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-bash: initPipeline: command not found
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
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?
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.
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.
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?
