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-bash: initPipeline: command not found #213

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zhangws119 opened this issue May 31, 2015 · 4 comments
Open

-bash: initPipeline: command not found #213

zhangws119 opened this issue May 31, 2015 · 4 comments

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@zhangws119
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Dear metAMOS developers,
I am having an error about "initpipeline"
I hope you can help me finding the solution.
Thank you for your attention
James Version

as follows：drwxr-xr-x. 3 root root 4096 May 5 17:58 AMOS
drwxr-xr-x. 5 root root 4096 May 21 21:43 build
drwxr-xr-x. 6 13121 13121 4096 May 20 17:37 CA
-rw-r--r--. 1 root root 1948 Apr 7 04:34 check_install.py
drwxr-xr-x. 2 root root 4096 Apr 7 04:34 doc
drwxr-xr-x. 4 root root 4096 Apr 7 04:34 docs
-rw-r--r--. 1 root root 326269 May 20 16:36 ea-utils.1.1.2-537.tar.gz
-rw-r--r--. 1 root root 647296 May 20 16:37 EdenaV3_130110.tar.gz
-rw-r--r--. 1 root root 8596 May 5 19:39 ez_setup.py
drwxr-xr-x. 6 root root 4096 May 12 22:18 FastQC
-rw-r--r--. 1 root root 732 May 19 18:58 formatdb.log
-rw-r--r--. 1 root root 119 Apr 7 04:34 gitAMOS.sh
drwxr-xr-x. 2 root root 4096 Apr 7 04:34 img
-rwxr-xr-x. 1 root root 17571 May 21 21:33 initPipeline
-rw-r--r--. 1 root root 99154 May 21 17:53 INSTALL.py
-rw-r--r--. 1 root root 1067138 May 9 18:20 jellyfish.tar.gz
drwxr-xr-x. 9 root root 4096 May 12 17:26 KronaTools
drwxrwxr-x. 4 root root 4096 Sep 7 2013 LAP
-rw-r--r--. 1 root root 649999 Apr 7 04:34 LICENSE.txt
drwxr-xr-x. 2 root root 4096 Apr 7 04:34 Log
drwxr-xr-x. 2 root root 4096 May 21 21:32 metAMOS.egg-info
-rw-r--r--. 1 root root 263436565 May 19 18:57 metaphyler.tar.gz
drwxr-xr-x. 9 1002 1002 4096 May 19 19:22 phylosift
drwxr-xr-x. 4 zhangws games 4096 Oct 5 2013 quast
-rw-r--r--. 1 root root 738 Apr 7 04:34 README.md
-rw-r--r--. 1 root root 11075 Apr 7 04:34 required_file_list.txt
-rwxr-xr-x. 1 root root 43150 May 21 21:33 runPipeline
-rw-r--r--. 1 root root 1388 Apr 7 04:34 setup.py
-rw-r--r--. 1 root root 755541 May 5 19:39 setuptools-0.7.4.tar.gz
-rw-r--r--. 1 root root 340514 May 20 16:38 sparsehash-2.0.2.tar.gz
drwxr-xr-x. 2 root root 4096 May 25 23:12 src
drwxr-xr-x. 4 root root 4096 May 25 23:28 Test
drwxr-xr-x. 2 root root 4096 May 31 16:51 test_wmh
drwxr-xr-x. 4 root root 4096 Apr 7 04:34 Tutorial
drwxr-xr-x. 14 root root 4096 May 21 02:02 Utilities
[root@MTB metAMOS-1.5rc3]# initPipeline -q -1 /home/weilin/SoftWares/velvet_1.2.10/data/WMH_1.fq -2 /home/weilin/SoftWares/velvet_1.2.10/data/WMH_2.fq -d test_wmh -i 300:500
-bash: initPipeline: command not found
@skoren
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skoren commented May 31, 2015

I don't think this is a metAMOS issue but an issue with the shell not including the current directory in your path. Have you tried ./initPipeline instead of initPipeline?

@zhangws119
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Dear metAMOS developers:

Thanks for your help,I have solved this problem with your help ,but now I have a new issue about runPipeline , I hope you can help me finding the solution. Thank you very much.

as follows :
Starting Task = preprocess.PREPROCESS
Job = [[WMH_1.fq, WMH_2.fq] -> preprocess.success] completed
Completed Task = preprocess.Preprocess
Starting Task = assemble.ASSEMBLE
Job = [preprocess.success -> .run] completed
Completed Task = assemble.SplitAssemblers
Job = [soapdenovo.31.run -> soapdenovo.31.asm.contig] completed
Completed Task = assemble.Assemble
Job = [[soapdenovo.31.asm.contig] -> [assemble.ok]] completed
Completed Task = assemble.CheckAsmResults
Uptodate Task = assemble.SplitMappers
Starting Task = mapreads.MAPREADS
Job = [soapdenovo.31.asm.contig -> soapdenovo.31.contig.cvg] completed
Completed Task = mapreads.MapReads
Job = [[soapdenovo.31.contig.cvg] -> [mapreads.ok]] completed
Completed Task = mapreads.CheckMapResults
Uptodate Task = mapreads.SplitForORFs
Starting Task = findorfs.FINDORFS
Job = [soapdenovo.31.contig.cvg -> soapdenovo.31.faa] completed
Completed Task = findorfs.FindORFS
Starting Task = validate.VALIDATE
Job = [[soapdenovo.31.faa] -> [validate.ok]] completed
Completed Task = validate.Validate
Starting Task = findrepeats.FINDREPEATS
Job = [proba.fna -> proba.repeats] completed
Completed Task = findreps.FindRepeats
Starting Task = annotate.ANNOTATE
Job = [proba.faa -> proba.hits] completed
Completed Task = annotate.Annotate
Starting Task = functionalannotation.FUNCTIONALANNOTATION
Job = [proba.faa -> [blast.out, krona.ec.input]] completed
Completed Task = fannotate.FunctionalAnnotation
Starting Task = scaffold.SCAFFOLD
[91m****************************************************************
_ERROR_**********
During scaffold, the following command failed with return code -11:

/home/zhangws/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/OrientContigs -minRedundancy 5 -all -redundancy 10 -b /home/zhangws/software/metAMOS-1.5rc3/test_wmh/Scaffold/in/proba.bnk -repeats /home/zhangws/software/metAMOS-1.5rc3/test_wmh/Scaffold/in/proba.reps

_DETAILS_**********
Last 10 commands run before the error (/home/zhangws/software/metAMOS-1.5rc3/test_wmh/Logs/COMMANDS.log)
|2015-06-02 09:27:55|# [SCAFFOLD]
|2015-06-02 09:27:56| rm -rf /home/zhangws/software/metAMOS-1.5rc3/test_wmh/Scaffold/in/proba.bnk
|2015-06-02 09:33:00| /home/zhangws/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/toAmos_new -Q /home/zhangws/software/metAMOS-1.5rc3/test_wmh/Preprocess/out/lib1.seq -i --min 2 --max 3808 --libname lib1 -b /home/zhangws/software/metAMOS-1.5rc3/test_wmh/Scaffold/in/proba.bnk
|2015-06-02 09:34:15| /home/zhangws/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/toAmos_new -c /home/zhangws/software/metAMOS-1.5rc3/test_wmh/Assemble/out/proba.asm.tigr -b /home/zhangws/software/metAMOS-1.5rc3/test_wmh/Scaffold/in/proba.bnk
|2015-06-02 09:36:57| /home/zhangws/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/asmQC -b /home/zhangws/software/metAMOS-1.5rc3/test_wmh/Scaffold/in/proba.bnk -scaff -recompute -update -numsd 2
|2015-06-02 09:36:57| perl /home/zhangws/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/bank-unlock /home/zhangws/software/metAMOS-1.5rc3/test_wmh/Scaffold/in/proba.bnk
|2015-06-02 09:39:07| /home/zhangws/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/clk -b /home/zhangws/software/metAMOS-1.5rc3/test_wmh/Scaffold/in/proba.bnk
|2015-06-02 09:40:04| /home/zhangws/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/Bundler -b /home/zhangws/software/metAMOS-1.5rc3/test_wmh/Scaffold/in/proba.bnk
|2015-06-02 10:28:31| /home/zhangws/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/MarkRepeats -redundancy 50 -b /home/zhangws/software/metAMOS-1.5rc3/test_wmh/Scaffold/in/proba.bnk > /home/zhangws/software/metAMOS-1.5rc3/test_wmh/Scaffold/in/proba.reps
|2015-06-02 10:42:50| /home/zhangws/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/OrientContigs -minRedundancy 5 -all -redundancy 10 -b /home/zhangws/software/metAMOS-1.5rc3/test_wmh/Scaffold/in/proba.bnk -repeats /home/zhangws/software/metAMOS-1.5rc3/test_wmh/Scaffold/in/proba.reps

Last 10 lines of output (/home/zhangws/software/metAMOS-1.5rc3/test_wmh/Logs/SCAFFOLD.log)
FOR SKIPPED EDGE 339352 SET EDGE STATUS TO BE 5
FOR SKIPPED EDGE 340101 SET EDGE STATUS TO BE 5
FOR SKIPPED EDGE 340706 SET EDGE STATUS TO BE 5
FOR SKIPPED EDGE 343496 SET EDGE STATUS TO BE 5
FOR SKIPPED EDGE 344745 SET EDGE STATUS TO BE 5
FOR SKIPPED EDGE 347237 SET EDGE STATUS TO BE 5
FOR SKIPPED EDGE 347476 SET EDGE STATUS TO BE 5
FOR SKIPPED EDGE 350808 SET EDGE STATUS TO BE 5
FOR SKIPPED EDGE 358382 SET EDGE STATUS TO BE 5
FOR SKIPPED EDGE 359477 SET EDGE STATUS TO BE 5

Please veryify input data and restart MetAMOS. If the problem persists please contact the MetAMOS development team.
_ERROR_**********

rm: cannot remove `/home/zhangws/software/metAMOS-1.5rc3/test_wmh/Logs/scaffold.ok': No such file or directory
Oops, MetAMOS finished with errors! see text in red above for details.

@skoren
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skoren commented Jun 2, 2015

You can set -n Scaffold as a workaround to skip the scaffolding step.

From your output it looks like there may be an issue with your input paired sequences. You specified the min/max as 300-500 but during the run, they were re-estimated to be 2-4000 which seems to be too large. You can check the outputs in Assemble/out/*.lib1.meanstdev to see the library estimate for the sequence mapping to see the mean/stdev computed. If they are significantly different from what you expect for the library, there is most likely an issue with the input data pairing being inconsistent.

@izaakm
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izaakm commented Jun 11, 2015

What are the headers for the columns in "Assemble/out/*.lib1.meanstdev"?

In general, where might I find headers for output files that don't include headers by default?

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@skoren @izaakm @zhangws119