BowtieToPileupforewardReadsFileNames11/data2/Nasonia/s_1_1_sequence.txt2010-07-14 16:12:19.137 CEST/data2/Nasonia/2010-07-14 16:12:08.916 CESTA list of all forward reads files. These are generally the files starting with s_N_1, where N is the number of the pair.2010-07-14 16:11:49.846 CESTreverseReadsFileNames11/data2/Nasonia/s_1_2_sequence.txt2010-07-14 16:12:56.21 CESTA list of all reverse reads files. These are generally the files starting with s_N_2, where N is the number of the pair.2010-07-14 16:12:38.160 CESTalignmentBasename00bowtie_alignment2010-07-14 16:10:34.664 CESTFull path and name of the desired alignment file, but without an extension. A logfile with the same name (with .log) will be created.2010-07-14 16:10:20.676 CESTreferenceGenome00Full path and name of reference genome file.2010-07-14 16:14:58.509 CEST/data2/Nasonia/ref_genome/Nvit_2.0.linear.fa2010-07-14 16:15:26.803 CEST/data2/Nasonia/ref_genome/2010-07-14 16:15:12.49 CESTindexBasename00Nvitripennis2010-07-14 16:09:16.534 CESTDesired bowtie index base name. Bowtie-build will generate 6 files with this base name: .1.ebwt, .2.ebwt, .3.ebwt, .4.ebwt, .rev.1.ebwt, and .rev.2.ebwt. Bowtie will use this index, the original reference genome file is no longer used by bowtie.2010-07-14 16:09:09.642 CESTrelativeIndexLocation00Location to write index to. Is relative to the reference genome. Do not use leading slashes unless you wish to move up in the directory structure using '../'.2010-09-16 11:52:08.714 CESTLocation to write index to. Is relative to the reference genome. Do nut use leading slashes unless you wish to move up in the directory structure using '../'.2010-07-14 16:08:14.408 CESTbowtie_index2010-07-14 16:08:34.699 CESTpileupBasename00Desired name for the pileup file (without path)2010-07-14 16:57:33.993 CESTraw.pileup2010-07-14 16:57:49.772 CESTra2010-07-14 16:57:37.92 CESTbowtie_errString that may contain some of Bowties error output.2010-09-16 11:52:49.987 CESTbowtieBuild_errString that may contain some of Bowties error output.2010-09-16 11:53:04.507 CESTPileup_rawPileupFinal workflow output: location and name of the pileup file.2010-09-16 11:56:55.458 CESTintermediate_bowtieIndexBasenameIntermediate output for bowtie-build: the basename of the index files.2010-09-16 11:54:18.152 CESTintermediate_bowtie_samLocationAndBasenameIntermediate output for Bowtie: the path and base name of the created SAM alignment file.2010-09-16 11:53:48.740 CESTintermediate_samToBam_bamNameIntermediate output for samToBam: the resulting BAM file.2010-09-16 11:56:08.761 CESTintermediate_filterAndSort_sortedBamNameIntermediate output for filterAndSort: resulting BAM file.2010-09-16 11:54:58.863 CESTintermediate_refIndexIntermediate output for indexReference: the SAMtools index.2010-09-16 11:55:38.667 CESTBowtie_buildreferenceGenome0indexBasename0indexLocation0bowtieBuild_bowtieIndexBasename00err00bowtieBuild creates a Bowite-specific index of the reference genome.2010-09-16 11:58:49.86 CESTbowtieBuild creates a Bowtie-specific index of the reference genome.2010-09-16 11:59:21.447 CESTnet.sf.taverna.t2.activitiesdataflow-activity1.2net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBowtiebowtie_readsFileNames1bowtie_reverseReadsFileNames1bowtie_alignmentBasename0bowtie_indexBasename0bowtie_err00bowtie_samLocationAndBasename00Bowtie aligns the reads to the reference genome.2010-09-16 11:58:17.245 CESTnet.sf.taverna.t2.activitiesdataflow-activity1.2net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesamToBamsamToBam_samName0samToBam_bamName00SAMtools SAM to BAM conversion.2010-09-16 12:00:58.379 CESTnet.sf.taverna.t2.activitiesdataflow-activity1.2net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeFilterAndSortfilterAndSort_bamName0sortedBamName00Filters all unaligned reads from the input BAM file and sorts the rest. Outputs the name and location of the filtered and sorted BAM file.2010-09-16 12:00:13.113 CESTnet.sf.taverna.t2.activitiesdataflow-activity1.2net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokePileupfaidx0pileupName0referenceGenomeFilename0sortedBamName0rawPileup00Generates a pileup (list with information on each genomic position) from a filtered and sorted BAM file.2010-09-16 12:00:45.322 CESTnet.sf.taverna.t2.activitiesdataflow-activity1.2net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeindexReferencereferenceGenomeFilename0refIndex00indexReference creates a SAMtools-specific index of the reference genome.2010-09-16 11:59:10.423 CESTnet.sf.taverna.t2.activitiesdataflow-activity1.2net.sf.taverna.t2.activities.dataflow.DataflowActivitynet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeBowtie_buildreferenceGenomeBowtie_buildindexBasenameBowtie_buildindexLocationBowtiebowtie_readsFileNamesBowtiebowtie_reverseReadsFileNamesBowtiebowtie_alignmentBasenameBowtiebowtie_indexBasenamesamToBamsamToBam_samNameFilterAndSortfilterAndSort_bamNamePileupfaidxPileuppileupNamePileupreferenceGenomeFilenamePileupsortedBamNameindexReferencereferenceGenomeFilenamebowtie_errbowtieBuild_errPileup_rawPileupintermediate_bowtieIndexBasenameintermediate_bowtie_samLocationAndBasenameintermediate_samToBam_bamNameintermediate_filterAndSort_sortedBamNameintermediate_refIndexdb85225f-f384-4d67-aa4d-8deb0381e7b12010-07-14 16:15:27.950 CEST0c8e27d0-8631-4ca4-a8ac-c819f99b0ccb2010-07-14 16:12:56.993 CESTeeef4890-923c-461f-b73e-5b94dfd36c8d2010-09-16 12:01:17.718 CESTWBKoetsier2010-07-14 15:53:30.84 CESTThis example workflow aligns short sequencing reads to a reference genome using Bowtie and generates a SAMtools pileup file. The main problem with sequencing data is the sheer amount. By analysing an actual data set (SNP detection in N. vitripennis) and translating this pipeline into a Taverna workflow, I was able to come up with an easy way of using Taverna for such analysis. I created a Java API (with my limited Java experience) that wraps the command line programs used in the analysis pipeline: Bowtie and some of the SAMtools. Instead of passing Taverna or the API data, only references to files are used. The API does not have a main entry point, instead, each step in the analysis pipeline is represented by a short Beanshell script that calls the appropriate method of the API. These scripts are used as services. This workflow is part of my bachelors thesis (bioinformatics at the Hanze University Groningen, the Netherlands).2010-09-16 11:46:42.100 CEST6731624c-555d-413f-aa13-73a219acc8692010-07-14 16:12:19.543 CEST281758c3-029e-4ee8-bcec-c9a10638d2d02010-07-14 16:57:52.828 CEST48e52609-9e53-4454-be5d-8fcee2226f462010-09-16 11:42:44.943 CEST284cc100-cfaf-404a-9a6c-6249adf1a8432010-07-14 16:08:34.994 CESTThis workflow
This workflow is part of my bachelors thesis (bioinformatics at the Hanze University Groningen, the Netherlands).2010-09-16 11:36:33.997 CEST75105663-5942-4bce-8945-a0119a7a2c772010-07-14 16:56:55.128 CESTc13e9eee-2aa6-4c52-8623-4214f1aaf7b52010-07-14 16:01:44.651 CESTafb2b38b-b35e-4dca-97be-4358656f21d82010-09-16 11:46:44.300 CESTThis example workflow aligns short sequencing reads to a reference genome using Bowtie and generates a SAMtools pileup file. The main problem with sequencing data is the sheer amount. By analysing an actual data set (SNP detection in N. vitripennis) and translating this pipeline into a Taverna workflow, I was able to come up with an easy way of using Taverna for such analysis. I created a Java API (with my limited Java experience) that wraps the command line programs used in the analysis pipeline: Bowtie and SAMtools/Picard
This workflow is part of my bachelors thesis (bioinformatics at the Hanze University Groningen, the Netherlands).2010-09-16 11:41:56.862 CESTBowtieToPileup2010-07-14 15:53:41.892 CEST6f194cf9-4d62-4a49-87aa-ca34b4ed98642010-07-14 16:10:35.564 CESTThis example workflow aligns short sequencing reads to a reference genome using Bowtie and generates a SAMtools pileup file. By analysing an actual data set (SNP detection in N. vitripennis) and translating this analysis pipeline into a Taverna workflow, I was able to come up with an easy way of using Taverna for such analysis. I created a Java API (with my limited Java experience) that wraps the command line programs used in the analysis pipeline: Bowtie and some of the SAMtools. Instead of passing Taverna or the API data, only references to files are used. The API does not have a main entry point, instead, each step in the analysis pipeline is represented by a short Beanshell script that calls the appropriate method of the API. These scripts are used as services. This workflow is part of my bachelors thesis (bioinformatics at the Hanze University Groningen, the Netherlands). Please note that Bowtie and the SAMtools need to be installed and in the path. The API needs to be present in the .taverna/lib directory, please check dependencies of the Beanshell services. Assumes Linux.2010-09-16 11:51:08.88 CESTTakes raw reads and reference genome and returns pileup2010-07-14 15:54:07.365 CEST958b89a5-1848-4c4f-9894-915706aee73b2010-07-14 15:54:14.492 CEST6640f876-4bba-45ed-a932-c61659bc03d02010-07-14 16:09:18.98 CESTa55bd66d-9c62-4727-9d7b-0690c02b4d1a2010-09-16 12:04:47.780 CESTf8631dd8-5947-48b3-ae40-6dba9c18330b2010-07-14 16:25:06.63 CESTPileupfaidx00/path/to/refGenome.fa.fai2010-07-14 15:46:57.665 CESTName and full path of an existing SAMtools reference genome index (*.fai)2010-07-14 15:46:44.542 CESTpileupName00raw.pileup2010-07-14 15:47:34.59 CESTDesired base name for the pileup. Defaults to raw.pileup.2010-07-14 15:47:30.607 CESTreferenceGenomeFilename00/path/to/Nvit_2.0.linear.fa2010-07-14 15:48:08.836 CESTFull path and name of reference genome.2010-07-14 15:47:50.528 CEST/path/to/2010-07-14 15:47:57.832 CESTsortedBamName00/path/to/sorted.bam2010-07-14 15:48:34.556 CESTName and full path of alignment file in BAM format.2010-07-14 15:48:43.578 CESTName and full path of alignment file2010-07-14 15:48:23.514 CESTrawPileupFull path and name of pileup file.2010-07-14 15:49:02.350 CESTpileupfaidx0pileupName0referenceGenomeFilename0sortedBamName0rawPileup00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivityworkflowNGSPipeline-0.3.jarjava.lang.StringtruesortedBamName0text/plainjava.lang.StringtruereferenceGenomeFilename0text/plainjava.lang.StringtruepileupName0text/plainjava.lang.Stringtruefaidx0text/plain0rawPileup0net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokepileupfaidxpileuppileupNamepileupreferenceGenomeFilenamepileupsortedBamNamerawPileupPileup2010-07-14 13:39:49.327 CEST9b33a75d-061a-4f40-8bd3-b2e7e04a4da62010-07-14 15:48:10.424 CESTWBKoetsier2010-07-14 13:39:41.639 CESTCreates a pileup from the alignment file using 'samtools pileup -c'.2010-07-14 13:41:51.414 CESTd4780d10-e633-403a-8a5f-d0b153113f0c2010-07-14 15:49:03.666 CEST66a227d5-c250-46f8-8267-30d48dc172e02010-07-14 15:46:59.326 CESTd2c01c50-fa34-4589-814a-1c6dce82fba22010-07-14 15:47:35.423 CEST538a762a-509a-4aac-885a-a4ba43d75db22010-07-14 15:48:43.698 CEST0eafce7f-2492-4515-a2b9-3c60d193a87f2010-07-14 13:41:59.713 CESTCreates a pileup from the alignment file using 'samtools pileup -2010-07-14 13:40:14.358 CESTsamToBamsamToBam_samName00Full path and name of sam file. It will be converted into a bamfile with the same name.2010-07-12 20:12:34.604 CEST/path/to/alignment.sam2010-07-12 20:12:43.194 CESTsamToBam_bamName/path/to/alignment.bam2010-07-12 20:13:05.46 CESTFull path and name of created bam file.2010-07-12 20:12:57.764 CESTsamToBamsamName0bamName00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivityworkflowNGSPipeline-0.3.jarjava.lang.StringtruesamName0text/plain0bamName0net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokesamToBamsamNamesamToBam_bamNamec1922db8-5a84-4e0a-8a7f-31003a0c96392010-07-14 12:18:03.498 CESTc060ad17-3113-4f50-a496-3f4d2e9d0ae42010-07-13 12:28:32.526 CESTbab6dd0a-4fb7-415d-996f-45e380e9d5322010-07-13 12:27:26.510 CESTsamToBam2010-07-13 12:28:05.802 CEST11aa98e0-614e-4b43-9b2d-d175c46741752010-07-14 12:17:25.101 CESTConverts given SAM file to BAM using samtools view -bS2010-07-13 12:28:32.400 CESTWBKoetsier2010-07-13 12:27:57.568 CESTindexReferencereferenceGenomeFilename00/home/Nikki/dev/testData/refGenome/2010-06-07 16:49:52.415 CEST/path/to/Nvit_2.0.linear.fa2010-07-14 13:11:59.554 CESTReference genome filename2010-06-07 16:49:34.144 CEST/home/Nikki/dev/testData/refGenome/Nvit_2.0.linear.fa2010-06-07 16:50:05.387 CESTrefIndexIndex of reference genome in 2010-07-14 13:12:14.762 CESTIndexReferencereferenceGenomeFilename0refIndex00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivityworkflowNGSPipeline-0.3.jarjava.lang.StringtruereferenceGenomeFilename0text/plain0refIndex0net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokeIndexReferencereferenceGenomeFilenamerefIndexIndex reference genome using 'samtools faidx'2010-07-14 13:11:25.232 CEST37688cbe-bd0c-469d-97b9-f602c9883ceb2010-07-14 13:11:35.29 CESTWBKoetsier2010-07-14 13:10:59.628 CESTindexReference2010-07-14 13:11:33.169 CESTc977075e-9861-4223-9816-7dbc96faf9b92010-07-14 13:31:09.607 CESTe3755d79-0de7-4080-888a-ee8cdb074e722010-07-14 13:36:26.247 CESTf3147cdf-26ec-410c-91b2-39b2ad3f55f92010-07-14 13:12:00.590 CESTBowtiebowtie_alignmentBasename00/path/to/desired/alignmentname2010-07-12 20:03:55.460 CEST/path/to/desired/alignmentname2010-07-12 20:04:01.271 CESTFull path and name of the desired alignment file, but without an extension. A logfile with the same name (with .log) will be created.2010-07-12 20:05:01.902 CESTbowtie_indexBasename00Full path and base name of the bowtie-build index.2010-07-12 20:05:23.916 CEST/path/to/genome2010-07-12 20:05:41.298 CESTFull path and base name of the bowtie-build index. This base name is the name of the 'ebwt' files, but without .N.ebwt.2010-07-12 20:06:20.736 CESTbowtie_readsFileNames11A list of all forward reads files. These are generally the files starting with s_N_1, where N is the number of the pair.2010-07-12 20:07:28.273 CEST/path/to/s_1_1_sequence.txt2010-07-12 20:07:48.939 CESTbowtie_reverseReadsFileNames11A list of all reverse reads files. These are generally the files starting with s_N_2, where N is the number of the pair.2010-07-12 20:08:06.551 CEST/path/to/s_1_2_sequence.txt2010-07-12 20:08:24.252 CESTbowtie_samLocationAndBasenameThis service returns the full path and name of the resulting alignment file (in SAM format). If an alignment base name was given, this is used. Otherwise the file will be called alignment.sam and written to the same directory as the reads files.2010-07-12 20:10:01.354 CEST/path/to/alignment.sam2010-07-12 20:10:08.496 CESTThis service returns the full path and name of the resulting alignment file (in SAM format).2010-07-12 20:08:59.812 CEST/path/to2010-07-12 20:09:05.773 CESTbowtie_errError string should the service fail.2010-07-12 20:40:27.804 CESTbowtiealignmentBasename0indexBasename0readsFileNames1reverseReadsFileNames1samLocationAndBasename00err00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivityworkflowNGSPipeline-0.3.jarjava.lang.StringtruereadsFileNames1text/plainjava.lang.StringtruereverseReadsFileNames1text/plainjava.lang.StringtrueindexBasename0text/plainjava.lang.StringtruealignmentBasename0text/plain0samLocationAndBasename00err0net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokebowtiealignmentBasenamebowtieindexBasenamebowtiereadsFileNamesbowtiereverseReadsFileNamesbowtie_samLocationAndBasenamebowtie_errBowtie: runs bowtie using these set options:
-a
-3 5
-n 2
-l 28
-y
-t
--sam
-p 16
--best2010-07-13 10:03:04.159 CEST45386c6b-cc44-477e-980c-331d954ee60a2010-07-13 09:56:58.798 CESTBowtie: runs bowtie using these set options:
-a
-3 5
-n 2
-l 28
-y
-t
--sam
-p 16
--best
If neccesary, these options can be changed by changing the bowtie.properties file in $HOME/.taverna/lib.
If bowtie should fail, the error will be written to the error output port 'err' and port 'samLocationAndBasename' will come up empty.2010-07-13 15:04:35.865 CEST53cb7c63-8c2f-4888-90a0-02971f1d2f102010-07-13 10:03:04.320 CESTBowtie2010-07-13 10:03:45.14 CESTBowtie: runs bowtie using these set options:
-a
-3 5
-n 2
-l 28
-y
-t
--sam
-p 16
--best
If bowtie should fail, the error will be written to the error output port 'err' and port 'samLocationAndBasename' will come up empty.2010-07-13 13:21:36.33 CEST5ffc112e-85b6-494b-84a6-811c93ec91782010-07-13 10:03:45.139 CESTBowtie: runs bowtie using these set options:
-a
-3 5
-n 2
-l 28
-y
-t
--sam
-p 16
--best
If bowtie should fail, the error will be written to the error output port 'err' and port 2010-07-13 13:20:51.988 CESTbfb24cf1-703e-4f34-a9d9-1527b15ea5f22010-07-13 09:59:44.252 CESTb34a296f-361c-4ba0-a0ad-735aa2f37b122010-07-12 20:44:08.678 CEST2010-07-13 10:03:32.845 CESTWBKoetsier2010-07-13 10:01:30.895 CEST99ae6bae-0810-4e33-9da1-13b214df6c912010-07-13 12:21:16.121 CESTBowtie: runs bowtie using these set options:
-a
-3 5
-n 2
-l 28
-y
-t
--sam
-p 16
--best2010-07-13 10:03:38.649 CESTd0ef063e-c6d1-4275-b42b-26e69d9772d12010-07-13 10:04:55.331 CESTb8273aa2-fb95-48f9-a460-5d855d7568d92010-07-13 13:21:36.159 CEST921d4d26-39e6-4ea5-9e16-c66a69bf77642010-07-12 20:40:28.934 CEST95b791a4-549e-4ae6-8932-5e86d67b9f812010-07-13 15:04:35.987 CEST5d9c174d-cb24-43d0-bc30-2bc233617b862010-07-13 15:34:24.651 CEST5f2a95d7-6d62-47f8-92ba-64bdffb0e9262010-07-13 12:19:11.671 CESTBowtie: runs bowtie using these set options:2010-07-13 10:01:48.151 CEST945aa086-0f72-446f-8761-537e673671b52010-07-13 14:26:07.310 CESTBowtie: runs bowtie using these set options:
-a
-3 5
-n 2
-l 28
-y
-t
--sam
-p 16
--best
If bowtie should fail, the error will be written to the error output port 'err'2010-07-13 13:20:32.642 CEST28f50309-c87e-493b-ac56-3e504c68894b2010-07-12 20:36:29.920 CEST9d08ecb0-0f1e-4886-8f30-dadcc67ba80f2010-07-13 10:54:36.687 CESTBowtie_buildindexBasename00Desired bowtie index base name. Bowtie-build will generate 6 files with this base name: .1.ebwt, .2.ebwt, .3.ebwt, .4.ebwt, .rev.1.ebwt, and .rev.2.ebwt.
Bowtie-build: runs bowtie-build.
Takes reference genome filename, index basename and index location as input. When index basename and location are left blank, default values will be read from the bowtie.properties file in $HOME/.taverna/lib.2010-07-14 10:36:19.239 CESTDesired bowtie index base name. Bowtie-build will generate 6 files with this base name: .1.ebwt, .2.ebwt, .3.ebwt, .4.ebwt, .rev.1.ebwt, and .rev.2.ebwt. Bowtie will use this index, the original reference genome file is no longer used by bowtie.2010-07-14 10:37:11.933 CESTDesired bowtie index basename. Bowtie-build will generate
Bowtie-build: runs bowtie-build.
Takes reference genome filename, index basename and index location as input. When index basename and location are left blank, default values will be read from the bowtie.properties file in $HOME/.taverna/lib.2010-07-14 10:34:55.201 CESTNvitripennis2010-07-14 10:37:20.144 CESTindexLocation00Location to write index to. Give full path.2010-07-14 10:37:50.958 CESTLocation to write index to. Is relative to the reference genome2010-07-14 10:38:51.821 CESTLocation to write index to. Is relative to the reference genome. Do nut use leading slashes unless you wish to move up in the directory structure using '../'.2010-07-14 10:58:12.3 CESTbowtie_index2010-07-14 10:58:38.443 CESTLocation to write index to. Is relative to the reference genome. Do nut use leading slashes2010-07-14 10:46:52.849 CEST/path/to/index/2010-07-14 10:38:13.887 CESTreferenceGenome00/data2/Nasonia/ref_genome/Nvit_2.0.linear.fa2010-07-14 10:59:41.59 CESTFull path and name of the reference genome file (must be in FASTA format)2010-07-14 10:59:07.33 CESTbowtieBuild_bowtieIndexBasenamefull path and base name of the created index2010-07-14 11:00:22.267 CESTerrError string should anything go wrong.2010-07-14 11:55:52.595 CESTbowtieBuildindexBasename0indexLocation0referenceGenome0bowtieIndexBasename00err00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivityworkflowNGSPipeline-0.3.jarjava.lang.StringtruereferenceGenome0text/plainjava.lang.StringtrueindexBasename0text/plainjava.lang.StringtrueindexLocation0text/plain0bowtieIndexBasename00err0net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokebowtieBuildindexBasenamebowtieBuildindexLocationbowtieBuildreferenceGenomebowtieBuild_bowtieIndexBasenameerr41375c4b-5795-4ba2-a081-e72cb612fd3a2010-07-13 18:19:50.830 CEST81085a74-5ed0-4c30-811e-5addc4908bc02010-07-14 11:00:26.459 CESTWBKoetsier2010-07-13 17:57:26.246 CESTBowtie-build2010-07-13 17:57:38.5 CEST5337636f-9508-4fed-a2db-f561c3ca5ab12010-07-14 11:55:52.722 CESTe0ec64a9-ed40-4985-8f18-e7d364418eaa2010-07-14 10:59:41.179 CEST65a7e8b5-ce7a-478a-ad8a-625a48dbfb222010-07-14 12:07:21.275 CESTBowtie-build: runs bowtie-build.
Takes reference genome filename, index basename and index location as input. When index basename and location are left blank, default values will be read from the bowtie.properties file in $HOME/.taverna/lib.2010-07-13 17:59:31.834 CEST85e9b539-6347-44c7-8cf7-5c831fe63b7a2010-07-14 10:58:38.576 CESTe055476f-ea13-4043-ade7-e9c8477327f82010-07-13 17:59:33.63 CEST010c2e3f-bf22-4b4c-b199-30942ab63f692010-07-14 12:06:06.820 CEST2a6c44fd-cd57-4948-8502-dfd3a5709ad12010-07-14 10:37:20.345 CESTFilterAndSortfilterAndSort_bamName00Name and location of BAM file2010-05-19 16:42:27.770 CEST/path/to/my_alignment.bam2010-05-19 16:42:38.793 CESTsortedBamNamefilterAndSortbamName0sortedBamName00net.sf.taverna.t2.activitiesbeanshell-activity1.2net.sf.taverna.t2.activities.beanshell.BeanshellActivityworkflowNGSPipeline-0.3.jarjava.lang.StringtruebamName0text/plain0sortedBamName0net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize1net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry1.0100050000net.sf.taverna.t2.coreworkflowmodel-impl1.2net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.InvokefilterAndSortbamNamesortedBamNameFilters and sorts the given BAM file using 2010-07-14 12:55:14.930 CESTFilters and sorts the given BAM file. First, all unaligned reads are removed using the Picard program 'ViewSam'.
using the following pipeline: java -jar ViewSam.jar ALIGNMENT_STATUS=Aligned I=alignment.bam 2> viewsam.err | sed '1d' | samtools view -bS - | samtools sort - sorted2010-07-14 12:57:08.554 CESTFilters and sorts the given BAM file. First, all unaligned reads are removed using the Picard program 'ViewSam'. The unwanted header is then removed using Unix 'sed', after which the reads are sorted according to chromosome position. Output is a BAM file.
2010-07-14 13:00:46.737 CEST2c46a18c-722c-46ed-9a77-427b8411d3962010-07-14 13:05:09.696 CESTFilterAndSort2010-07-14 12:54:55.283 CESTWBKoetsier2010-07-14 12:54:46.967 CEST5e2e4b3a-5eb3-48c6-9c30-ab9e2da2ada62010-07-14 13:00:46.903 CEST