Mercurial > repos > mbernt > maxbin2
diff test-data/1/out.log @ 2:6a638de7915c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
| author | iuc |
|---|---|
| date | Tue, 29 Oct 2019 08:45:20 -0400 |
| parents | 35aa0df55a62 |
| children |
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--- a/test-data/1/out.log Tue Oct 16 10:28:16 2018 -0400 +++ b/test-data/1/out.log Tue Oct 29 08:45:20 2019 -0400 @@ -1,17 +1,18 @@ -MaxBin 2.2.4 -Input contig: Bin_Sample3_contigs.fasta +MaxBin 2.2.7 +Input contig: /tmp/tmpkKUAw8/files/2/1/e/dataset_21ee7f6a-b141-4f58-9edf-40cf6498124b.dat out header: out -Located reads file [interleavedPE_unmapped_Sample3_total.fasta] -Running Bowtie2 on reads file [interleavedPE_unmapped_Sample3_total.fasta]...this may take a while... -Searching against 107 marker genes to find starting seed contigs for [Bin_Sample3_contigs.fasta]... +Thread: 1 +Located reads file [/tmp/tmpkKUAw8/files/e/9/9/dataset_e996d3cb-de7d-4e64-a9f8-75cd61e9f791.dat] +Running Bowtie2 on reads file [/tmp/tmpkKUAw8/files/e/9/9/dataset_e996d3cb-de7d-4e64-a9f8-75cd61e9f791.dat]...this may take a while... +Searching against 107 marker genes to find starting seed contigs for [/tmp/tmpkKUAw8/files/2/1/e/dataset_21ee7f6a-b141-4f58-9edf-40cf6498124b.dat]... Try harder to dig out marker genes from contigs. Done data collection. Running MaxBin... -Command: /home/berntm/miniconda3/envs/__maxbin2@2.2.4/opt/MaxBin-2.2.4/src/MaxBin -fasta out.contig.tmp -abund out.contig.tmp.reads.abund1 -seed out.seed -out out -min_contig_length 1000 +Command: /home/berntm/miniconda3/envs/__maxbin2@2.2.7/opt/MaxBin-2.2.7/src/MaxBin -fasta out.contig.tmp -abund out.contig.tmp.reads.abund1 -seed out.seed -out out -min_contig_length 1000 Minimum contig length set to 1000. Reading seed list... Looking for seeds in sequences. - contig-201_2 [11.293216] - contig-201_100 [10.048304] + contig-201_2 [2.848706] + contig-201_100 [2.993483] Get 2 seeds. Start EM process. @@ -36,13 +37,13 @@ Minimum probability for binning: 0.50 Ignoring 0 bins without any sequences. Number of unclassified sequences: 0 (0.00%) -Elapsed time: 0 days 00:00:00 +Elapsed time: 0 days 00:00:01 Deleting intermediate files. ========== Job finished ========== -Yielded 2 bins for contig (scaffold) file Bin_Sample3_contigs.fasta +Yielded 2 bins for contig (scaffold) file /tmp/tmpkKUAw8/files/2/1/e/dataset_21ee7f6a-b141-4f58-9edf-40cf6498124b.dat Here are the output files for this run. Please refer to the README file for further details. @@ -52,10 +53,11 @@ Marker genes for each bin: out.marker_of_each_gene.tar.gz Bin files: out.001.fasta - out.002.fasta Unbinned sequences: out.noclass +Marker plot: out.marker.pdf -Store abundance information of reads file [interleavedPE_unmapped_Sample3_total.fasta] in [out.abund1]. +Store abundance information of reads file [/tmp/tmpkKUAw8/files/e/9/9/dataset_e996d3cb-de7d-4e64-a9f8-75cd61e9f791.dat] in [out.abund1]. ========== Elapsed Time ========== -0 hours 0 minutes and 14 seconds. +0 hours 0 minutes and 6 seconds.