ V-Sorting samples time: 00:00:00\n+ Allocating rank array\n+ Ranking v-sort output\n+ Ranking v-sort output time: 00:00:00\n+ Invoking Larsson-Sadakane on ranks\n+ Invoking Larsson-Sadakane on ranks time: 00:00:00\n+ Sanity-checking and returning\n+Building samples\n+Reserving space for 12 sample suffixes\n+Generating random suffixes\n+QSorting 12 sample offsets, eliminating duplicates\n+QSorting sample offsets, eliminating duplicates time: 00:00:00\n+Multikey QSorting 12 samples\n+ (Using difference cover)\n+ Multikey QSorting samples time: 00:00:00\n+Calculating bucket sizes\n+Splitting and merging\n+ Splitting and merging time: 00:00:00\n+Avg bucket size: 756159 (target: 141779)\n+Converting suffix-array elements to index image\n+Allocating ftab, absorbFtab\n+Entering Ebwt loop\n+Getting block 1 of 1\n+ No samples; assembling all-inclusive block\n+ Sorting block of length 756159 for bucket 1\n+ (Using difference cover)\n+ Sorting block time: 00:00:00\n+Returning block of 756160 for bucket 1\n+Exited Ebwt loop\n+fchr[A]: 0\n+fchr[C]: 235897\n+fchr[G]: 235897\n+fchr[T]: 386401\n+fchr[$]: 756159\n+Exiting Ebwt::buildToDisk()\n+Returning from initFromVector\n+Wrote 4446745 bytes to primary EBWT file: BS_CT.1.bt2\n+Wrote 189044 bytes to secondary EBWT file: BS_CT.2.bt2\n+Re-opening _in1 and _in2 as input streams\n+Returning from Ebwt constructor\n+Headers:\n+ len: 756159\n+ bwtLen: 756160\n+ sz: 189040\n+ bwtSz: 189040\n+ lineRate: 6\n+ offRate: 4\n+ offMask: 0xfffffff0\n+ ftabChars: 10\n+ eftabLen: 20\n+ eftabSz: 80\n+ ftabLen: 1048577\n+ ftabSz: 4194308\n+ offsLen: 47260\n+ offsSz: 189040\n+ lineSz: 64\n+ sideSz: 64\n+ sideBwtSz: 48\n+ sideBwtLen: 192\n+ numSides: 3939\n+ numLines: 3939\n+ ebwtTotLen: 252096\n+ ebwtTotSz: 252096\n+ color: 0\n+ reverse: 0\n+Total time for call to driver() for forward index: 00:00:00\n+Reading reference sizes\n+ Time reading reference sizes: 00:00:00\n+Calculating joined length\n+Writing header\n+Reserving space for joined string\n+Joining reference sequences\n+ Time to join reference sequences: 00:00:00\n+ Time to reverse reference sequence: 00:00:00\n+bmax according to b'..b"eaded (default)\n+\n+Summary of all aligner options:\t-q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --quiet\n+Current working directory is: /tmp/tmpq6T4hb/job_working_directory/000/8/working\n+\n+Now reading in and storing sequence information of the genome specified in: /tmp/tmpVM2AEy/\n+\n+chr chrY_JH584300_random (182347 bp)\n+chr chrY_JH584301_random (259875 bp)\n+chr chrY_JH584302_random (155838 bp)\n+chr chrY_JH584303_random (158099 bp)\n+\n+Single-core mode: setting pid to 1\n+\n+Single-end alignments will be performed\n+=======================================\n+\n+Input file is in FastQ format\n+Writing a C -> T converted version of the input file input_1.fq to /tmp/tmpHOWuwJ/input_1.fq_C_to_T.fastq.gz\n+\n+Created C -> T converted version of the FastQ file input_1.fq (1000 sequences in total)\n+\n+Input file is input_1.fq_C_to_T.fastq.gz (FastQ)\n+\n+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\n+\n+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)\n+Using Bowtie 2 index: /tmp/tmpVM2AEy/Bisulfite_Genome/CT_conversion/BS_CT\n+\n+Found first alignment:\t1_1\t4\t*\t0\t0\t*\t*\t0\t0\tTTGTATATATTAGATAAATTAATTTTTTTTGTTTGTATGTTAAATTTTTTAATTAATTTATTAATATTTTGTGAATTTTTAGATA\tAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEE\tYT:Z:UU\n+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)\n+Using Bowtie 2 index: /tmp/tmpVM2AEy/Bisulfite_Genome/GA_conversion/BS_GA\n+\n+Found first alignment:\t1_1\t4\t*\t0\t0\t*\t*\t0\t0\tTTGTATATATTAGATAAATTAATTTTTTTTGTTTGTATGTTAAATTTTTTAATTAATTTATTAATATTTTGTGAATTTTTAGATA\tAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEAEEEEEE\tYT:Z:UU\n+\n+>>> Writing bisulfite mapping results to /tmp/tmpHOWuwJ/results/input_1_bismark_bt2.bam <<<\n+\n+Unmapped sequences will be written to /tmp/tmpHOWuwJ/results/input_1.fq_unmapped_reads.fq.gz\n+Ambiguously mapping sequences will be written to /tmp/tmpHOWuwJ/results/input_1.fq_ambiguous_reads.fq.gz\n+\n+Reading in the sequence file input_1.fq\n+Processed 1000 sequences in total\n+\n+\n+Successfully deleted the temporary file /tmp/tmpHOWuwJ/input_1.fq_C_to_T.fastq.gz\n+\n+Final Alignment report\n+======================\n+Sequences analysed in total:\t1000\n+Number of alignments with a unique best hit from the different alignments:\t8\n+Mapping efficiency:\t0.8%\n+\n+Sequences with no alignments under any condition:\t983\n+Sequences did not map uniquely:\t9\n+Sequences which were discarded because genomic sequence could not be extracted:\t0\n+\n+Number of sequences with unique best (first) alignment came from the bowtie output:\n+CT/CT:\t6\t((converted) top strand)\n+CT/GA:\t2\t((converted) bottom strand)\n+GA/CT:\t0\t(complementary to (converted) top strand)\n+GA/GA:\t0\t(complementary to (converted) bottom strand)\n+\n+Number of alignments to (merely theoretical) complementary strands being rejected in total:\t0\n+\n+Final Cytosine Methylation Report\n+=================================\n+Total number of C's analysed:\t143\n+\n+Total methylated C's in CpG context:\t3\n+Total methylated C's in CHG context:\t2\n+Total methylated C's in CHH context:\t3\n+Total methylated C's in Unknown context:\t0\n+\n+Total unmethylated C's in CpG context:\t1\n+Total unmethylated C's in CHG context:\t36\n+Total unmethylated C's in CHH context:\t98\n+Total unmethylated C's in Unknown context:\t0\n+\n+C methylated in CpG context:\t75.0%\n+C methylated in CHG context:\t5.3%\n+C methylated in CHH context:\t3.0%\n+Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0\n+\n+\n+Bismark completed in 0d 0h 0m 5s\n+\n+====================\n+Bismark run complete\n+====================\n+\n" |