Closed sebhtml closed 10 years ago
Issue by sebhtml Thursday May 15, 2014 at 22:05 GMT Originally opened as https://github.com/kbase/assembly/issues/6
https://bitbucket.org/levinas/assembly-rast/issue/6/python-subprocess-and-velvet-errors
Fangfang Xia created an issue 2013-10-13
I noticed the three pipelines Alex Copeland submitted on Oct 10 all failed. Not sure if this was looked into.
ubuntu@ar-comp-mem25:/mnt/data/accopeland/2/2/2_report.txt
Issue 1:
Command: sga preprocess -q 10 -f 20 -m 29 --permute-ambiguous -o SRR000066_10000.pp.fastq SRR000066_10000.fastq ERROR TRACE: [' File "/home/ubuntu/assembly-v0.1.0/lib/ar_server/consume.py", line 328, in compute\n result_files, summary, contig_files = self.run_pipeline(pipelines, job_data, contigs_only=contigs)\n', ' File "/home/ubuntu/assembly-v0.1.0/lib/ar_server/consume.py", line 503, in run_pipeline\n module_name, job_data, all_data=True, reads=include_reads)\n', ' File "/home/ubuntu/assembly-v0.1.0/lib/ar_server/plugins.py", line 594, in run_module\n output = plugin.plugin_object(settings, job_data, self)\n', ' File "/home/ubuntu/assembly-v0.1.0/lib/ar_server/plugins.py", line 391, in call\n output = self.run(valid_files)\n', ' File "/home/ubuntu/assembly-v0.1.0/lib/ar_server/plugins/sga_preprocess.py", line 41, in run\n self.arast_popen(cmd_args, cwd=self.outpath)\n', ' File "/home/ubuntu/assembly-v0.1.0/lib/ar_server/plugins.py", line 77, in arast_popen\n stderr=subprocess.STDOUT, **kwargs)\n', ' File "/usr/lib/python2.7/subprocess.py", line 679, in init\n errread, errwrite)\n', ' File "/usr/lib/python2.7/subprocess.py", line 1249, in _execute_child\n raise child_exception\n']
Issue 2:
Command: velveth velvet_77ca39c8-f01a-4ad2-8ce8-9f61432659b0 29 -shortPaired -fastq -separate SRR000066_10000_1.00.cor.td_sync.fastq SRR000066_10000_2.00.cor.td_sync.fastq -short -fastq SRR000066_10000__unpaired.00.cor.td.fastq velveth: Right sequence file '/mnt/data/accopeland/2/2/tagdust_5c2583d5-f390-4ac2-8850-ad766f2e1646/SRR000066_10000_2.00.cor.td_sync.fastq' has too many sequences [0.000000] Reading FastQ file /mnt/data/accopeland/2/2/tagdust_5c2583d5-f390-4ac2-8850-ad766f2e1646/SRR000066_10000_1.00.cor.td_sync.fastq; [0.000422] Reading FastQ file /mnt/data/accopeland/2/2/tagdust_5c2583d5-f390-4ac2-8850-ad766f2e1646/SRR000066_10000_2.00.cor.td_sync.fastq; Command: velvetg velvet_77ca39c8-f01a-4ad2-8ce8-9f61432659b0 -exp_cov auto -ins_length 100 -ins_length_sd 20 [0.000000] No Roadmap file to build upon! Please run velveth (see manual)
Resolved.
cbun
commented
10 years ago cbun
commented
10 years ago
https://bitbucket.org/levinas/assembly-rast/issue/6/python-subprocess-and-velvet-errors
Fangfang Xia created an issue 2013-10-13
I noticed the three pipelines Alex Copeland submitted on Oct 10 all failed. Not sure if this was looked into.
ubuntu@ar-comp-mem25:/mnt/data/accopeland/2/2/2_report.txt
Issue 1:
Command: sga preprocess -q 10 -f 20 -m 29 --permute-ambiguous -o SRR000066_10000.pp.fastq SRR000066_10000.fastq ERROR TRACE: [' File "/home/ubuntu/assembly-v0.1.0/lib/ar_server/consume.py", line 328, in compute\n result_files, summary, contig_files = self.run_pipeline(pipelines, job_data, contigs_only=contigs)\n', ' File "/home/ubuntu/assembly-v0.1.0/lib/ar_server/consume.py", line 503, in run_pipeline\n module_name, job_data, all_data=True, reads=include_reads)\n', ' File "/home/ubuntu/assembly-v0.1.0/lib/ar_server/plugins.py", line 594, in run_module\n output = plugin.plugin_object(settings, job_data, self)\n', ' File "/home/ubuntu/assembly-v0.1.0/lib/ar_server/plugins.py", line 391, in call\n output = self.run(valid_files)\n', ' File "/home/ubuntu/assembly-v0.1.0/lib/ar_server/plugins/sga_preprocess.py", line 41, in run\n self.arast_popen(cmd_args, cwd=self.outpath)\n', ' File "/home/ubuntu/assembly-v0.1.0/lib/ar_server/plugins.py", line 77, in arast_popen\n stderr=subprocess.STDOUT, **kwargs)\n', ' File "/usr/lib/python2.7/subprocess.py", line 679, in init\n errread, errwrite)\n', ' File "/usr/lib/python2.7/subprocess.py", line 1249, in _execute_child\n raise child_exception\n']
Issue 2:
Command: velveth velvet_77ca39c8-f01a-4ad2-8ce8-9f61432659b0 29 -shortPaired -fastq -separate SRR000066_10000_1.00.cor.td_sync.fastq SRR000066_10000_2.00.cor.td_sync.fastq -short -fastq SRR000066_10000__unpaired.00.cor.td.fastq velveth: Right sequence file '/mnt/data/accopeland/2/2/tagdust_5c2583d5-f390-4ac2-8850-ad766f2e1646/SRR000066_10000_2.00.cor.td_sync.fastq' has too many sequences [0.000000] Reading FastQ file /mnt/data/accopeland/2/2/tagdust_5c2583d5-f390-4ac2-8850-ad766f2e1646/SRR000066_10000_1.00.cor.td_sync.fastq; [0.000422] Reading FastQ file /mnt/data/accopeland/2/2/tagdust_5c2583d5-f390-4ac2-8850-ad766f2e1646/SRR000066_10000_2.00.cor.td_sync.fastq; Command: velvetg velvet_77ca39c8-f01a-4ad2-8ce8-9f61432659b0 -exp_cov auto -ins_length 100 -ins_length_sd 20 [0.000000] No Roadmap file to build upon! Please run velveth (see manual)