Closed ScarecrowFu closed 8 years ago
roryk
commented
8 years ago Hi @ScarecrowFu,
Sorry about that-- we have moved over a lot of tools to be able to be found by searching the conda paths but not all of them. It looks like the tools directory is missing from your path, so bcbio-nextgen doesn't know where to find many of the tools. If you add the /iron/bioinfo/share/bcbio/anaconda/bin directory to your path it will work around this issue.
ScarecrowFu
commented
8 years ago hi @roryk
I had add the /iron/bioinfo/share/bcbio/anaconda/bin directory to my path,but it still got errors:
[2016-08-09T07:07Z] Uncaught exception occurred Traceback (most recent call last): File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run _do_run(cmd, checks, log_stdout) File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run raise subprocess.CalledProcessError(exitcode, error_msg) CalledProcessError: Command 'set -o pipefail; /iron/bioinfo/share/bcbio/anaconda/bin/samtools sort -@ 1 -m 2G -n /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/align/Test1/1_110907_ERP000591.bam /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/align/Test1/tx/tmp2NfKWq/1_110907_ERP000591.nsorted [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files Usage: samtools sort [options...] [in.bam] Options: -l INT Set compression level, from 0 (uncompressed) to 9 (best) -m INT Set maximum memory per thread; suffix K/M/G recognized [768M] -n Sort by read name -o FILE Write final output to FILE rather than standard output -T PREFIX Write temporary files to PREFIX.nnnn.bam -@, --threads INT Set number of sorting and compression threads [1] --input-fmt-option OPT[=VAL] Specify a single input file format option in the form of OPTION or OPTION=VALUE -O, --output-fmt FORMAT[,OPT[=VAL]]... Specify output format (SAM, BAM, CRAM) --output-fmt-option OPT[=VAL] Specify a single output file format option in the form of OPTION or OPTION=VALUE --reference FILE Reference sequence FASTA FILE [null] ' returned non-zero exit status 1
[2016-08-09T07:07Z] Multi-core sorting failed, reverting to single core Traceback (most recent call last): File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/bam/__init__.py", line 372, in sort os.path.basename(sort_file))) File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run _do_run(cmd, checks, log_stdout) File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run raise subprocess.CalledProcessError(exitcode, error_msg) CalledProcessError: Command 'set -o pipefail; /iron/bioinfo/share/bcbio/anaconda/bin/samtools sort -@ 1 -m 2G -n /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/align/Test1/1_110907_ERP000591.bam /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/align/Test1/tx/tmp2NfKWq/1_110907_ERP000591.nsorted [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files Usage: samtools sort [options...] [in.bam] Options: -l INT Set compression level, from 0 (uncompressed) to 9 (best) -m INT Set maximum memory per thread; suffix K/M/G recognized [768M] -n Sort by read name -o FILE Write final output to FILE rather than standard output -T PREFIX Write temporary files to PREFIX.nnnn.bam -@, --threads INT Set number of sorting and compression threads [1] --input-fmt-option OPT[=VAL] Specify a single input file format option in the form of OPTION or OPTION=VALUE -O, --output-fmt FORMAT[,OPT[=VAL]]... Specify output format (SAM, BAM, CRAM) --output-fmt-option OPT[=VAL] Specify a single output file format option in the form of OPTION or OPTION=VALUE --reference FILE Reference sequence FASTA FILE [null] ' returned non-zero exit status 1
chapmanb
commented
8 years ago Thanks for following up and all the work debugging. I'm unable to replicate this with the same tests so am confused as to what is going on. I wonder if it's possible you have a different version of samtools, what does:
/iron/bioinfo/share/bcbio/anaconda/bin/samtools --versionreport? It should be running 1.3.1 which is working cleanly for me with the latest development code. Thanks for any help so we can reproduce and fix.
Run a fast RNA-seq analysis ... [2016-08-08T09:57Z] System YAML configuration: /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml [2016-08-08T09:57Z] Resource requests: picard; memory: 3.50; cores: 1 [2016-08-08T09:57Z] Configuring 1 jobs to run, using 1 cores each with 3.50g of memory reserved for each job [2016-08-08T09:57Z] Timing: organize samples [2016-08-08T09:57Z] multiprocessing: organize_samples [2016-08-08T09:57Z] Using input YAML configuration: /iron/bioinfo/src/bcbio-nextgen/tests/data/automated/run_info-fastrnaseq.yaml [2016-08-08T09:57Z] Checking sample YAML configuration: /iron/bioinfo/src/bcbio-nextgen/tests/data/automated/run_info-fastrnaseq.yaml [2016-08-08T09:57Z] Testing minimum versions of installed programs [2016-08-08T09:57Z] multiprocessing: prepare_sample [2016-08-08T09:57Z] Preparing Test1 [2016-08-08T09:57Z] Resource requests: samtools; memory: 2.00; cores: 16 [2016-08-08T09:57Z] Configuring 1 jobs to run, using 1 cores each with 2.00g of memory reserved for each job [2016-08-08T09:57Z] Timing: fastrnaseq [2016-08-08T09:57Z] multiprocessing: run_salmon_reads [2016-08-08T09:57Z] Extracting genomic sequences of /iron/bioinfo/src/bcbio-nextgen/tests/data/genomes/mm9/rnaseq/ref-transcripts.gtf. [2016-08-08T09:57Z] Reading the annotation file: /iron/bioinfo/src/bcbio-nextgen/tests/data/genomes/mm9/rnaseq/ref-transcripts.gtf [2016-08-08T09:57Z] Creating Salmon index for /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/salmon/Test1/index/mm9/mm9.fa. [2016-08-08T09:57Z] Version Info: This is the most recent version of Salmon. [2016-08-08T09:57Z] index ["/iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/salmon/Test1/index/tx/tmpTFXwBX/mm9"] did not previously exist . . . creating it [2016-08-08T09:57Z] [2016-08-08 17:57:28.993] [jointLog] [info] building index [2016-08-08T09:57Z] RapMap Indexer [2016-08-08T09:57Z] [2016-08-08T09:57Z] [Step 1 of 4] : counting k-mers [2016-08-08T09:57Z] Elapsed time: 0.000502748s [2016-08-08T09:57Z] [2016-08-08T09:57Z] Replaced 0 non-ATCG nucleotides [2016-08-08T09:57Z] Clipped poly-A tails from 0 transcripts [2016-08-08T09:57Z] Building rank-select dictionary and saving to disk done [2016-08-08T09:57Z] Elapsed time: 2.9736e-05s [2016-08-08T09:57Z] Writing sequence data to file . . . done [2016-08-08T09:57Z] Elapsed time: 4.9893e-05s [2016-08-08T09:57Z] [info] Building 32-bit suffix array (length of generalized text is 15574) [2016-08-08T09:57Z] Building suffix array . . . success [2016-08-08T09:57Z] saving to disk . . . done [2016-08-08T09:57Z] Elapsed time: 6.9579e-05s [2016-08-08T09:57Z] done [2016-08-08T09:57Z] Elapsed time: 0.0335442s processed 0 positions [2016-08-08T09:57Z] khash had 14382 keys [2016-08-08T09:57Z] saving hash to disk . . . done [2016-08-08T09:57Z] Elapsed time: 0.00102314s [2016-08-08T09:57Z] [2016-08-08 17:57:29.159] [jointLog] [info] done building index [2016-08-08T09:57Z] Quantifying transcripts in /iron/bioinfo/src/bcbio-nextgen/tests/data/110907_ERP000591/1_110907_ERP000591_1_fastq.txt.gz and /iron/bioinfo/src/bcbio-nextgen/tests/data/110907_ERP000591/1_110907_ERP000591_2_fastq.txt.gz with Salmon. [2016-08-08T09:57Z] Version Info: This is the most recent version of Salmon. [2016-08-08T09:57Z] # salmon (mapping-based) v0.6.0 [2016-08-08T09:57Z] # [ program ] => salmon [2016-08-08T09:57Z] # [ command ] => quant [2016-08-08T09:57Z] # [ libType ] => { IU } [2016-08-08T09:57Z] # [ index ] => { /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/salmon/Test1/index/mm9 } [2016-08-08T09:57Z] # [ threads ] => { 1 } [2016-08-08T09:57Z] # [ output ] => { /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/salmon/Test1/tx/tmprrMmSM/quant } [2016-08-08T09:57Z] # [ mates1 ] => { /dev/fd/63 } [2016-08-08T09:57Z] # [ mates2 ] => { /dev/fd/62 } [2016-08-08T09:57Z] # [ numBootstraps ] => { 30 } [2016-08-08T09:57Z] Logs will be written to /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/salmon/Test1/tx/tmprrMmSM/quant/logs [2016-08-08T09:57Z] [2016-08-08 17:57:31.155] [jointLog] [info] parsing read library format [2016-08-08T09:57Z] there is 1 lib [2016-08-08T09:57Z] Loading 32-bit quasi indexIndex contained 38 targets [2016-08-08T09:57Z] [2016-08-08 17:57:31.209] [jointLog] [info] Loading Quasi index [2016-08-08T09:57Z] [2016-08-08 17:57:31.210] [jointLog] [info] done [2016-08-08T09:57Z] [2016-08-08T09:57Z] [2016-08-08T09:57Z] [2016-08-08T09:57Z] [2016-08-08T09:57Z] [2016-08-08 17:57:31.209] [stderrLog] [info] Loading Suffix Array [2016-08-08T09:57Z] [2016-08-08 17:57:31.209] [stderrLog] [info] Loading Position Hash [2016-08-08T09:57Z] [2016-08-08 17:57:31.209] [stderrLog] [info] Loading Transcript Info [2016-08-08T09:57Z] [2016-08-08 17:57:31.209] [stderrLog] [info] Loading Rank-Select Bit Array [2016-08-08T09:57Z] [2016-08-08 17:57:31.209] [stderrLog] [info] There were 38 set bits in the bit array [2016-08-08T09:57Z] [2016-08-08 17:57:31.209] [stderrLog] [info] Computing transcript lengths [2016-08-08T09:57Z] [2016-08-08 17:57:31.209] [stderrLog] [info] Waiting to finish loading hash [2016-08-08T09:57Z] [2016-08-08 17:57:31.210] [stderrLog] [info] Done loading index [2016-08-08T09:57Z] [2016-08-08T09:57Z] [2016-08-08T09:57Z] [2016-08-08T09:57Z] [2016-08-08T09:57Z] [2016-08-08T09:57Z] [2016-08-08T09:57Z] [2016-08-08T09:57Z] [2016-08-08T09:57Z] [2016-08-08 17:57:31.679] [jointLog] [info] Computed 10 rich equivalence classes for further processing [2016-08-08T09:57Z] [2016-08-08 17:57:31.679] [jointLog] [info] Counted 24996 total reads in the equivalence classes [2016-08-08T09:57Z] [2016-08-08 17:57:31.683] [jointLog] [warning] Only 24996 fragments were mapped, but the number of burn-in fragments was set to 5000000. [2016-08-08T09:57Z] The effective lengths have been computed using the observed mappings. [2016-08-08T09:57Z] [2016-08-08T09:57Z] [2016-08-08 17:57:31.683] [jointLog] [info] Mapping rate = 99.984% [2016-08-08T09:57Z] [2016-08-08T09:57Z] [2016-08-08 17:57:31.683] [jointLog] [info] finished quantifyLibrary() [2016-08-08T09:57Z] [2016-08-08 17:57:31.683] [jointLog] [info] Starting optimizer [2016-08-08T09:57Z] [2016-08-08 17:57:31.684] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2016-08-08T09:57Z] [2016-08-08 17:57:31.684] [jointLog] [info] iteration = 0 | max rel diff. = 0.754468 [2016-08-08T09:57Z] [2016-08-08 17:57:31.684] [jointLog] [info] iteration = 50 | max rel diff. = 4.16666e-11 [2016-08-08T09:57Z] [2016-08-08 17:57:31.684] [jointLog] [info] Finished optimizer [2016-08-08T09:57Z] [2016-08-08 17:57:31.684] [jointLog] [info] writing output [2016-08-08T09:57Z] [2016-08-08T09:57Z] [2016-08-08 17:57:31.740] [jointLog] [info] Staring Bootstrapping [2016-08-08T09:57Z] [2016-08-08 17:57:31.740] [jointLog] [info] Will draw 30 bootstrap samples [2016-08-08T09:57Z] [2016-08-08 17:57:31.740] [jointLog] [info] Optimizing over 10 equivalence classes [2016-08-08T09:57Z] [2016-08-08 17:57:31.740] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2016-08-08T09:57Z] [2016-08-08 17:57:31.741] [jointLog] [info] wrote 1 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.742] [jointLog] [info] wrote 2 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.743] [jointLog] [info] wrote 3 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.744] [jointLog] [info] wrote 4 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.745] [jointLog] [info] wrote 5 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.746] [jointLog] [info] wrote 6 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.747] [jointLog] [info] wrote 7 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.748] [jointLog] [info] wrote 8 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.750] [jointLog] [info] wrote 9 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.751] [jointLog] [info] wrote 10 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.752] [jointLog] [info] wrote 11 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.753] [jointLog] [info] wrote 12 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.754] [jointLog] [info] wrote 13 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.755] [jointLog] [info] wrote 14 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.756] [jointLog] [info] wrote 15 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.757] [jointLog] [info] wrote 16 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.758] [jointLog] [info] wrote 17 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.759] [jointLog] [info] wrote 18 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.760] [jointLog] [info] wrote 19 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.761] [jointLog] [info] wrote 20 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.762] [jointLog] [info] wrote 21 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.763] [jointLog] [info] wrote 22 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.764] [jointLog] [info] wrote 23 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.765] [jointLog] [info] wrote 24 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.766] [jointLog] [info] wrote 25 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.767] [jointLog] [info] wrote 26 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.768] [jointLog] [info] wrote 27 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.769] [jointLog] [info] wrote 28 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.770] [jointLog] [info] wrote 29 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.772] [jointLog] [info] wrote 30 bootstraps [2016-08-08T09:57Z] [2016-08-08 17:57:31.772] [jointLog] [info] Finished Bootstrapping [2016-08-08T09:57Z] [2016-08-08 17:57:31.782] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : [2016-08-08T09:57Z] [2016-08-08T09:57Z] Greater than 5% of the alignments (but not, necessarily reads) disagreed with the provided library type; check the file: /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/salmon/Test1/tx/tmprrMmSM/quant/libFormatCounts.txt for details [2016-08-08T09:57Z] [2016-08-08T09:57Z] Combining count files into /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/sailfish/combined.sf. [2016-08-08T09:57Z] Finished combining count files into /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/sailfish/combined.sf. [2016-08-08T09:57Z] Timing: quality control [2016-08-08T09:57Z] multiprocessing: qsignature_summary [2016-08-08T09:57Z] multiprocessing: multiqc_summary [2016-08-08T09:57Z] skipping report. No bcbreport installed. [2016-08-08T09:57Z] Timing: upload [2016-08-08T09:57Z] multiprocessing: upload_samples [2016-08-08T09:57Z] Storing directory in local filesystem: /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/upload/Test1/sailfish [2016-08-08T09:57Z] Storing directory in local filesystem: /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/upload/Test1/salmon [2016-08-08T09:57Z] multiprocessing: upload_samples_project [2016-08-08T09:57Z] Storing in local filesystem: /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/upload/110907_ERP000591/programs.txt [2016-08-08T09:57Z] Storing in local filesystem: /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/upload/110907_ERP000591/bcbio-nextgen.log [2016-08-08T09:57Z] Storing in local filesystem: /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/upload/110907_ERP000591/bcbio-nextgen-commands.log [2016-08-08T09:57Z] Storing in local filesystem: /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/upload/110907_ERP000591/project-summary.yaml [2016-08-08T09:57Z] Storing in local filesystem: /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/upload/110907_ERP000591/combined.sf [2016-08-08T09:57Z] Storing in local filesystem: /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/upload/110907_ERP000591/combined.isoform.sf.tpm [2016-08-08T09:57Z] Storing in local filesystem: /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/upload/110907_ERP000591/combined.gene.sf.tpm [2016-08-08T09:57Z] Storing in local filesystem: /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/upload/110907_ERP000591/tx2gene.csv [2016-08-08T09:57Z] Timing: finished ok Run an RNA-seq analysis with hisat2 and generate gene-level counts. ... [2016-08-08T09:57Z] System YAML configuration: /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml [2016-08-08T09:57Z] Resource requests: cutadapt, picard; memory: 2.00, 3.50; cores: 16, 1 [2016-08-08T09:57Z] Configuring 1 jobs to run, using 1 cores each with 3.50g of memory reserved for each job [2016-08-08T09:57Z] Timing: organize samples [2016-08-08T09:57Z] multiprocessing: organize_samples [2016-08-08T09:57Z] Using input YAML configuration: /iron/bioinfo/src/bcbio-nextgen/tests/data/automated/run_info-hisat2.yaml [2016-08-08T09:57Z] Checking sample YAML configuration: /iron/bioinfo/src/bcbio-nextgen/tests/data/automated/run_info-hisat2.yaml [2016-08-08T09:57Z] GTF not compatible with Qualimap, skipping. [2016-08-08T09:57Z] Testing minimum versions of installed programs [2016-08-08T09:57Z] multiprocessing: prepare_sample [2016-08-08T09:57Z] Preparing Test1 [2016-08-08T09:57Z] Timing: adapter trimming [2016-08-08T09:57Z] multiprocessing: trim_sample [2016-08-08T09:57Z] Trimming low quality ends and read through adapter sequence from /iron/bioinfo/src/bcbio-nextgen/tests/data/110907_ERP000591/1_110907_ERP000591_1_fastq.txt.gz, /iron/bioinfo/src/bcbio-nextgen/tests/data/110907_ERP000591/1_110907_ERP000591_2_fastq.txt.gz. [2016-08-08T09:57Z] Trimming /iron/bioinfo/src/bcbio-nextgen/tests/data/110907_ERP000591/1_110907_ERP000591_1_fastq.txt.gz and /iron/bioinfo/src/bcbio-nextgen/tests/data/110907_ERP000591/1_110907_ERP000591_2_fastq.txt.gz in paired end mode with cutadapt. [2016-08-08T09:57Z] This is cutadapt 1.10 with Python 2.7.12 [2016-08-08T09:57Z] Command line parameters: --times=2 --quality-base=33 --quality-cutoff=5 --format=fastq --adapter=AAAAAAAAAAAAA --adapter=TTTTTTTTTTTTT --adapter=AGATCGGAAGAG --adapter=CTCTTCCGATCT --minimum-length=25 -o /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/trimmed/tx/tmpS8ffgV/1_110907_ERP000591_2_fastq_Test1.trimmed.txt.gz -p /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/trimmed/tx/tmpS8ffgV/1_110907_ERP000591_1_fastq_Test1.trimmed.txt.gz /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/trimmed/tx/tmpS8ffgV/1_110907_ERP000591_2_fastq_Test1.trimmed.tmp.txt.gz /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/trimmed/tx/tmpS8ffgV/1_110907_ERP000591_1_fastq_Test1.trimmed.tmp.txt.gz [2016-08-08T09:57Z] Trimming 4 adapters with at most 10.0% errors in paired-end legacy mode ... [2016-08-08T09:57Z] WARNING: Requested read modifications are applied only to the first [2016-08-08T09:57Z] read since backwards compatibility mode is enabled. To modify both [2016-08-08T09:57Z] reads, also use any of the -A/-B/-G/-U options. Use a dummy adapter [2016-08-08T09:57Z] sequence when necessary: -A XXX [2016-08-08T09:57Z] Finished in 1.08 s (43 us/read; 1.39 M reads/minute). [2016-08-08T09:57Z] [2016-08-08T09:57Z] === Summary === [2016-08-08T09:57Z] [2016-08-08T09:57Z] Total read pairs processed: 25,000 [2016-08-08T09:57Z] Read 1 with adapter: 1,783 (7.1%) [2016-08-08T09:57Z] Read 2 with adapter: 0 (0.0%) [2016-08-08T09:57Z] Pairs that were too short: 0 (0.0%) [2016-08-08T09:57Z] Pairs written (passing filters): 25,000 (100.0%) [2016-08-08T09:57Z] [2016-08-08T09:57Z] Total basepairs processed: 3,793,683 bp [2016-08-08T09:57Z] Read 1: 1,900,000 bp [2016-08-08T09:57Z] Read 2: 1,893,683 bp [2016-08-08T09:57Z] Quality-trimmed: 50 bp (0.0%) [2016-08-08T09:57Z] Read 1: 50 bp [2016-08-08T09:57Z] Read 2: 0 bp [2016-08-08T09:57Z] Total written (filtered): 3,787,674 bp (99.8%) [2016-08-08T09:57Z] Read 1: 1,893,991 bp [2016-08-08T09:57Z] Read 2: 1,893,683 bp [2016-08-08T09:57Z] [2016-08-08T09:57Z] === First read: Adapter 1 === [2016-08-08T09:57Z] [2016-08-08T09:57Z] Sequence: AAAAAAAAAAAAA; Type: regular 3'; Length: 13; Trimmed: 629 times. [2016-08-08T09:57Z] [2016-08-08T09:57Z] No. of allowed errors: [2016-08-08T09:57Z] 0-9 bp: 0; 10-13 bp: 1 [2016-08-08T09:57Z] [2016-08-08T09:57Z] Bases preceding removed adapters: [2016-08-08T09:57Z] A: 0.0% [2016-08-08T09:57Z] C: 34.7% [2016-08-08T09:57Z] G: 22.6% [2016-08-08T09:57Z] T: 42.6% [2016-08-08T09:57Z] none/other: 0.2% [2016-08-08T09:57Z] [2016-08-08T09:57Z] Overview of removed sequences [2016-08-08T09:57Z] length count expect max.err error counts [2016-08-08T09:57Z] 3 481 390.6 0 481 [2016-08-08T09:57Z] 4 138 97.7 0 138 [2016-08-08T09:57Z] 5 9 24.4 0 9 [2016-08-08T09:57Z] 7 1 1.5 0 1 [2016-08-08T09:57Z] [2016-08-08T09:57Z] === First read: Adapter 2 === [2016-08-08T09:57Z] [2016-08-08T09:57Z] Sequence: TTTTTTTTTTTTT; Type: regular 3'; Length: 13; Trimmed: 487 times. [2016-08-08T09:57Z] [2016-08-08T09:57Z] No. of allowed errors: [2016-08-08T09:57Z] 0-9 bp: 0; 10-13 bp: 1 [2016-08-08T09:57Z] [2016-08-08T09:57Z] Bases preceding removed adapters: [2016-08-08T09:57Z] A: 37.8% [2016-08-08T09:57Z] C: 24.4% [2016-08-08T09:57Z] G: 37.8% [2016-08-08T09:57Z] T: 0.0% [2016-08-08T09:57Z] none/other: 0.0% [2016-08-08T09:57Z] [2016-08-08T09:57Z] Overview of removed sequences [2016-08-08T09:57Z] length count expect max.err error counts [2016-08-08T09:57Z] 3 359 390.6 0 359 [2016-08-08T09:57Z] 4 122 97.7 0 122 [2016-08-08T09:57Z] 5 6 24.4 0 6 [2016-08-08T09:57Z] [2016-08-08T09:57Z] === First read: Adapter 3 === [2016-08-08T09:57Z] [2016-08-08T09:57Z] Sequence: AGATCGGAAGAG; Type: regular 3'; Length: 12; Trimmed: 353 times. [2016-08-08T09:57Z] [2016-08-08T09:57Z] No. of allowed errors: [2016-08-08T09:57Z] 0-9 bp: 0; 10-12 bp: 1 [2016-08-08T09:57Z] [2016-08-08T09:57Z] Bases preceding removed adapters: [2016-08-08T09:57Z] A: 23.8% [2016-08-08T09:57Z] C: 23.2% [2016-08-08T09:57Z] G: 17.0% [2016-08-08T09:57Z] T: 36.0% [2016-08-08T09:57Z] none/other: 0.0% [2016-08-08T09:57Z] [2016-08-08T09:57Z] Overview of removed sequences [2016-08-08T09:57Z] length count expect max.err error counts [2016-08-08T09:57Z] 3 266 390.6 0 266 [2016-08-08T09:57Z] 4 87 97.7 0 87 [2016-08-08T09:57Z] [2016-08-08T09:57Z] === First read: Adapter 4 === [2016-08-08T09:57Z] [2016-08-08T09:57Z] Sequence: CTCTTCCGATCT; Type: regular 3'; Length: 12; Trimmed: 344 times. [2016-08-08T09:57Z] [2016-08-08T09:57Z] No. of allowed errors: [2016-08-08T09:57Z] 0-9 bp: 0; 10-12 bp: 1 [2016-08-08T09:57Z] [2016-08-08T09:57Z] Bases preceding removed adapters: [2016-08-08T09:57Z] A: 11.0% [2016-08-08T09:57Z] C: 28.5% [2016-08-08T09:57Z] G: 22.1% [2016-08-08T09:57Z] T: 38.4% [2016-08-08T09:57Z] none/other: 0.0% [2016-08-08T09:57Z] [2016-08-08T09:57Z] Overview of removed sequences [2016-08-08T09:57Z] length count expect max.err error counts [2016-08-08T09:57Z] 3 269 390.6 0 269 [2016-08-08T09:57Z] 4 63 97.7 0 63 [2016-08-08T09:57Z] 6 2 6.1 0 2 [2016-08-08T09:57Z] 10 10 0.0 1 0 10 [2016-08-08T09:57Z] [2016-08-08T09:57Z] Resource requests: hisat2, picard; memory: 2.00, 3.50; cores: 16, 1 [2016-08-08T09:57Z] Configuring 1 jobs to run, using 1 cores each with 8.00g of memory reserved for each job [2016-08-08T09:57Z] Timing: alignment [2016-08-08T09:57Z] multiprocessing: disambiguate_split [2016-08-08T09:57Z] multiprocessing: process_alignment [2016-08-08T09:57Z] Aligning lane 1_110907_ERP000591 with hisat2 aligner [2016-08-08T09:57Z] Aligning /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/trimmed/1_110907_ERP000591_1_fastq_Test1.trimmed.txt.gz and /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/trimmed/1_110907_ERP000591_2_fastq_Test1.trimmed.txt.gz with hisat2. [2016-08-08T09:57Z] 25000 reads; of these: [2016-08-08T09:57Z] 25000 (100.00%) were paired; of these: [2016-08-08T09:57Z] 213 (0.85%) aligned concordantly 0 times [2016-08-08T09:57Z] 23706 (94.82%) aligned concordantly exactly 1 time [2016-08-08T09:57Z] 1081 (4.32%) aligned concordantly >1 times [2016-08-08T09:57Z] ---- [2016-08-08T09:57Z] 213 pairs aligned concordantly 0 times; of these: [2016-08-08T09:57Z] 198 (92.96%) aligned discordantly 1 time [2016-08-08T09:57Z] ---- [2016-08-08T09:57Z] 15 pairs aligned 0 times concordantly or discordantly; of these: [2016-08-08T09:57Z] 30 mates make up the pairs; of these: [2016-08-08T09:57Z] 6 (20.00%) aligned 0 times [2016-08-08T09:57Z] 14 (46.67%) aligned exactly 1 time [2016-08-08T09:57Z] 10 (33.33%) aligned >1 times [2016-08-08T09:57Z] 99.99% overall alignment rate [2016-08-08T09:57Z] Index BAM file: 1_110907_ERP000591.bam [2016-08-08T09:57Z] Resource requests: cufflinks, samtools; memory: 3.00, 2.00; cores: 16, 16 [2016-08-08T09:57Z] Configuring 1 jobs to run, using 1 cores each with 3.00g of memory reserved for each job [2016-08-08T09:57Z] Timing: disambiguation [2016-08-08T09:57Z] Timing: transcript assembly [2016-08-08T09:57Z] Timing: estimate expression (threaded) [2016-08-08T09:57Z] multiprocessing: generate_transcript_counts [2016-08-08T09:57Z] Sort BAM file (multi core, queryname): 1_110907_ERP000591.bam to 1_110907_ERP000591.nsorted.bam [2016-08-08T09:57Z] [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files [2016-08-08T09:57Z] Uncaught exception occurred Traceback (most recent call last): File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run _do_run(cmd, checks, log_stdout) File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run raise subprocess.CalledProcessError(exitcode, error_msg) CalledProcessError: Command 'set -o pipefail; /iron/bioinfo/share/bcbio/anaconda/bin/samtools sort -@ 1 -m 2G -n /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/align/Test1/1_110907_ERP000591.bam /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/align/Test1/tx/tmpv_U8im/1_110907_ERP000591.nsorted [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files Usage: samtools sort [options...] [in.bam] Options: -l INT Set compression level, from 0 (uncompressed) to 9 (best) -m INT Set maximum memory per thread; suffix K/M/G recognized [768M] -n Sort by read name -o FILE Write final output to FILE rather than standard output -T PREFIX Write temporary files to PREFIX.nnnn.bam -@, --threads INT Set number of sorting and compression threads [1] --input-fmt-option OPT[=VAL] Specify a single input file format option in the form of OPTION or OPTION=VALUE -O, --output-fmt FORMAT[,OPT[=VAL]]... Specify output format (SAM, BAM, CRAM) --output-fmt-option OPT[=VAL] Specify a single output file format option in the form of OPTION or OPTION=VALUE --reference FILE Reference sequence FASTA FILE [null] ' returned non-zero exit status 1 [2016-08-08T09:57Z] Multi-core sorting failed, reverting to single core Traceback (most recent call last): File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/bam/init.py", line 372, in sort os.path.basename(sort_file))) File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run _do_run(cmd, checks, log_stdout) File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run raise subprocess.CalledProcessError(exitcode, error_msg) CalledProcessError: Command 'set -o pipefail; /iron/bioinfo/share/bcbio/anaconda/bin/samtools sort -@ 1 -m 2G -n /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/align/Test1/1_110907_ERP000591.bam /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/align/Test1/tx/tmpv_U8im/1_110907_ERP000591.nsorted [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files Usage: samtools sort [options...] [in.bam] Options: -l INT Set compression level, from 0 (uncompressed) to 9 (best) -m INT Set maximum memory per thread; suffix K/M/G recognized [768M] -n Sort by read name -o FILE Write final output to FILE rather than standard output -T PREFIX Write temporary files to PREFIX.nnnn.bam -@, --threads INT Set number of sorting and compression threads [1] --input-fmt-option OPT[=VAL] Specify a single input file format option in the form of OPTION or OPTION=VALUE -O, --output-fmt FORMAT[,OPT[=VAL]]... Specify output format (SAM, BAM, CRAM) --output-fmt-option OPT[=VAL] Specify a single output file format option in the form of OPTION or OPTION=VALUE --reference FILE Reference sequence FASTA FILE [null] ' returned non-zero exit status 1 [2016-08-08T09:57Z] Sort BAM file (single core, queryname): 1_110907_ERP000591.bam to 1_110907_ERP000591.nsorted.bam [2016-08-08T09:57Z] [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files [2016-08-08T09:57Z] Uncaught exception occurred Traceback (most recent call last): File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run _do_run(cmd, checks, log_stdout) File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run raise subprocess.CalledProcessError(exitcode, error_msg) CalledProcessError: Command 'set -o pipefail; /iron/bioinfo/share/bcbio/anaconda/bin/samtools sort -@ 1 -m 2G -n /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/align/Test1/1_110907_ERP000591.bam /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/align/Test1/tx/tmpv_U8im/1_110907_ERP000591.nsorted [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files Usage: samtools sort [options...] [in.bam] Options: -l INT Set compression level, from 0 (uncompressed) to 9 (best) -m INT Set maximum memory per thread; suffix K/M/G recognized [768M] -n Sort by read name -o FILE Write final output to FILE rather than standard output -T PREFIX Write temporary files to PREFIX.nnnn.bam -@, --threads INT Set number of sorting and compression threads [1] --input-fmt-option OPT[=VAL] Specify a single input file format option in the form of OPTION or OPTION=VALUE -O, --output-fmt FORMAT[,OPT[=VAL]]... Specify output format (SAM, BAM, CRAM) --output-fmt-option OPT[=VAL] Specify a single output file format option in the form of OPTION or OPTION=VALUE --reference FILE Reference sequence FASTA FILE [null] ' returned non-zero exit status 1 Traceback (most recent call last): File "/iron/bioinfo/share/bcbio/anaconda/bin/bcbio_nextgen.py", line 4, in
import('pkg_resources').run_script('bcbio-nextgen==0.9.9', 'bcbio_nextgen.py')
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/init.py", line 726, in run_script
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/init.py", line 1484, in run_script
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_nextgen.py", line 226, in
main(kwargs)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_nextgen.py", line 43, in main
run_main(kwargs)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 43, in run_main
fc_dir, run_info_yaml)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 87, in _run_toplevel
for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 252, in rnaseqpipeline
samples = rnaseq.quantitate_expression_parallel(samples, run_parallel)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/rnaseq.py", line 83, in quantitate_expression_parallel
samples = run_parallel("generate_transcript_counts", samples)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
return run_multicore(fn, items, config, parallel=parallel)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore
for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items):
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 800, in call
while self.dispatch_one_batch(iterator):
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 658, in dispatch_one_batch
self._dispatch(tasks)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 566, in _dispatch
job = ImmediateComputeBatch(batch)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 180, in init
self.results = batch()
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 72, in call
return [func(_args, _kwargs) for func, args, kwargs in self.items]
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 51, in wrapper
return apply(f, _args, _kwargs)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 148, in generate_transcript_counts
return rnaseq.generate_transcript_counts(*args)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/rnaseq.py", line 104, in generate_transcript_counts
data["count_file"] = featureCounts.count(data)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/featureCounts.py", line 22, in count
sorted_bam = bam.sort(in_bam, dd.get_config(data), order="queryname")
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/bam/init.py", line 382, in sort
os.path.basename(sort_file)))
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
_do_run(cmd, checks, log_stdout)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'set -o pipefail; /iron/bioinfo/share/bcbio/anaconda/bin/samtools sort -@ 1 -m 2G -n /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/align/Test1/1_110907_ERP000591.bam /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/align/Test1/tx/tmpv_U8im/1_110907_ERP000591.nsorted
[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files
Usage: samtools sort [options...] [in.bam]
Options:
-l INT Set compression level, from 0 (uncompressed) to 9 (best)
-m INT Set maximum memory per thread; suffix K/M/G recognized [768M]
-n Sort by read name
-o FILE Write final output to FILE rather than standard output
-T PREFIX Write temporary files to PREFIX.nnnn.bam
-@, --threads INT
Set number of sorting and compression threads [1]
--input-fmt-option OPT[=VAL]
Specify a single input file format option in the form
of OPTION or OPTION=VALUE
-O, --output-fmt FORMAT[,OPT[=VAL]]...
Specify output format (SAM, BAM, CRAM)
--output-fmt-option OPT[=VAL]
Specify a single output file format option in the form
of OPTION or OPTION=VALUE
--reference FILE
Reference sequence FASTA FILE [null]
' returned non-zero exit status 1
ERROR
Run an RNA-seq analysis with TopHat and generate gene-level counts. ... [2016-08-08T09:57Z] System YAML configuration: /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml
[2016-08-08T09:57Z] Resource requests: cutadapt, picard; memory: 2.00, 3.50; cores: 16, 1
[2016-08-08T09:57Z] Configuring 1 jobs to run, using 1 cores each with 3.50g of memory reserved for each job
[2016-08-08T09:57Z] Timing: organize samples
[2016-08-08T09:57Z] multiprocessing: organize_samples
[2016-08-08T09:57Z] Using input YAML configuration: /iron/bioinfo/src/bcbio-nextgen/tests/data/automated/run_info-rnaseq.yaml
[2016-08-08T09:57Z] Checking sample YAML configuration: /iron/bioinfo/src/bcbio-nextgen/tests/data/automated/run_info-rnaseq.yaml
[2016-08-08T09:57Z] GTF not compatible with Qualimap, skipping.
[2016-08-08T09:57Z] Testing minimum versions of installed programs
[2016-08-08T09:57Z] multiprocessing: prepare_sample
[2016-08-08T09:57Z] Preparing Test1
[2016-08-08T09:57Z] Timing: adapter trimming
[2016-08-08T09:57Z] multiprocessing: trim_sample
[2016-08-08T09:57Z] Trimming low quality ends and read through adapter sequence from /iron/bioinfo/src/bcbio-nextgen/tests/data/110907_ERP000591/1_110907_ERP000591_1_fastq.txt.gz, /iron/bioinfo/src/bcbio-nextgen/tests/data/110907_ERP000591/1_110907_ERP000591_2_fastq.txt.gz.
[2016-08-08T09:57Z] Trimming /iron/bioinfo/src/bcbio-nextgen/tests/data/110907_ERP000591/1_110907_ERP000591_1_fastq.txt.gz and /iron/bioinfo/src/bcbio-nextgen/tests/data/110907_ERP000591/1_110907_ERP000591_2_fastq.txt.gz in paired end mode with cutadapt.
[2016-08-08T09:57Z] This is cutadapt 1.10 with Python 2.7.12
[2016-08-08T09:57Z] Command line parameters: --times=2 --quality-base=33 --quality-cutoff=5 --format=fastq --adapter=AAAAAAAAAAAAA --adapter=TTTTTTTTTTTTT --adapter=AGATCGGAAGAG --adapter=CTCTTCCGATCT --minimum-length=25 -o /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/trimmed/tx/tmpDfrqJ7/1_110907_ERP000591_2_fastq_Test1.trimmed.txt.gz -p /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/trimmed/tx/tmpDfrqJ7/1_110907_ERP000591_1_fastq_Test1.trimmed.txt.gz /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/trimmed/tx/tmpDfrqJ7/1_110907_ERP000591_2_fastq_Test1.trimmed.tmp.txt.gz /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/trimmed/tx/tmpDfrqJ7/1_110907_ERP000591_1_fastq_Test1.trimmed.tmp.txt.gz
[2016-08-08T09:57Z] Trimming 4 adapters with at most 10.0% errors in paired-end legacy mode ...
[2016-08-08T09:57Z] WARNING: Requested read modifications are applied only to the first
[2016-08-08T09:57Z] read since backwards compatibility mode is enabled. To modify both
[2016-08-08T09:57Z] reads, also use any of the -A/-B/-G/-U options. Use a dummy adapter
[2016-08-08T09:57Z] sequence when necessary: -A XXX
[2016-08-08T09:57Z] Finished in 1.43 s (57 us/read; 1.05 M reads/minute).
[2016-08-08T09:57Z]
[2016-08-08T09:57Z] === Summary ===
[2016-08-08T09:57Z]
[2016-08-08T09:57Z] Total read pairs processed: 25,000
[2016-08-08T09:57Z] Read 1 with adapter: 1,783 (7.1%)
[2016-08-08T09:57Z] Read 2 with adapter: 0 (0.0%)
[2016-08-08T09:57Z] Pairs that were too short: 0 (0.0%)
[2016-08-08T09:57Z] Pairs written (passing filters): 25,000 (100.0%)
[2016-08-08T09:57Z]
[2016-08-08T09:57Z] Total basepairs processed: 3,793,683 bp
[2016-08-08T09:57Z] Read 1: 1,900,000 bp
[2016-08-08T09:57Z] Read 2: 1,893,683 bp
[2016-08-08T09:57Z] Quality-trimmed: 50 bp (0.0%)
[2016-08-08T09:57Z] Read 1: 50 bp
[2016-08-08T09:57Z] Read 2: 0 bp
[2016-08-08T09:57Z] Total written (filtered): 3,787,674 bp (99.8%)
[2016-08-08T09:57Z] Read 1: 1,893,991 bp
[2016-08-08T09:57Z] Read 2: 1,893,683 bp
[2016-08-08T09:57Z]
[2016-08-08T09:57Z] === First read: Adapter 1 ===
[2016-08-08T09:57Z]
[2016-08-08T09:57Z] Sequence: AAAAAAAAAAAAA; Type: regular 3'; Length: 13; Trimmed: 629 times.
[2016-08-08T09:57Z]
[2016-08-08T09:57Z] No. of allowed errors:
[2016-08-08T09:57Z] 0-9 bp: 0; 10-13 bp: 1
[2016-08-08T09:57Z]
[2016-08-08T09:57Z] Bases preceding removed adapters:
[2016-08-08T09:57Z] A: 0.0%
[2016-08-08T09:57Z] C: 34.7%
[2016-08-08T09:57Z] G: 22.6%
[2016-08-08T09:57Z] T: 42.6%
[2016-08-08T09:57Z] none/other: 0.2%
[2016-08-08T09:57Z]
[2016-08-08T09:57Z] Overview of removed sequences
[2016-08-08T09:57Z] length count expect max.err error counts
[2016-08-08T09:57Z] 3 481 390.6 0 481
[2016-08-08T09:57Z] 4 138 97.7 0 138
[2016-08-08T09:57Z] 5 9 24.4 0 9
[2016-08-08T09:57Z] 7 1 1.5 0 1
[2016-08-08T09:57Z]
[2016-08-08T09:57Z] === First read: Adapter 2 ===
[2016-08-08T09:57Z]
[2016-08-08T09:57Z] Sequence: TTTTTTTTTTTTT; Type: regular 3'; Length: 13; Trimmed: 487 times.
[2016-08-08T09:57Z]
[2016-08-08T09:57Z] No. of allowed errors:
[2016-08-08T09:57Z] 0-9 bp: 0; 10-13 bp: 1
[2016-08-08T09:57Z]
[2016-08-08T09:57Z] Bases preceding removed adapters:
[2016-08-08T09:57Z] A: 37.8%
[2016-08-08T09:57Z] C: 24.4%
[2016-08-08T09:57Z] G: 37.8%
[2016-08-08T09:57Z] T: 0.0%
[2016-08-08T09:57Z] none/other: 0.0%
[2016-08-08T09:57Z]
[2016-08-08T09:57Z] Overview of removed sequences
[2016-08-08T09:57Z] length count expect max.err error counts
[2016-08-08T09:57Z] 3 359 390.6 0 359
[2016-08-08T09:57Z] 4 122 97.7 0 122
[2016-08-08T09:57Z] 5 6 24.4 0 6
[2016-08-08T09:57Z]
[2016-08-08T09:57Z] === First read: Adapter 3 ===
[2016-08-08T09:57Z]
[2016-08-08T09:57Z] Sequence: AGATCGGAAGAG; Type: regular 3'; Length: 12; Trimmed: 353 times.
[2016-08-08T09:57Z]
[2016-08-08T09:57Z] No. of allowed errors:
[2016-08-08T09:57Z] 0-9 bp: 0; 10-12 bp: 1
[2016-08-08T09:57Z]
[2016-08-08T09:57Z] Bases preceding removed adapters:
[2016-08-08T09:57Z] A: 23.8%
[2016-08-08T09:57Z] C: 23.2%
[2016-08-08T09:57Z] G: 17.0%
[2016-08-08T09:57Z] T: 36.0%
[2016-08-08T09:57Z] none/other: 0.0%
[2016-08-08T09:57Z]
[2016-08-08T09:57Z] Overview of removed sequences
[2016-08-08T09:57Z] length count expect max.err error counts
[2016-08-08T09:57Z] 3 266 390.6 0 266
[2016-08-08T09:57Z] 4 87 97.7 0 87
[2016-08-08T09:57Z]
[2016-08-08T09:57Z] === First read: Adapter 4 ===
[2016-08-08T09:57Z]
[2016-08-08T09:57Z] Sequence: CTCTTCCGATCT; Type: regular 3'; Length: 12; Trimmed: 344 times.
[2016-08-08T09:57Z]
[2016-08-08T09:57Z] No. of allowed errors:
[2016-08-08T09:57Z] 0-9 bp: 0; 10-12 bp: 1
[2016-08-08T09:57Z]
[2016-08-08T09:57Z] Bases preceding removed adapters:
[2016-08-08T09:57Z] A: 11.0%
[2016-08-08T09:57Z] C: 28.5%
[2016-08-08T09:57Z] G: 22.1%
[2016-08-08T09:57Z] T: 38.4%
[2016-08-08T09:57Z] none/other: 0.0%
[2016-08-08T09:57Z]
[2016-08-08T09:57Z] Overview of removed sequences
[2016-08-08T09:57Z] length count expect max.err error counts
[2016-08-08T09:57Z] 3 269 390.6 0 269
[2016-08-08T09:57Z] 4 63 97.7 0 63
[2016-08-08T09:57Z] 6 2 6.1 0 2
[2016-08-08T09:57Z] Resource requests: picard, tophat2; memory: 3.50, 2.00; cores: 1, 16
[2016-08-08T09:57Z] Configuring 1 jobs to run, using 1 cores each with 10.00g of memory reserved for each job
[2016-08-08T09:57Z] Timing: alignment
[2016-08-08T09:57Z] multiprocessing: disambiguate_split
[2016-08-08T09:57Z] multiprocessing: process_alignment
[2016-08-08T09:57Z] Aligning lane 1_110907_ERP000591 with tophat2 aligner
Traceback (most recent call last):
File "/iron/bioinfo/share/bcbio/anaconda/bin/bcbio_nextgen.py", line 4, in
import('pkg_resources').run_script('bcbio-nextgen==0.9.9', 'bcbio_nextgen.py')
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/init.py", line 726, in run_script
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/init.py", line 1484, in run_script
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_nextgen.py", line 226, in
main(kwargs)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_nextgen.py", line 43, in main
run_main(kwargs)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 43, in run_main
fc_dir, run_info_yaml)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 87, in _run_toplevel
for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 244, in rnaseqpipeline
samples = run_parallel("process_alignment", samples)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
return run_multicore(fn, items, config, parallel=parallel)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore
for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items):
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 800, in call
while self.dispatch_one_batch(iterator):
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 658, in dispatch_one_batch
self._dispatch(tasks)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 566, in _dispatch
job = ImmediateComputeBatch(batch)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 180, in init
self.results = batch()
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 72, in call
return [func(_args, _kwargs) for func, args, kwargs in self.items]
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 51, in wrapper
return apply(f, _args, _kwargs)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 72, in process_alignment
return sample.process_alignment(_args)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.py", line 112, in process_alignment
data = align_to_sort_bam(fastq1, fastq2, aligner, data)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.py", line 64, in align_to_sort_bam
names, align_dir, data)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.py", line 117, in _align_from_fastq
out = align_fn(fastq1, fastq2, align_ref, names, align_dir, data)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/tophat.py", line 242, in align
align_dir, data, names)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/tophat.py", line 132, in tophat_align
tx_out_dir, data)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/tophat.py", line 252, in _estimate_paired_innerdist
out_base, out_dir, data, True)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/tophat.py", line 272, in _bowtie_for_innerdist
work_dir, data, extra_args)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/bowtie2.py", line 42, in align
with postalign.tobam_cl(data, out_file, pair_file is not None) as (tobam_cl, tx_out_file):
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/contextlib.py", line 17, in enter
return self.gen.next()
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/postalign.py", line 39, in tobam_cl
yield (samblaster_dedup_sort(data, tx_out_file, tx_sr_file, tx_disc_file),
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/postalign.py", line 78, in samblaster_dedup_sort
sambamba = config_utils.get_program("sambamba", data["config"])
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/config_utils.py", line 186, in get_program
return _get_program_cmd(name, pconfig, config, default)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/config_utils.py", line 212, in wrap
raise CmdNotFound(" ".join(map(repr, (fn.func_name, name, pconfig, default))))
bcbio.pipeline.config_utils.CmdNotFound: '_get_program_cmd' 'sambamba' {} None
ERROR
Run a single-cell RNA-seq analysis ... [2016-08-08T09:58Z] System YAML configuration: /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml
[2016-08-08T09:58Z] Resource requests: picard; memory: 3.50; cores: 1
[2016-08-08T09:58Z] Configuring 1 jobs to run, using 1 cores each with 3.50g of memory reserved for each job
[2016-08-08T09:58Z] Timing: organize samples
[2016-08-08T09:58Z] multiprocessing: organize_samples
[2016-08-08T09:58Z] Using input YAML configuration: /iron/bioinfo/src/bcbio-nextgen/tests/data/automated/run_info-scrnaseq.yaml
[2016-08-08T09:58Z] Checking sample YAML configuration: /iron/bioinfo/src/bcbio-nextgen/tests/data/automated/run_info-scrnaseq.yaml
[2016-08-08T09:58Z] Testing minimum versions of installed programs
[2016-08-08T09:58Z] multiprocessing: prepare_sample
[2016-08-08T09:58Z] Preparing Test1
[2016-08-08T09:58Z] Resource requests: samtools; memory: 2.00; cores: 16
[2016-08-08T09:58Z] Configuring 1 jobs to run, using 1 cores each with 2.00g of memory reserved for each job
[2016-08-08T09:58Z] Timing: singlecell-rnaseq
[2016-08-08T09:58Z] multiprocessing: run_umi_transform
[2016-08-08T09:58Z] Inserting UMI and barcode information into the read name of /iron/bioinfo/src/bcbio-nextgen/tests/data/Harvard-inDrop/r1.fq.gz
[2016-08-08T09:58Z] /usr/bin/bash: seqtk: command not found
[2016-08-08T09:58Z] Traceback (most recent call last):
[2016-08-08T09:58Z] File "/iron/bioinfo/share/bcbio/anaconda/bin/umis", line 9, in
[2016-08-08T09:58Z] load_entry_point('umis==0.2.2', 'console_scripts', 'umis')()
[2016-08-08T09:58Z] File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/click/core.py", line 716, in call
[2016-08-08T09:58Z] return self.main(_args, _kwargs)
[2016-08-08T09:58Z] File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/click/core.py", line 696, in main
[2016-08-08T09:58Z] rv = self.invoke(ctx)
[2016-08-08T09:58Z] File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/click/core.py", line 1060, in invoke
[2016-08-08T09:58Z] return _process_result(sub_ctx.command.invoke(sub_ctx))
[2016-08-08T09:58Z] File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/click/core.py", line 889, in invoke
[2016-08-08T09:58Z] return ctx.invoke(self.callback, _ctx.params)
[2016-08-08T09:58Z] File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/click/core.py", line 534, in invoke
[2016-08-08T09:58Z] return callback(_args, _kwargs)
[2016-08-08T09:58Z] File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/umis-0.2.2-py2.7-linux-x86_64.egg/umis/umis.py", line 109, in fastqtransform
[2016-08-08T09:58Z] IOError: [Errno 32] Broken pipe
[2016-08-08T09:58Z] Uncaught exception occurred
Traceback (most recent call last):
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
_do_run(cmd, checks, log_stdout)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'set -o pipefail; /iron/bioinfo/share/bcbio/anaconda/bin/umis fastqtransform --dual_index /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/umis/harvard-indrop.json /iron/bioinfo/src/bcbio-nextgen/tests/data/Harvard-inDrop/r1.fq.gz /iron/bioinfo/src/bcbio-nextgen/tests/data/Harvard-inDrop/r2.fq.gz | seqtk seq -L 20 - | gzip > /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/umis/tx/tmpG1P_fa/Test1.umitransformed.fq.gz
/usr/bin/bash: seqtk: command not found
Traceback (most recent call last):
File "/iron/bioinfo/share/bcbio/anaconda/bin/umis", line 9, in
load_entry_point('umis==0.2.2', 'console_scripts', 'umis')()
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/click/core.py", line 716, in call
return self.main(_args, _kwargs)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/click/core.py", line 696, in main
rv = self.invoke(ctx)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/click/core.py", line 1060, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/click/core.py", line 889, in invoke
return ctx.invoke(self.callback, *_ctx.params)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/click/core.py", line 534, in invoke
return callback(_args, kwargs)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/umis-0.2.2-py2.7-linux-x86_64.egg/umis/umis.py", line 109, in fastqtransform
IOError: [Errno 32] Broken pipe
' returned non-zero exit status 127
Traceback (most recent call last):
File "/iron/bioinfo/share/bcbio/anaconda/bin/bcbio_nextgen.py", line 4, in
import('pkg_resources').run_script('bcbio-nextgen==0.9.9', 'bcbio_nextgen.py')
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/ init**.py", line 726, in run_script
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/init.py", line 1484, in run_script
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_nextgen.py", line 226, in
main(kwargs)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_nextgen.py", line 43, in main
run_main(kwargs)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 43, in run_main
fc_dir, run_info_yaml)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 87, in _run_toplevel
for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 295, in singlecellrnaseqpipeline
samples = rnaseq.singlecell_rnaseq(samples, run_parallel)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/rnaseq.py", line 21, in singlecell_rnaseq
samples = run_parallel("run_umi_transform", samples)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
return run_multicore(fn, items, config, parallel=parallel)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore
for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items):
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 800, in call
while self.dispatch_one_batch(iterator):
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 658, in dispatch_one_batch
self._dispatch(tasks)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 566, in _dispatch
job = ImmediateComputeBatch(batch)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 180, in init
self.results = batch()
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 72, in call
return [func(_args, _kwargs) for func, args, kwargs in self.items]
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 51, in wrapper
return apply(f, _args, _kwargs)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 32, in run_umi_transform
return umi.umi_transform(_args)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/umi.py", line 87, in umi_transform
do.run(cmd.format(__locals()), message)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
_do_run(cmd, checks, log_stdout)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'set -o pipefail; /iron/bioinfo/share/bcbio/anaconda/bin/umis fastqtransform --dual_index /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/umis/harvard-indrop.json /iron/bioinfo/src/bcbio-nextgen/tests/data/Harvard-inDrop/r1.fq.gz /iron/bioinfo/src/bcbio-nextgen/tests/data/Harvard-inDrop/r2.fq.gz | seqtk seq -L 20 - | gzip > /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/umis/tx/tmpG1P_fa/Test1.umitransformed.fq.gz
/usr/bin/bash: seqtk: command not found
Traceback (most recent call last):
File "/iron/bioinfo/share/bcbio/anaconda/bin/umis", line 9, in
load_entry_point('umis==0.2.2', 'console_scripts', 'umis')()
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/click/core.py", line 716, in call
return self.main(_args, _kwargs)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/click/core.py", line 696, in main
rv = self.invoke(ctx)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/click/core.py", line 1060, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/click/core.py", line 889, in invoke
return ctx.invoke(self.callback, _ctx.params)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/click/core.py", line 534, in invoke
return callback(_args, *_kwargs)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/umis-0.2.2-py2.7-linux-x86_64.egg/umis/umis.py", line 109, in fastqtransform
IOError: [Errno 32] Broken pipe
' returned non-zero exit status 127
SKIP
Run an RNA-seq analysis with STAR and generate gene-level counts. ... [2016-08-08T09:58Z] System YAML configuration: /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml
[2016-08-08T09:58Z] Resource requests: cutadapt, picard; memory: 2.00, 3.50; cores: 16, 1
[2016-08-08T09:58Z] Configuring 1 jobs to run, using 1 cores each with 3.50g of memory reserved for each job
[2016-08-08T09:58Z] Timing: organize samples
[2016-08-08T09:58Z] multiprocessing: organize_samples
[2016-08-08T09:58Z] Using input YAML configuration: /iron/bioinfo/src/bcbio-nextgen/tests/data/automated/run_info-star.yaml
[2016-08-08T09:58Z] Checking sample YAML configuration: /iron/bioinfo/src/bcbio-nextgen/tests/data/automated/run_info-star.yaml
[2016-08-08T09:58Z] GTF not compatible with Qualimap, skipping.
[2016-08-08T09:58Z] Testing minimum versions of installed programs
[2016-08-08T09:58Z] multiprocessing: prepare_sample
[2016-08-08T09:58Z] Preparing Test1
[2016-08-08T09:58Z] Timing: adapter trimming
[2016-08-08T09:58Z] multiprocessing: trim_sample
[2016-08-08T09:58Z] Trimming low quality ends and read through adapter sequence from /iron/bioinfo/src/bcbio-nextgen/tests/data/110907_ERP000591/1_110907_ERP000591_1_fastq.txt.gz, /iron/bioinfo/src/bcbio-nextgen/tests/data/110907_ERP000591/1_110907_ERP000591_2_fastq.txt.gz.
[2016-08-08T09:58Z] Trimming /iron/bioinfo/src/bcbio-nextgen/tests/data/110907_ERP000591/1_110907_ERP000591_1_fastq.txt.gz and /iron/bioinfo/src/bcbio-nextgen/tests/data/110907_ERP000591/1_110907_ERP000591_2_fastq.txt.gz in paired end mode with cutadapt.
[2016-08-08T09:58Z] This is cutadapt 1.10 with Python 2.7.12
[2016-08-08T09:58Z] Command line parameters: --times=2 --quality-base=33 --quality-cutoff=5 --format=fastq --adapter=AAAAAAAAAAAAA --adapter=TTTTTTTTTTTTT --adapter=AGATCGGAAGAG --adapter=CTCTTCCGATCT --minimum-length=25 -o /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/trimmed/tx/tmpXlbZIz/1_110907_ERP000591_2_fastq_Test1.trimmed.txt.gz -p /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/trimmed/tx/tmpXlbZIz/1_110907_ERP000591_1_fastq_Test1.trimmed.txt.gz /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/trimmed/tx/tmpXlbZIz/1_110907_ERP000591_2_fastq_Test1.trimmed.tmp.txt.gz /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/trimmed/tx/tmpXlbZIz/1_110907_ERP000591_1_fastq_Test1.trimmed.tmp.txt.gz
[2016-08-08T09:58Z] Trimming 4 adapters with at most 10.0% errors in paired-end legacy mode ...
[2016-08-08T09:58Z] WARNING: Requested read modifications are applied only to the first
[2016-08-08T09:58Z] read since backwards compatibility mode is enabled. To modify both
[2016-08-08T09:58Z] reads, also use any of the -A/-B/-G/-U options. Use a dummy adapter
[2016-08-08T09:58Z] sequence when necessary: -A XXX
[2016-08-08T09:58Z] Finished in 1.29 s (52 us/read; 1.16 M reads/minute).
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] === Summary ===
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] Total read pairs processed: 25,000
[2016-08-08T09:58Z] Read 1 with adapter: 1,783 (7.1%)
[2016-08-08T09:58Z] Read 2 with adapter: 0 (0.0%)
[2016-08-08T09:58Z] Pairs that were too short: 0 (0.0%)
[2016-08-08T09:58Z] Pairs written (passing filters): 25,000 (100.0%)
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] Total basepairs processed: 3,793,683 bp
[2016-08-08T09:58Z] Read 1: 1,900,000 bp
[2016-08-08T09:58Z] Read 2: 1,893,683 bp
[2016-08-08T09:58Z] Quality-trimmed: 50 bp (0.0%)
[2016-08-08T09:58Z] Read 1: 50 bp
[2016-08-08T09:58Z] Read 2: 0 bp
[2016-08-08T09:58Z] Total written (filtered): 3,787,674 bp (99.8%)
[2016-08-08T09:58Z] Read 1: 1,893,991 bp
[2016-08-08T09:58Z] Read 2: 1,893,683 bp
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] === First read: Adapter 1 ===
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] Sequence: AAAAAAAAAAAAA; Type: regular 3'; Length: 13; Trimmed: 629 times.
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] No. of allowed errors:
[2016-08-08T09:58Z] 0-9 bp: 0; 10-13 bp: 1
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] Bases preceding removed adapters:
[2016-08-08T09:58Z] A: 0.0%
[2016-08-08T09:58Z] C: 34.7%
[2016-08-08T09:58Z] G: 22.6%
[2016-08-08T09:58Z] T: 42.6%
[2016-08-08T09:58Z] none/other: 0.2%
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] Overview of removed sequences
[2016-08-08T09:58Z] length count expect max.err error counts
[2016-08-08T09:58Z] 3 481 390.6 0 481
[2016-08-08T09:58Z] 4 138 97.7 0 138
[2016-08-08T09:58Z] 5 9 24.4 0 9
[2016-08-08T09:58Z] 7 1 1.5 0 1
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] === First read: Adapter 2 ===
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] Sequence: TTTTTTTTTTTTT; Type: regular 3'; Length: 13; Trimmed: 487 times.
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] No. of allowed errors:
[2016-08-08T09:58Z] 0-9 bp: 0; 10-13 bp: 1
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] Bases preceding removed adapters:
[2016-08-08T09:58Z] A: 37.8%
[2016-08-08T09:58Z] C: 24.4%
[2016-08-08T09:58Z] G: 37.8%
[2016-08-08T09:58Z] T: 0.0%
[2016-08-08T09:58Z] none/other: 0.0%
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] Overview of removed sequences
[2016-08-08T09:58Z] length count expect max.err error counts
[2016-08-08T09:58Z] 3 359 390.6 0 359
[2016-08-08T09:58Z] 4 122 97.7 0 122
[2016-08-08T09:58Z] 5 6 24.4 0 6
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] === First read: Adapter 3 ===
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] Sequence: AGATCGGAAGAG; Type: regular 3'; Length: 12; Trimmed: 353 times.
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] No. of allowed errors:
[2016-08-08T09:58Z] 0-9 bp: 0; 10-12 bp: 1
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] Bases preceding removed adapters:
[2016-08-08T09:58Z] A: 23.8%
[2016-08-08T09:58Z] C: 23.2%
[2016-08-08T09:58Z] G: 17.0%
[2016-08-08T09:58Z] T: 36.0%
[2016-08-08T09:58Z] none/other: 0.0%
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] Overview of removed sequences
[2016-08-08T09:58Z] Resource requests: picard, star; memory: 3.50, 2.00; cores: 1, 16
[2016-08-08T09:58Z] Configuring 1 jobs to run, using 1 cores each with 3.50g of memory reserved for each job
[2016-08-08T09:58Z] Timing: alignment
[2016-08-08T09:58Z] multiprocessing: disambiguate_split
[2016-08-08T09:58Z] multiprocessing: process_alignment
[2016-08-08T09:58Z] Aligning lane 1_110907_ERP000591 with star aligner
[2016-08-08T09:58Z] Running STAR aligner on /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/trimmed/1_110907_ERP000591_1_fastq_Test1.trimmed.txt.gz and /iron/bioinfo/src/bcbio-nextgen/tests/data/genomes/mm9/star/
[2016-08-08T09:58Z] Index BAM file: Test1.bam
[2016-08-08T09:58Z] Resource requests: cufflinks, samtools; memory: 3.00, 2.00; cores: 16, 16
[2016-08-08T09:58Z] Configuring 1 jobs to run, using 1 cores each with 3.00g of memory reserved for each job
[2016-08-08T09:58Z] Timing: disambiguation
[2016-08-08T09:58Z] Timing: transcript assembly
[2016-08-08T09:58Z] multiprocessing: cufflinks_assemble
[2016-08-08T09:58Z] Assembling transcripts with Cufflinks using /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/align/Test1/1_110907_ERP000591_star/Test1.bam.
[2016-08-08T09:58Z] /usr/bin/bash: cufflinks: command not found
[2016-08-08T09:58Z] Uncaught exception occurred
Traceback (most recent call last):
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
_do_run(cmd, checks, log_stdout)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'set -o pipefail; cufflinks --output-dir /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/assembly/tx/tmpo_HyRf/Test1 --num-threads 1 --frag-bias-correct /iron/bioinfo/src/bcbio-nextgen/tests/data/genomes/mm9/seq/mm9.fa --library-type fr-unstranded --multi-read-correct --upper-quartile-norm /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/align/Test1/1_110907_ERP000591_star/Test1.bam
/usr/bin/bash: cufflinks: command not found
' returned non-zero exit status 127
Traceback (most recent call last):
File "/iron/bioinfo/share/bcbio/anaconda/bin/bcbio_nextgen.py", line 4, in
import('pkg_resources').run_script('bcbio-nextgen==0.9.9', 'bcbio_nextgen.py')
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/init.py", line 726, in run_script
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/init.py", line 1484, in run_script
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_nextgen.py", line 226, in
main(kwargs)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_nextgen.py", line 43, in main
run_main(kwargs)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 43, in run_main
fc_dir, run_info_yaml)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 87, in _run_toplevel
for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 250, in rnaseqpipeline
samples = rnaseq.assemble_transcripts(run_parallel, samples)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/rnaseq.py", line 234, in assemble_transcripts
samples = run_parallel("cufflinks_assemble", samples)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
return run_multicore(fn, items, config, parallel=parallel)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore
for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items):
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 800, in call
while self.dispatch_one_batch(iterator):
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 658, in dispatch_one_batch
self._dispatch(tasks)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 566, in _dispatch
job = ImmediateComputeBatch(batch)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 180, in init
self.results = batch()
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 72, in call
return [func(_args, _kwargs) for func, args, kwargs in self.items]
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 51, in wrapper
return apply(f, _args, _kwargs)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 288, in cufflinks_assemble
return rnaseq.cufflinks_assemble(*args)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/rnaseq.py", line 189, in cufflinks_assemble
assembled_gtf = cufflinks.assemble(bam_file, ref_file, num_cores, out_dir, data)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/cufflinks.py", line 112, in assemble
do.run(cmd, "Assembling transcripts with Cufflinks using %s." % bam_file)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
_do_run(cmd, checks, log_stdout)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'set -o pipefail; cufflinks --output-dir /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/assembly/tx/tmpo_HyRf/Test1 --num-threads 1 --frag-bias-correct /iron/bioinfo/src/bcbio-nextgen/tests/data/genomes/mm9/seq/mm9.fa --library-type fr-unstranded --multi-read-correct --upper-quartile-norm /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/align/Test1/1_110907_ERP000591_star/Test1.bam
/usr/bin/bash: cufflinks: command not found
' returned non-zero exit status 127
ERROR
Run an RNA-seq analysis with TopHat and generate gene-level counts. ... [2016-08-08T09:58Z] System YAML configuration: /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml
[2016-08-08T09:58Z] Resource requests: cutadapt, picard; memory: 2.00, 3.50; cores: 16, 1
[2016-08-08T09:58Z] Configuring 1 jobs to run, using 1 cores each with 3.50g of memory reserved for each job
[2016-08-08T09:58Z] Timing: organize samples
[2016-08-08T09:58Z] multiprocessing: organize_samples
[2016-08-08T09:58Z] Using input YAML configuration: /iron/bioinfo/src/bcbio-nextgen/tests/data/automated/run_info-stranded.yaml
[2016-08-08T09:58Z] Checking sample YAML configuration: /iron/bioinfo/src/bcbio-nextgen/tests/data/automated/run_info-stranded.yaml
[2016-08-08T09:58Z] Testing minimum versions of installed programs
[2016-08-08T09:58Z] multiprocessing: prepare_sample
[2016-08-08T09:58Z] Preparing Test1
[2016-08-08T09:58Z] Timing: adapter trimming
[2016-08-08T09:58Z] multiprocessing: trim_sample
[2016-08-08T09:58Z] Trimming low quality ends and read through adapter sequence from /iron/bioinfo/src/bcbio-nextgen/tests/data/test_stranded/test_1.fq.gz, /iron/bioinfo/src/bcbio-nextgen/tests/data/test_stranded/test_2.fq.gz.
[2016-08-08T09:58Z] Trimming /iron/bioinfo/src/bcbio-nextgen/tests/data/test_stranded/test_1.fq.gz and /iron/bioinfo/src/bcbio-nextgen/tests/data/test_stranded/test_2.fq.gz in paired end mode with cutadapt.
[2016-08-08T09:58Z] This is cutadapt 1.10 with Python 2.7.12
[2016-08-08T09:58Z] Command line parameters: --times=2 --quality-base=33 --quality-cutoff=5 --format=fastq --adapter=AAAAAAAAAAAAA --adapter=TTTTTTTTTTTTT --adapter=AGATCGGAAGAG --adapter=CTCTTCCGATCT --minimum-length=25 -o /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/trimmed/tx/tmpseED9f/test_2_Test1.trimmed.fq.gz -p /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/trimmed/tx/tmpseED9f/test_1_Test1.trimmed.fq.gz /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/trimmed/tx/tmpseED9f/test_2_Test1.trimmed.tmp.fq.gz /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/trimmed/tx/tmpseED9f/test_1_Test1.trimmed.tmp.fq.gz
[2016-08-08T09:58Z] Trimming 4 adapters with at most 10.0% errors in paired-end legacy mode ...
[2016-08-08T09:58Z] WARNING: Requested read modifications are applied only to the first
[2016-08-08T09:58Z] read since backwards compatibility mode is enabled. To modify both
[2016-08-08T09:58Z] reads, also use any of the -A/-B/-G/-U options. Use a dummy adapter
[2016-08-08T09:58Z] sequence when necessary: -A XXX
[2016-08-08T09:58Z] Finished in 0.01 s (100 us/read; 0.60 M reads/minute).
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] === Summary ===
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] Total read pairs processed: 100
[2016-08-08T09:58Z] Read 1 with adapter: 12 (12.0%)
[2016-08-08T09:58Z] Read 2 with adapter: 0 (0.0%)
[2016-08-08T09:58Z] Pairs that were too short: 0 (0.0%)
[2016-08-08T09:58Z] Pairs written (passing filters): 100 (100.0%)
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] Total basepairs processed: 19,948 bp
[2016-08-08T09:58Z] Read 1: 10,000 bp
[2016-08-08T09:58Z] Read 2: 9,948 bp
[2016-08-08T09:58Z] Quality-trimmed: 0 bp (0.0%)
[2016-08-08T09:58Z] Read 1: 0 bp
[2016-08-08T09:58Z] Read 2: 0 bp
[2016-08-08T09:58Z] Total written (filtered): 19,855 bp (99.5%)
[2016-08-08T09:58Z] Read 1: 9,907 bp
[2016-08-08T09:58Z] Read 2: 9,948 bp
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] === First read: Adapter 1 ===
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] Sequence: AAAAAAAAAAAAA; Type: regular 3'; Length: 13; Trimmed: 2 times.
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] No. of allowed errors:
[2016-08-08T09:58Z] 0-9 bp: 0; 10-13 bp: 1
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] Bases preceding removed adapters:
[2016-08-08T09:58Z] A: 0.0%
[2016-08-08T09:58Z] C: 0.0%
[2016-08-08T09:58Z] G: 100.0%
[2016-08-08T09:58Z] T: 0.0%
[2016-08-08T09:58Z] none/other: 0.0%
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] Overview of removed sequences
[2016-08-08T09:58Z] length count expect max.err error counts
[2016-08-08T09:58Z] 3 2 1.6 0 2
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] === First read: Adapter 2 ===
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] Sequence: TTTTTTTTTTTTT; Type: regular 3'; Length: 13; Trimmed: 6 times.
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] No. of allowed errors:
[2016-08-08T09:58Z] 0-9 bp: 0; 10-13 bp: 1
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] Bases preceding removed adapters:
[2016-08-08T09:58Z] A: 33.3%
[2016-08-08T09:58Z] C: 50.0%
[2016-08-08T09:58Z] G: 16.7%
[2016-08-08T09:58Z] T: 0.0%
[2016-08-08T09:58Z] none/other: 0.0%
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] Overview of removed sequences
[2016-08-08T09:58Z] length count expect max.err error counts
[2016-08-08T09:58Z] 3 2 1.6 0 2
[2016-08-08T09:58Z] 4 1 0.4 0 1
[2016-08-08T09:58Z] 5 1 0.1 0 1
[2016-08-08T09:58Z] 11 1 0.0 1 0 1
[2016-08-08T09:58Z] 49 1 0.0 1 0 1
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] === First read: Adapter 3 ===
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] Sequence: AGATCGGAAGAG; Type: regular 3'; Length: 12; Trimmed: 1 times.
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] No. of allowed errors:
[2016-08-08T09:58Z] 0-9 bp: 0; 10-12 bp: 1
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] Bases preceding removed adapters:
[2016-08-08T09:58Z] A: 0.0%
[2016-08-08T09:58Z] C: 0.0%
[2016-08-08T09:58Z] G: 100.0%
[2016-08-08T09:58Z] T: 0.0%
[2016-08-08T09:58Z] none/other: 0.0%
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] Overview of removed sequences
[2016-08-08T09:58Z] length count expect max.err error counts
[2016-08-08T09:58Z] 3 1 1.6 0 1
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] === First read: Adapter 4 ===
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] Sequence: CTCTTCCGATCT; Type: regular 3'; Length: 12; Trimmed: 3 times.
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] No. of allowed errors:
[2016-08-08T09:58Z] 0-9 bp: 0; 10-12 bp: 1
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] Bases preceding removed adapters:
[2016-08-08T09:58Z] A: 33.3%
[2016-08-08T09:58Z] C: 0.0%
[2016-08-08T09:58Z] G: 33.3%
[2016-08-08T09:58Z] T: 33.3%
[2016-08-08T09:58Z] none/other: 0.0%
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] Overview of removed sequences
[2016-08-08T09:58Z] Resource requests: picard, star; memory: 3.50, 2.00; cores: 1, 16
[2016-08-08T09:58Z] Configuring 1 jobs to run, using 1 cores each with 3.50g of memory reserved for each job
[2016-08-08T09:58Z] Timing: alignment
[2016-08-08T09:58Z] multiprocessing: disambiguate_split
[2016-08-08T09:58Z] multiprocessing: process_alignment
[2016-08-08T09:58Z] Aligning lane Test1 with star aligner
[2016-08-08T09:58Z] Running STAR aligner on /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/trimmed/test_1_Test1.trimmed.fq.gz and /iron/bioinfo/src/bcbio-nextgen/tests/data/genomes/hg19/star/
[2016-08-08T09:58Z] Index BAM file: Test1.bam
[2016-08-08T09:58Z] Resource requests: cufflinks, samtools; memory: 3.00, 2.00; cores: 16, 16
[2016-08-08T09:58Z] Configuring 1 jobs to run, using 1 cores each with 3.00g of memory reserved for each job
[2016-08-08T09:58Z] Timing: disambiguation
[2016-08-08T09:58Z] Timing: transcript assembly
[2016-08-08T09:58Z] Timing: estimate expression (threaded)
[2016-08-08T09:58Z] multiprocessing: generate_transcript_counts
[2016-08-08T09:58Z] Sort BAM file (multi core, queryname): Test1.bam to Test1.nsorted.bam
[2016-08-08T09:58Z] [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files
[2016-08-08T09:58Z] Uncaught exception occurred
Traceback (most recent call last):
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
_do_run(cmd, checks, log_stdout)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'set -o pipefail; /iron/bioinfo/share/bcbio/anaconda/bin/samtools sort -@ 1 -m 2G -n /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1_star/Test1.bam /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1_star/tx/tmp28vrGQ/Test1.nsorted
[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files
Usage: samtools sort [options...] [in.bam]
Options:
-l INT Set compression level, from 0 (uncompressed) to 9 (best)
-m INT Set maximum memory per thread; suffix K/M/G recognized [768M]
-n Sort by read name
-o FILE Write final output to FILE rather than standard output
-T PREFIX Write temporary files to PREFIX.nnnn.bam
-@, --threads INT
Set number of sorting and compression threads [1]
--input-fmt-option OPT[=VAL]
Specify a single input file format option in the form
of OPTION or OPTION=VALUE
-O, --output-fmt FORMAT[,OPT[=VAL]]...
Specify output format (SAM, BAM, CRAM)
--output-fmt-option OPT[=VAL]
Specify a single output file format option in the form
of OPTION or OPTION=VALUE
--reference FILE
Reference sequence FASTA FILE [null]
' returned non-zero exit status 1
[2016-08-08T09:58Z] Multi-core sorting failed, reverting to single core
Traceback (most recent call last):
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/bam/init.py", line 372, in sort
os.path.basename(sort_file)))
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
_do_run(cmd, checks, log_stdout)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'set -o pipefail; /iron/bioinfo/share/bcbio/anaconda/bin/samtools sort -@ 1 -m 2G -n /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1_star/Test1.bam /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1_star/tx/tmp28vrGQ/Test1.nsorted
[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files
Usage: samtools sort [options...] [in.bam]
Options:
-l INT Set compression level, from 0 (uncompressed) to 9 (best)
-m INT Set maximum memory per thread; suffix K/M/G recognized [768M]
-n Sort by read name
-o FILE Write final output to FILE rather than standard output
-T PREFIX Write temporary files to PREFIX.nnnn.bam
-@, --threads INT
Set number of sorting and compression threads [1]
--input-fmt-option OPT[=VAL]
Specify a single input file format option in the form
of OPTION or OPTION=VALUE
-O, --output-fmt FORMAT[,OPT[=VAL]]...
Specify output format (SAM, BAM, CRAM)
--output-fmt-option OPT[=VAL]
Specify a single output file format option in the form
of OPTION or OPTION=VALUE
--reference FILE
Reference sequence FASTA FILE [null]
' returned non-zero exit status 1
[2016-08-08T09:58Z] Sort BAM file (single core, queryname): Test1.bam to Test1.nsorted.bam
[2016-08-08T09:58Z] [bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files
[2016-08-08T09:58Z] Uncaught exception occurred
Traceback (most recent call last):
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
_do_run(cmd, checks, log_stdout)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'set -o pipefail; /iron/bioinfo/share/bcbio/anaconda/bin/samtools sort -@ 1 -m 2G -n /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1_star/Test1.bam /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1_star/tx/tmp28vrGQ/Test1.nsorted
[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files
Usage: samtools sort [options...] [in.bam]
Options:
-l INT Set compression level, from 0 (uncompressed) to 9 (best)
-m INT Set maximum memory per thread; suffix K/M/G recognized [768M]
-n Sort by read name
-o FILE Write final output to FILE rather than standard output
-T PREFIX Write temporary files to PREFIX.nnnn.bam
-@, --threads INT
Set number of sorting and compression threads [1]
--input-fmt-option OPT[=VAL]
Specify a single input file format option in the form
of OPTION or OPTION=VALUE
-O, --output-fmt FORMAT[,OPT[=VAL]]...
Specify output format (SAM, BAM, CRAM)
--output-fmt-option OPT[=VAL]
Specify a single output file format option in the form
of OPTION or OPTION=VALUE
--reference FILE
Reference sequence FASTA FILE [null]
' returned non-zero exit status 1
Traceback (most recent call last):
File "/iron/bioinfo/share/bcbio/anaconda/bin/bcbio_nextgen.py", line 4, in
import('pkg_resources').run_script('bcbio-nextgen==0.9.9', 'bcbio_nextgen.py')
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/init.py", line 726, in run_script
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/init.py", line 1484, in run_script
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_nextgen.py", line 226, in
main(kwargs)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_nextgen.py", line 43, in main
run_main(kwargs)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 43, in run_main
fc_dir, run_info_yaml)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 87, in _run_toplevel
for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 252, in rnaseqpipeline
samples = rnaseq.quantitate_expression_parallel(samples, run_parallel)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/rnaseq.py", line 83, in quantitate_expression_parallel
samples = run_parallel("generate_transcript_counts", samples)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
return run_multicore(fn, items, config, parallel=parallel)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore
for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items):
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 800, in call
while self.dispatch_one_batch(iterator):
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 658, in dispatch_one_batch
self._dispatch(tasks)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 566, in _dispatch
job = ImmediateComputeBatch(batch)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 180, in init
self.results = batch()
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 72, in call
return [func(_args, _kwargs) for func, args, kwargs in self.items]
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 51, in wrapper
return apply(f, _args, _kwargs)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 148, in generate_transcript_counts
return rnaseq.generate_transcript_counts(*args)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/rnaseq.py", line 104, in generate_transcript_counts
data["count_file"] = featureCounts.count(data)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/rnaseq/featureCounts.py", line 22, in count
sorted_bam = bam.sort(in_bam, dd.get_config(data), order="queryname")
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/bam/init.py", line 382, in sort
os.path.basename(sort_file)))
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
_do_run(cmd, checks, log_stdout)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'set -o pipefail; /iron/bioinfo/share/bcbio/anaconda/bin/samtools sort -@ 1 -m 2G -n /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1_star/Test1.bam /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/align/Test1/Test1_star/tx/tmp28vrGQ/Test1.nsorted
[bam_sort] Use -T PREFIX / -o FILE to specify temporary and final output files
Usage: samtools sort [options...] [in.bam]
Options:
-l INT Set compression level, from 0 (uncompressed) to 9 (best)
-m INT Set maximum memory per thread; suffix K/M/G recognized [768M]
-n Sort by read name
-o FILE Write final output to FILE rather than standard output
-T PREFIX Write temporary files to PREFIX.nnnn.bam
-@, --threads INT
Set number of sorting and compression threads [1]
--input-fmt-option OPT[=VAL]
Specify a single input file format option in the form
of OPTION or OPTION=VALUE
-O, --output-fmt FORMAT[,OPT[=VAL]]...
Specify output format (SAM, BAM, CRAM)
--output-fmt-option OPT[=VAL]
Specify a single output file format option in the form
of OPTION or OPTION=VALUE
--reference FILE
Reference sequence FASTA FILE [null]
' returned non-zero exit status 1
ERROR
Run an explant RNA-seq analysis with TopHat and generate gene-level counts. ... [2016-08-08T09:58Z] System YAML configuration: /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml
[2016-08-08T09:58Z] Resource requests: cutadapt, picard; memory: 2.00, 3.50; cores: 16, 1
[2016-08-08T09:58Z] Configuring 1 jobs to run, using 1 cores each with 3.50g of memory reserved for each job
[2016-08-08T09:58Z] Timing: organize samples
[2016-08-08T09:58Z] multiprocessing: organize_samples
[2016-08-08T09:58Z] Using input YAML configuration: /iron/bioinfo/src/bcbio-nextgen/tests/data/automated/run_info-explant.yaml
[2016-08-08T09:58Z] Checking sample YAML configuration: /iron/bioinfo/src/bcbio-nextgen/tests/data/automated/run_info-explant.yaml
[2016-08-08T09:58Z] GTF not compatible with Qualimap, skipping.
[2016-08-08T09:58Z] GTF not compatible with Qualimap, skipping.
[2016-08-08T09:58Z] Testing minimum versions of installed programs
[2016-08-08T09:58Z] multiprocessing: prepare_sample
[2016-08-08T09:58Z] Preparing Test1
[2016-08-08T09:58Z] Preparing Test2
[2016-08-08T09:58Z] Timing: adapter trimming
[2016-08-08T09:58Z] multiprocessing: trim_sample
[2016-08-08T09:58Z] Trimming low quality ends and read through adapter sequence from /iron/bioinfo/src/bcbio-nextgen/tests/data/1_explant/Hsapiens_Mmusculus_1.fq.gz.
[2016-08-08T09:58Z] Trimming /iron/bioinfo/src/bcbio-nextgen/tests/data/1_explant/Hsapiens_Mmusculus_1.fq.gz in single end mode with cutadapt.
[2016-08-08T09:58Z] Trimming low quality ends and read through adapter sequence from /iron/bioinfo/src/bcbio-nextgen/tests/data/1_explant/Hsapiens_Mmusculus_rep2.fq.gz.
[2016-08-08T09:58Z] Trimming /iron/bioinfo/src/bcbio-nextgen/tests/data/1_explant/Hsapiens_Mmusculus_rep2.fq.gz in single end mode with cutadapt.
[2016-08-08T09:58Z] Resource requests: picard, tophat2; memory: 3.50, 2.00; cores: 1, 16
[2016-08-08T09:58Z] Configuring 1 jobs to run, using 1 cores each with 10.00g of memory reserved for each job
[2016-08-08T09:58Z] Timing: alignment
[2016-08-08T09:58Z] multiprocessing: disambiguate_split
[2016-08-08T09:58Z] multiprocessing: process_alignment
[2016-08-08T09:58Z] Aligning lane Test1 with tophat2 aligner
[2016-08-08T09:58Z] Running Tophat on /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/trimmed/Hsapiens_Mmusculus_1_Test1.trimmed.fq.gz and None.
[2016-08-08T09:58Z]
[2016-08-08T09:58Z] [2016-08-08 17:58:46] Beginning TopHat run (v2.1.1)
[2016-08-08T09:58Z] -----------------------------------------------
[2016-08-08T09:58Z] [2016-08-08 17:58:46] Checking for Bowtie
[2016-08-08T09:58Z] Bowtie 2 not found, checking for older version..
[2016-08-08T09:58Z] Error: Bowtie not found on this system.
[2016-08-08T09:58Z] Uncaught exception occurred
Traceback (most recent call last):
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
_do_run(cmd, checks, log_stdout)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'set -o pipefail; /iron/bioinfo/share/bcbio/anaconda/bin/python /iron/bioinfo/share/bcbio/anaconda/bin/tophat --library-type=fr-unstranded --no-mixed --rg-id=Test1 --no-coverage-search --rg-library=illumina --rg-platform-unit=Test1 --rg-sample=Test1 --GTF=/iron/bioinfo/src/bcbio-nextgen/tests/data/genomes/mm9/rnaseq/ref-transcripts.gtf --output-dir=/iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/align/Test1/mm9/tx/tmpXoYYTr/Test1_tophat --no-convert-bam /iron/bioinfo/src/bcbio-nextgen/tests/data/genomes/mm9/bowtie2/mm9 /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/trimmed/Hsapiens_Mmusculus_1_Test1.trimmed.fq.gz
[2016-08-08 17:58:46] Beginning TopHat run (v2.1.1)
[2016-08-08 17:58:46] Checking for Bowtie Bowtie 2 not found, checking for older version.. Error: Bowtie not found on this system. ' returned non-zero exit status 1 Traceback (most recent call last): File "/iron/bioinfo/share/bcbio/anaconda/bin/bcbio_nextgen.py", line 4, in
import('pkg_resources').run_script('bcbio-nextgen==0.9.9', 'bcbio_nextgen.py')
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/init.py", line 726, in run_script
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/setuptools-20.3-py2.7.egg/pkg_resources/init.py", line 1484, in run_script
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_nextgen.py", line 226, in
main(kwargs)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio_nextgen-0.9.9-py2.7.egg-info/scripts/bcbio_nextgen.py", line 43, in main
run_main(kwargs)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 43, in run_main
fc_dir, run_info_yaml)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 87, in _run_toplevel
for xs in pipeline(config, run_info_yaml, parallel, dirs, samples):
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/main.py", line 244, in rnaseqpipeline
samples = run_parallel("process_alignment", samples)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 28, in run_parallel
return run_multicore(fn, items, config, parallel=parallel)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multi.py", line 86, in run_multicore
for data in joblib.Parallel(parallel["num_jobs"])(joblib.delayed(fn)(x) for x in items):
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 800, in call
while self.dispatch_one_batch(iterator):
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 658, in dispatch_one_batch
self._dispatch(tasks)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 566, in _dispatch
job = ImmediateComputeBatch(batch)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 180, in init
self.results = batch()
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/joblib/parallel.py", line 72, in call
return [func(_args, _kwargs) for func, args, kwargs in self.items]
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/utils.py", line 51, in wrapper
return apply(f, _args, _kwargs)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/distributed/multitasks.py", line 72, in process_alignment
return sample.process_alignment(*args)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/sample.py", line 112, in process_alignment
data = align_to_sort_bam(fastq1, fastq2, aligner, data)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.py", line 64, in align_to_sort_bam
names, align_dir, data)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/pipeline/alignment.py", line 117, in _align_from_fastq
out = align_fn(fastq1, fastq2, align_ref, names, align_dir, data)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/tophat.py", line 242, in align
align_dir, data, names)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/ngsalign/tophat.py", line 149, in tophat_align
do.run(cmd, "Running Tophat on %s and %s." % (fastq_file, pair_file), None)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
_do_run(cmd, checks, log_stdout)
File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run
raise subprocess.CalledProcessError(exitcode, error_msg)
subprocess.CalledProcessError: Command 'set -o pipefail; /iron/bioinfo/share/bcbio/anaconda/bin/python /iron/bioinfo/share/bcbio/anaconda/bin/tophat --library-type=fr-unstranded --no-mixed --rg-id=Test1 --no-coverage-search --rg-library=illumina --rg-platform-unit=Test1 --rg-sample=Test1 --GTF=/iron/bioinfo/src/bcbio-nextgen/tests/data/genomes/mm9/rnaseq/ref-transcripts.gtf --output-dir=/iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/align/Test1/mm9/tx/tmpXoYYTr/Test1_tophat --no-convert-bam /iron/bioinfo/src/bcbio-nextgen/tests/data/genomes/mm9/bowtie2/mm9 /iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/trimmed/Hsapiens_Mmusculus_1_Test1.trimmed.fq.gz
[2016-08-08 17:58:46] Beginning TopHat run (v2.1.1)
[2016-08-08 17:58:46] Checking for Bowtie Bowtie 2 not found, checking for older version.. Error: Bowtie not found on this system. ' returned non-zero exit status 1 ERROR
ERROR: Run an RNA-seq analysis with hisat2 and generate gene-level counts.
Traceback (most recent call last): File "/iron/bioinfo/src/bcbio-nextgen/tests/test_automated_analysis.py", line 235, in test_2_hisat2 subprocess.check_call(cl) File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/subprocess.py", line 541, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command '['bcbio_nextgen.py', '/iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml', '/iron/bioinfo/src/bcbio-nextgen/tests/data/automated/../110907_ERP000591', '/iron/bioinfo/src/bcbio-nextgen/tests/data/automated/run_info-hisat2.yaml']' returned non-zero exit status 1
ERROR: Run an RNA-seq analysis with TopHat and generate gene-level counts.
Traceback (most recent call last): File "/iron/bioinfo/src/bcbio-nextgen/tests/test_automated_analysis.py", line 167, in test_2_rnaseq subprocess.check_call(cl) File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/subprocess.py", line 541, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command '['bcbio_nextgen.py', '/iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml', '/iron/bioinfo/src/bcbio-nextgen/tests/data/automated/../110907_ERP000591', '/iron/bioinfo/src/bcbio-nextgen/tests/data/automated/run_info-rnaseq.yaml']' returned non-zero exit status 1
ERROR: Run an RNA-seq analysis with STAR and generate gene-level counts.
Traceback (most recent call last): File "/iron/bioinfo/src/bcbio-nextgen/tests/test_automated_analysis.py", line 193, in test_2_star subprocess.check_call(cl) File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/subprocess.py", line 541, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command '['bcbio_nextgen.py', '/iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml', '/iron/bioinfo/src/bcbio-nextgen/tests/data/automated/../110907_ERP000591', '/iron/bioinfo/src/bcbio-nextgen/tests/data/automated/run_info-star.yaml']' returned non-zero exit status 1
ERROR: Run an RNA-seq analysis with TopHat and generate gene-level counts.
Traceback (most recent call last): File "/iron/bioinfo/src/bcbio-nextgen/tests/test_automated_analysis.py", line 154, in test_2_stranded subprocess.check_call(cl) File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/subprocess.py", line 541, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command '['bcbio_nextgen.py', '/iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml', '/iron/bioinfo/src/bcbio-nextgen/tests/data/automated/../test_stranded', '/iron/bioinfo/src/bcbio-nextgen/tests/data/automated/run_info-stranded.yaml']' returned non-zero exit status 1
ERROR: Run an explant RNA-seq analysis with TopHat and generate gene-level counts.
Traceback (most recent call last): File "/iron/bioinfo/src/bcbio-nextgen/tests/test_automated_analysis.py", line 250, in test_explant subprocess.check_call(cl) File "/iron/bioinfo/share/bcbio/anaconda/lib/python2.7/subprocess.py", line 541, in check_call raise CalledProcessError(retcode, cmd) CalledProcessError: Command '['bcbio_nextgen.py', '/iron/bioinfo/src/bcbio-nextgen/tests/test_automated_output/bcbio_system.yaml', '/iron/bioinfo/src/bcbio-nextgen/tests/data/automated/../1_explant', '/iron/bioinfo/src/bcbio-nextgen/tests/data/automated/run_info-explant.yaml']' returned non-zero exit status 1
Ran 7 tests in 107.363s
FAILED (SKIP=1, errors=5)