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marbl / metAMOS

A metagenomic and isolate assembly and analysis pipeline built with AMOS
http://marbl.github.io/metAMOS
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1.5rc1 FragGeneScan segfault while running test #122

Closed ghuntress closed 10 years ago

ghuntress commented 10 years ago

Release: 1.5rc1 Frozen Binary (February 18th) Arch: x86_64 OS: Centos 6.5

Starting Task = findscaffoldorfs.FINDSCAFFOLDORFS *\ metAMOS running command: /tmp/_MEIkUbeTQ/Utilities/cpp/Linux-x86_64/FragGeneScan -s /home/mdavison/bin/Test/test1/Scaffold/out/proba.linearize.scaffolds.final -o /home/mdavison/bin/Test/test1/FindScaffoldORFS/out/proba.orfs -w 0 -t complete

****ERROR****** During findscaffoldorfs, the following command failed with return code -11:

/tmp/_MEIkUbeTQ/Utilities/cpp/Linux-x86_64/FragGeneScan -s /home/mdavison/bin/Test/test1/Scaffold/out/proba.linearize.scaffolds.final -o /home/mdavison/bin/Test/test1/FindScaffoldORFS/out/proba.orfs -w 0 -t complete

****DETAILS****** Last 10 commands run before the error (/home/mdavison/bin/Test/test1/Logs/COMMANDS.log) |2014-03-04 19:00:16| /tmp/_MEIkUbeTQ/AMOS/Linux-x86_64/bin/OrientContigs -minRedundancy 5 -all -redundancy 10 -b /home/mdavison/bin/Test/test1/Scaffold/in/proba.bnk -repeats /home/mdavison/bin/Test/test1/Scaffold/in/proba.reps |2014-03-04 19:00:16| /tmp/_MEIkUbeTQ/AMOS/Linux-x86_64/bin/bank2fasta -eid -b /home/mdavison/bin/Test/test1/Scaffold/in/proba.bnk > /home/mdavison/bin/Test/test1/Scaffold/out/proba.contigs |2014-03-04 19:00:16| /tmp/_MEIkUbeTQ/AMOS/Linux-x86_64/bin/OutputMotifs -b /home/mdavison/bin/Test/test1/Scaffold/in/proba.bnk > /home/mdavison/bin/Test/test1/Scaffold/out/proba.motifs |2014-03-04 19:00:16| /tmp/_MEIkUbeTQ/AMOS/Linux-x86_64/bin/OutputResults -b /home/mdavison/bin/Test/test1/Scaffold/in/proba.bnk -p /home/mdavison/bin/Test/test1/Scaffold/out/proba |2014-03-04 19:00:16| /tmp/_MEIkUbeTQ/AMOS/Linux-x86_64/bin/OutputScaffolds -b /home/mdavison/bin/Test/test1/Scaffold/in/proba.bnk > /home/mdavison/bin/Test/test1/Scaffold/out/proba.scaffolds.final |2014-03-04 19:00:16| /tmp/_MEIkUbeTQ/AMOS/Linux-x86_64/bin/Linearize -b /home/mdavison/bin/Test/test1/Scaffold/in/proba.bnk |2014-03-04 19:00:16| /tmp/_MEIkUbeTQ/AMOS/Linux-x86_64/bin/OutputResults -b /home/mdavison/bin/Test/test1/Scaffold/in/proba.bnk -p /home/mdavison/bin/Test/test1/Scaffold/out/proba.linearize |2014-03-04 19:00:16| /tmp/_MEIkUbeTQ/AMOS/Linux-x86_64/bin/OutputScaffolds -b /home/mdavison/bin/Test/test1/Scaffold/in/proba.bnk > /home/mdavison/bin/Test/test1/Scaffold/out/proba.linearize.scaffolds.final |2014-03-04 19:00:17|# [FINDSCAFFOLDORFS] |2014-03-04 19:00:18| /tmp/_MEIkUbeTQ/Utilities/cpp/Linux-x86_64/FragGeneScan -s /home/mdavison/bin/Test/test1/Scaffold/out/proba.linearize.scaffolds.final -o /home/mdavison/bin/Test/test1/FindScaffoldORFS/out/proba.orfs -w 0 -t complete

Last 10 lines of output (/home/mdavison/bin/Test/test1/Logs/FINDSCAFFOLDORFS.log)

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

In the dmesg (from the multiple times running the test):

FragGeneScan[27795]: segfault at 7fc6bd737fdb ip 000000000040499f sp 00007ffefff63470 error 4 in FragGeneScan[400000+c000] FragGeneScan[28459]: segfault at 7fd72621dfdb ip 000000000040499f sp 00007fffb3d11da0 error 4 in FragGeneScan[400000+c000] FragGeneScan[28971]: segfault at 7f2075576fdb ip 000000000040499f sp 00007fff5a13cd00 error 4 in FragGeneScan[400000+c000] FragGeneScan[29375]: segfault at 7f72fce7bfdb ip 000000000040499f sp 00007fffe802b570 error 4 in FragGeneScan[400000+c000] FragGeneScan[30146]: segfault at 7fc4de440fdb ip 000000000040499f sp 00007fff5d427550 error 4 in FragGeneScan[400000+c000] FragGeneScan[12496]: segfault at 7fa49394efdb ip 000000000040499f sp 00007fff1cdf77e0 error 4 in FragGeneScan[400000+c000] FragGeneScan[13145]: segfault at 7fe7d19dbfdb ip 000000000040499f sp 00007fff9bcb5f00 error 4 in FragGeneScan[400000+c000] FragGeneScan[13153]: segfault at 7f13c4d01fdb ip 000000000040499f sp 00007fff5570ff60 error 4 in FragGeneScan[400000+c000] FragGeneScan[24992]: segfault at 7f9124bddfdb ip 000000000040499f sp 00007fffd30d5360 error 4 in FragGeneScan[400000+c000]

Let me know if you need any additional files or logs.

-Garret

skoren commented 10 years ago

Hi,

This most likely means a library FragGeneScan was built with is not compatible with your system. Could you try running:

ldd Utilities/cpp/Linux-x86_64/FragGeneScan 
./Utilities/cpp/Linux-x86_64/FragGeneScan

and post the output?

ghuntress commented 10 years ago

ldd looks ok to me:

[mdavison@dge-calc Linux-x86_64]$ pwd
/tmp/_MEIhCV44D/Utilities/cpp/Linux-x86_64

[mdavison@dge-calc Linux-x86_64]$ ldd FragGeneScan 
    linux-vdso.so.1 =>  (0x00007fff453ff000)
    libm.so.6 => /lib64/libm.so.6 (0x0000003d16000000)
    libc.so.6 => /lib64/libc.so.6 (0x0000003d15c00000)
    /lib64/ld-linux-x86-64.so.2 (0x0000003d15800000)

[mdavison@dge-calc Linux-x86_64]$ ./FragGeneScan 
ERROR: You missed some parameters for input
USAGE: ./FragGeneScan.pl -s [seq_file_name] -o [output_file_name] -w [1 or 0] -t [train_file_name]
       [seq_file_name]:    sequence file name including the full path
       [output_file_name]: output file name including the full path
       [1 or 0]:           1 if the sequence file has complete genomic sequences
                           0 if the sequence file has short sequence reads
       [train_file_name]:  file name that contains model parameters; this file should be in the "train" directory
                           Note that four files containing model parameters already exist in the "train" directory
                           [complete] for complete genomic sequences or short sequence reads without sequencing error
                           [sanger_5] for Sanger sequencing reads with about 0.5% error rate
                           [sanger_10] for Sanger sequencing reads with about 1% error rate
                           [454_5] for 454 pyrosequencing reads with about 0.5% error rate
                           [454_10] for 454 pyrosequencing reads with about 1% error rate
                           [454_30] for 454 pyrosequencing reads with about 3% error rate
                           [illumina_5] for Illumina sequencing reads with about 0.5% error rate
                           [illumina_10] for Illumina sequencing reads with about 1% error rate
skoren commented 10 years ago

Based on your output, this is run_test.sh? Could you post the full output from runPipeline along with Logs/COMMANDS.log, Logs/FINDORFS.LOG, Logs/ASSEMBLE.log, and Logs/SCAFFOLD.log

Could you also try running AMOS/Linux-x86_64/bin/toAmos_new -h

ghuntress commented 10 years ago

A reboot later and now the test runs successfully... Sorry for the false positive.

fwhelan commented 9 years ago

I've been having the same problem as above, but multiple reboots hasn't solved the issue. Release: 1.5rc3 Arch: x86_64 OS: Linux -ldd looked similar to ghuntress's -I've been running ./run_pipeline_test.sh ; exact same error message as above.

Logs/COMMANDS.log:

|2014-11-28 11:18:31|# [RUNPIPELINE]
|2014-11-28 11:18:31| touch /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.seq
|2014-11-28 11:18:31| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/*.contig.cvg
|2014-11-28 11:18:31| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Logs/mapreads.ok
|2014-11-28 11:18:31| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Logs/propagate.ok
|2014-11-28 11:18:31| touch /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/out/proba.annots
|2014-11-28 11:18:31| touch /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/out/proba.linearize.scaffolds.final
|2014-11-28 11:18:31| touch /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.faa
|2014-11-28 11:18:31| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Abundance/out/proba.taxprof.pct.txt
|2014-11-28 11:18:31| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/out/proba.hits
|2014-11-28 11:18:31| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/*.faa
|2014-11-28 11:18:31| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/*.fna
|2014-11-28 11:18:31| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/*.faa
|2014-11-28 11:18:31| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/*.fna
|2014-11-28 11:18:31| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Logs/assemble.ok
|2014-11-28 11:18:31| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/*.asm.contig
|2014-11-28 11:18:31| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Logs/classify.ok
|2014-11-28 11:18:37|# [PREPROCESS]
|2014-11-28 11:18:38| java -cp /home/surette-1/software/metAMOS-1.5rc3/Utilities/java:.:. outputDefaultQuality /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/in/carsonella_pe_filt.fna > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/in/carsonella_pe_filt.fna.qual
|2014-11-28 11:18:38| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/all.seq.mates
|2014-11-28 11:18:40| cp /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/carsonella_pe_filt.fna /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.seq
|2014-11-28 11:18:40| cp /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/carsonella_pe_filt.fna.qual /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.seq.qual
|2014-11-28 11:18:40| which python
|2014-11-28 11:18:40| echo $PYTHONPATH
|2014-11-28 11:18:40| perl /home/surette-1/software/metAMOS-1.5rc3/Utilities/perl/split_fasta.pl /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.seq /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.1.fasta /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.2.fasta
|2014-11-28 11:18:40| perl /home/surette-1/software/metAMOS-1.5rc3/Utilities/perl/split_fasta.pl /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.seq.qual /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.1.fasta.qual /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.2.fasta.qual
|2014-11-28 11:18:40| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.seq /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.fasta
|2014-11-28 11:18:43| java -cp /home/surette-1/software/metAMOS-1.5rc3/Utilities/java:. convertFastaAndQualToFastq /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.seq /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.seq.qual > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.fastq
|2014-11-28 11:18:45| java -cp /home/surette-1/software/metAMOS-1.5rc3/Utilities/java:. convertFastaAndQualToFastq /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.1.fasta /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.1.fasta.qual > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.1.fastq
|2014-11-28 11:18:46| java -cp /home/surette-1/software/metAMOS-1.5rc3/Utilities/java:. convertFastaAndQualToFastq /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.2.fasta /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.2.fasta.qual > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.2.fastq
|2014-11-28 11:18:46| touch /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/preprocess.success
|2014-11-28 11:18:47|# [ASSEMBLE]
|2014-11-28 11:18:47| touch /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.run
|2014-11-28 11:18:48| cat /home/surette-1/software/metAMOS-1.5rc3/Test/test1/soapconfig.txt |grep -v max_rd_len > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/soap2config.txt
|2014-11-28 11:18:49| /home/surette-1/software/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/SOAPdenovo-63mer pregraph -p 15 -K 55 -R  -D   -s /home/surette-1/software/metAMOS-1.5rc3/Test/test1/soapconfig.txt -o /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.asm
|2014-11-28 11:18:49| /home/surette-1/software/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/SOAPdenovo-63mer contig -g /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.asm -R  -M 3 
|2014-11-28 11:18:50| mv /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.asm.contigWIUPAC.fa
|2014-11-28 11:18:50| java -cp /home/surette-1/software/metAMOS-1.5rc3/Utilities/java:. RemoveIUPAC /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.asm.contigWIUPAC.fa >/home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.asm.contig
|2014-11-28 11:18:50| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.run
|2014-11-28 11:18:50| touch /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/assemble.success
|2014-11-28 11:18:52|# [MAPREADS]
|2014-11-28 11:18:52| /home/surette-1/software/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.IDX
|2014-11-28 11:18:52| /home/surette-1/software/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/bowtie -p 15 -f -l 25 -e 140 --best --strata -m 10 -k 1 --un /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.lib1.unaligned.fasta /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.IDX /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.seq > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/lib1.bout
|2014-11-28 11:18:58| cat /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.lib1.mappedmates >> /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.lib1.hdr 
|2014-11-28 11:18:58| cp /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.lib1.hdr /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.lib1.mappedmates 
|2014-11-28 11:19:00|# [FINDORFS]
|2014-11-28 11:19:00| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/in/soapdenovo.55.asm.contig
|2014-11-28 11:19:00| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/in/soapdenovo.55.asm.contig
|2014-11-28 11:19:02| /home/surette-1/software/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/FragGeneScan -s /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/in/soapdenovo.55.asm.contig -o /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.orfs -w 0 -t complete
|2014-11-28 11:19:02| mv /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.orfs.ffn /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.ctg.fna
|2014-11-28 11:19:02| mv /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.orfs.faa /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.ctg.faa
|2014-11-28 11:19:02| mv /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.gene.cvg /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.ctg.gene.cvg
|2014-11-28 11:19:02| mv /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.gene.map /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.ctg.gene.map
|2014-11-28 11:19:02| rm -r /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.fna
|2014-11-28 11:19:02| cat /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55*.fna > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.fna
|2014-11-28 11:19:02| rm -r /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.fna.bnk
|2014-11-28 11:19:02| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/toAmos_new -s /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.fna -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.fna.bnk
|2014-11-28 11:19:02| rm -r /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.faa
|2014-11-28 11:19:02| cat /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55*.faa > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.faa
|2014-11-28 11:19:02| rm -r /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.faa.bnk
|2014-11-28 11:19:02| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/toAmos_new -s /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.faa -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.faa.bnk
|2014-11-28 11:19:02| rm -r /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.gene.cvg
|2014-11-28 11:19:02| cat /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55*.gene.cvg > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.gene.cvg
|2014-11-28 11:19:02| rm -r /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.gene.map
|2014-11-28 11:19:02| cat /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55*.gene.map > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.gene.map
|2014-11-28 11:19:02| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.faa /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.faa
|2014-11-28 11:19:02| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.fna /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.fna
|2014-11-28 11:19:03|# [VALIDATE]
|2014-11-28 11:19:03| touch /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Logs/validate.skip
|2014-11-28 11:19:03| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.asm.contig
|2014-11-28 11:19:03| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.asm.contig
|2014-11-28 11:19:03| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.linearize.scaffolds.final
|2014-11-28 11:19:03| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.linearize.scaffolds.final
|2014-11-28 11:19:03| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.asm.tigr
|2014-11-28 11:19:03| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.asm.tigr /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.asm.tigr
|2014-11-28 11:19:03| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.contig.cnt
|2014-11-28 11:19:03| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.contig.cnt /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.contig.cnt
|2014-11-28 11:19:03| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.contig.cvg
|2014-11-28 11:19:03| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.contig.cvg /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.contig.cvg
|2014-11-28 11:19:03| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.afg
|2014-11-28 11:19:03| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Logs/findorfs.ok
|2014-11-28 11:19:03| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/in/proba.asm.contig
|2014-11-28 11:19:03| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.asm.contig /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/in/proba.asm.contig
|2014-11-28 11:19:05| /home/surette-1/software/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/FragGeneScan -s /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/in/proba.asm.contig -o /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.orfs -w 0 -t complete
|2014-11-28 11:19:05| mv /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.orfs.ffn /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.ctg.fna
|2014-11-28 11:19:05| mv /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.orfs.faa /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.ctg.faa
|2014-11-28 11:19:05| mv /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.gene.cvg /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.ctg.gene.cvg
|2014-11-28 11:19:05| mv /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.gene.map /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.ctg.gene.map
|2014-11-28 11:19:05| rm -r /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.fna
|2014-11-28 11:19:05| cat /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba*.fna > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.fna
|2014-11-28 11:19:05| rm -r /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.fna.bnk
|2014-11-28 11:19:05| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/toAmos_new -s /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.fna -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.fna.bnk
|2014-11-28 11:19:05| rm -r /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.faa
|2014-11-28 11:19:05| cat /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba*.faa > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.faa
|2014-11-28 11:19:05| rm -r /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.faa.bnk
|2014-11-28 11:19:05| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/toAmos_new -s /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.faa -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.faa.bnk
|2014-11-28 11:19:05| rm -r /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.gene.cvg
|2014-11-28 11:19:05| cat /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba*.gene.cvg > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.gene.cvg
|2014-11-28 11:19:05| rm -r /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.gene.map
|2014-11-28 11:19:05| cat /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba*.gene.map > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.gene.map
|2014-11-28 11:19:05| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.faa /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.faa
|2014-11-28 11:19:05| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.fna /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.fna
|2014-11-28 11:19:05| touch /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Logs/findorfs.ok
|2014-11-28 11:19:05| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.faa
|2014-11-28 11:19:05| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.faa /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.faa
|2014-11-28 11:19:05| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindRepeats/in/proba.fna
|2014-11-28 11:19:05| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.fna /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindRepeats/in/proba.fna
|2014-11-28 11:19:05| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindRepeats/in/proba.faa
|2014-11-28 11:19:05| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.faa /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindRepeats/in/proba.faa
|2014-11-28 11:19:05| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/in/proba.fna
|2014-11-28 11:19:05| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.fna /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/in/proba.fna
|2014-11-28 11:19:05| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/in/proba.faa
|2014-11-28 11:19:05| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.faa /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/in/proba.faa
|2014-11-28 11:19:05| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.lib1.badmates
|2014-11-28 11:19:05| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.lib1.badmates /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.lib1.badmates
|2014-11-28 11:19:05| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.lib1.hdr
|2014-11-28 11:19:05| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.lib1.hdr /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.lib1.hdr
|2014-11-28 11:19:05| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.lib1.mappedmates
|2014-11-28 11:19:05| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.lib1.mappedmates /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.lib1.mappedmates
|2014-11-28 11:19:05| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.lib1.mates_in_diff_contigs
|2014-11-28 11:19:05| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.lib1.mates_in_diff_contigs /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.lib1.mates_in_diff_contigs
|2014-11-28 11:19:05| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.lib1contig.reads
|2014-11-28 11:19:05| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.lib1contig.reads /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.lib1contig.reads
|2014-11-28 11:19:05| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/lib1.unaligned.fasta
|2014-11-28 11:19:05| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.lib1.unaligned.fasta /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/lib1.unaligned.fasta
|2014-11-28 11:19:05| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/lib1.unaligned.fastq
|2014-11-28 11:19:06|# [FINDREPEATS]
|2014-11-28 11:19:06| touch /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Logs/findrepeats.skip
|2014-11-28 11:19:07|# [ANNOTATE]
|2014-11-28 11:19:07| touch /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/out/proba.annots
|2014-11-28 11:19:07| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/in/proba.asm.contig
|2014-11-28 11:19:07| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.asm.contig /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/in/proba.asm.contig
|2014-11-28 11:19:07| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/out/proba.hits
|2014-11-28 11:19:07| rm -f /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/out/*.hits
|2014-11-28 11:19:07| rm -f /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/out/*.epsilon-nb_results.txt
|2014-11-28 11:19:07| rm -f /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/out/*.phymm.out
|2014-11-28 11:19:48| /home/surette-1/software/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/kraken/bin/kraken --threads 15 -db /home/surette-1/software/metAMOS-1.5rc3/Utilities/DB//kraken /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/in/proba.asm.contig --preload   | kraken-filter --db /home/surette-1/software/metAMOS-1.5rc3/Utilities/DB//kraken --threshold 0.05 > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/out/proba.hits
|2014-11-28 11:19:51| perl /home/surette-1/software/metAMOS-1.5rc3/Utilities/perl/ImportKraken.pl  -c -i -f /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/in/proba.asm.contig /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/out/proba.hits:/home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.contig.cnt:class
|2014-11-28 11:19:51| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Postprocess/in/proba.hits
|2014-11-28 11:19:51| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Postprocess/out/proba.hits
|2014-11-28 11:19:51| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/out/proba.hits /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Postprocess/in/proba.hits
|2014-11-28 11:19:51| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/out/proba.hits /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Postprocess/out/proba.hits
|2014-11-28 11:19:52|# [FUNCTIONALANNOTATION]
|2014-11-28 11:19:52| touch /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Logs/functionalannotation.skip
|2014-11-28 11:19:52| touch /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FunctionalAnnotation/out/blast.out
|2014-11-28 11:19:53|# [SCAFFOLD]
|2014-11-28 11:19:53| rm -rf /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk
|2014-11-28 11:19:55| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/toAmos_new -s /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.seq -m /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.lib1.mappedmates -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk 
|2014-11-28 11:19:55| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/toAmos_new -c /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.asm.tigr -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk 
|2014-11-28 11:19:56| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/asmQC -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk -scaff -recompute -update -numsd 2 
|2014-11-28 11:19:56| perl /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/bank-unlock /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk
|2014-11-28 11:19:57| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/clk -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk
|2014-11-28 11:19:57| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/Bundler -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk
|2014-11-28 11:19:57| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/MarkRepeats -redundancy 50  -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.reps
|2014-11-28 11:19:58| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/OrientContigs -minRedundancy 5 -all  -redundancy 10  -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk -repeats /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.reps 
|2014-11-28 11:19:58| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/bank2fasta -eid  -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/out/proba.contigs
|2014-11-28 11:19:58| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/OutputMotifs -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/out/proba.motifs
|2014-11-28 11:19:58| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/OutputScaffolds -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/out/proba.scaffolds.final
|2014-11-28 11:19:58| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/Linearize -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk
|2014-11-28 11:19:58| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/OutputScaffolds -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/out/proba.linearize.scaffolds.final
|2014-11-28 11:19:59|# [FINDSCAFFOLDORFS]
|2014-11-28 11:19:59| /home/surette-1/software/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/FragGeneScan -s /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/out/proba.linearize.scaffolds.final -o /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindScaffoldORFS/out/proba.orfs -w 0 -t complete

Logs/FINDORFS.log

|2014-11-28 11:18:31|# [RUNPIPELINE]
|2014-11-28 11:18:31| touch /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.seq
|2014-11-28 11:18:31| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/*.contig.cvg
|2014-11-28 11:18:31| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Logs/mapreads.ok
|2014-11-28 11:18:31| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Logs/propagate.ok
|2014-11-28 11:18:31| touch /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/out/proba.annots
|2014-11-28 11:18:31| touch /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/out/proba.linearize.scaffolds.final
|2014-11-28 11:18:31| touch /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.faa
|2014-11-28 11:18:31| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Abundance/out/proba.taxprof.pct.txt
|2014-11-28 11:18:31| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/out/proba.hits
|2014-11-28 11:18:31| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/*.faa
|2014-11-28 11:18:31| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/*.fna
|2014-11-28 11:18:31| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/*.faa
|2014-11-28 11:18:31| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/*.fna
|2014-11-28 11:18:31| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Logs/assemble.ok
|2014-11-28 11:18:31| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/*.asm.contig
|2014-11-28 11:18:31| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Logs/classify.ok
|2014-11-28 11:18:37|# [PREPROCESS]
|2014-11-28 11:18:38| java -cp /home/surette-1/software/metAMOS-1.5rc3/Utilities/java:.:. outputDefaultQuality /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/in/carsonella_pe_filt.fna > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/in/carsonella_pe_filt.fna.qual
|2014-11-28 11:18:38| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/all.seq.mates
|2014-11-28 11:18:40| cp /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/carsonella_pe_filt.fna /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.seq
|2014-11-28 11:18:40| cp /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/carsonella_pe_filt.fna.qual /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.seq.qual
|2014-11-28 11:18:40| which python
|2014-11-28 11:18:40| echo $PYTHONPATH
|2014-11-28 11:18:40| perl /home/surette-1/software/metAMOS-1.5rc3/Utilities/perl/split_fasta.pl /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.seq /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.1.fasta /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.2.fasta
|2014-11-28 11:18:40| perl /home/surette-1/software/metAMOS-1.5rc3/Utilities/perl/split_fasta.pl /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.seq.qual /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.1.fasta.qual /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.2.fasta.qual
|2014-11-28 11:18:40| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.seq /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.fasta
|2014-11-28 11:18:43| java -cp /home/surette-1/software/metAMOS-1.5rc3/Utilities/java:. convertFastaAndQualToFastq /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.seq /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.seq.qual > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.fastq
|2014-11-28 11:18:45| java -cp /home/surette-1/software/metAMOS-1.5rc3/Utilities/java:. convertFastaAndQualToFastq /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.1.fasta /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.1.fasta.qual > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.1.fastq
|2014-11-28 11:18:46| java -cp /home/surette-1/software/metAMOS-1.5rc3/Utilities/java:. convertFastaAndQualToFastq /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.2.fasta /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.2.fasta.qual > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.2.fastq
|2014-11-28 11:18:46| touch /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/preprocess.success
|2014-11-28 11:18:47|# [ASSEMBLE]
|2014-11-28 11:18:47| touch /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.run
|2014-11-28 11:18:48| cat /home/surette-1/software/metAMOS-1.5rc3/Test/test1/soapconfig.txt |grep -v max_rd_len > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/soap2config.txt
|2014-11-28 11:18:49| /home/surette-1/software/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/SOAPdenovo-63mer pregraph -p 15 -K 55 -R  -D   -s /home/surette-1/software/metAMOS-1.5rc3/Test/test1/soapconfig.txt -o /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.asm
|2014-11-28 11:18:49| /home/surette-1/software/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/SOAPdenovo-63mer contig -g /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.asm -R  -M 3 
|2014-11-28 11:18:50| mv /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.asm.contigWIUPAC.fa
|2014-11-28 11:18:50| java -cp /home/surette-1/software/metAMOS-1.5rc3/Utilities/java:. RemoveIUPAC /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.asm.contigWIUPAC.fa >/home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.asm.contig
|2014-11-28 11:18:50| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.run
|2014-11-28 11:18:50| touch /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/assemble.success
|2014-11-28 11:18:52|# [MAPREADS]
|2014-11-28 11:18:52| /home/surette-1/software/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.IDX
|2014-11-28 11:18:52| /home/surette-1/software/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/bowtie -p 15 -f -l 25 -e 140 --best --strata -m 10 -k 1 --un /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.lib1.unaligned.fasta /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.IDX /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.seq > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/lib1.bout
|2014-11-28 11:18:58| cat /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.lib1.mappedmates >> /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.lib1.hdr 
|2014-11-28 11:18:58| cp /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.lib1.hdr /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.lib1.mappedmates 
|2014-11-28 11:19:00|# [FINDORFS]
|2014-11-28 11:19:00| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/in/soapdenovo.55.asm.contig
|2014-11-28 11:19:00| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/in/soapdenovo.55.asm.contig
|2014-11-28 11:19:02| /home/surette-1/software/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/FragGeneScan -s /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/in/soapdenovo.55.asm.contig -o /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.orfs -w 0 -t complete
|2014-11-28 11:19:02| mv /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.orfs.ffn /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.ctg.fna
|2014-11-28 11:19:02| mv /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.orfs.faa /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.ctg.faa
|2014-11-28 11:19:02| mv /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.gene.cvg /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.ctg.gene.cvg
|2014-11-28 11:19:02| mv /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.gene.map /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.ctg.gene.map
|2014-11-28 11:19:02| rm -r /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.fna
|2014-11-28 11:19:02| cat /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55*.fna > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.fna
|2014-11-28 11:19:02| rm -r /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.fna.bnk
|2014-11-28 11:19:02| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/toAmos_new -s /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.fna -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.fna.bnk
|2014-11-28 11:19:02| rm -r /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.faa
|2014-11-28 11:19:02| cat /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55*.faa > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.faa
|2014-11-28 11:19:02| rm -r /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.faa.bnk
|2014-11-28 11:19:02| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/toAmos_new -s /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.faa -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.faa.bnk
|2014-11-28 11:19:02| rm -r /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.gene.cvg
|2014-11-28 11:19:02| cat /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55*.gene.cvg > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.gene.cvg
|2014-11-28 11:19:02| rm -r /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.gene.map
|2014-11-28 11:19:02| cat /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55*.gene.map > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.gene.map
|2014-11-28 11:19:02| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.faa /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.faa
|2014-11-28 11:19:02| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.fna /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.fna
|2014-11-28 11:19:03|# [VALIDATE]
|2014-11-28 11:19:03| touch /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Logs/validate.skip
|2014-11-28 11:19:03| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.asm.contig
|2014-11-28 11:19:03| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.asm.contig
|2014-11-28 11:19:03| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.linearize.scaffolds.final
|2014-11-28 11:19:03| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.asm.contig /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.linearize.scaffolds.final
|2014-11-28 11:19:03| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.asm.tigr
|2014-11-28 11:19:03| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.asm.tigr /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.asm.tigr
|2014-11-28 11:19:03| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.contig.cnt
|2014-11-28 11:19:03| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.contig.cnt /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.contig.cnt
|2014-11-28 11:19:03| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.contig.cvg
|2014-11-28 11:19:03| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.contig.cvg /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.contig.cvg
|2014-11-28 11:19:03| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.afg
|2014-11-28 11:19:03| rm /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Logs/findorfs.ok
|2014-11-28 11:19:03| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/in/proba.asm.contig
|2014-11-28 11:19:03| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.asm.contig /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/in/proba.asm.contig
|2014-11-28 11:19:05| /home/surette-1/software/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/FragGeneScan -s /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/in/proba.asm.contig -o /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.orfs -w 0 -t complete
|2014-11-28 11:19:05| mv /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.orfs.ffn /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.ctg.fna
|2014-11-28 11:19:05| mv /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.orfs.faa /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.ctg.faa
|2014-11-28 11:19:05| mv /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.gene.cvg /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.ctg.gene.cvg
|2014-11-28 11:19:05| mv /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.gene.map /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.ctg.gene.map
|2014-11-28 11:19:05| rm -r /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.fna
|2014-11-28 11:19:05| cat /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba*.fna > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.fna
|2014-11-28 11:19:05| rm -r /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.fna.bnk
|2014-11-28 11:19:05| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/toAmos_new -s /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.fna -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.fna.bnk
|2014-11-28 11:19:05| rm -r /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.faa
|2014-11-28 11:19:05| cat /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba*.faa > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.faa
|2014-11-28 11:19:05| rm -r /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.faa.bnk
|2014-11-28 11:19:05| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/toAmos_new -s /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.faa -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.faa.bnk
|2014-11-28 11:19:05| rm -r /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.gene.cvg
|2014-11-28 11:19:05| cat /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba*.gene.cvg > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.gene.cvg
|2014-11-28 11:19:05| rm -r /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.gene.map
|2014-11-28 11:19:05| cat /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba*.gene.map > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.gene.map
|2014-11-28 11:19:05| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.faa /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.faa
|2014-11-28 11:19:05| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.fna /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.fna
|2014-11-28 11:19:05| touch /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Logs/findorfs.ok
|2014-11-28 11:19:05| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.faa
|2014-11-28 11:19:05| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.faa /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.faa
|2014-11-28 11:19:05| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindRepeats/in/proba.fna
|2014-11-28 11:19:05| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.fna /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindRepeats/in/proba.fna
|2014-11-28 11:19:05| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindRepeats/in/proba.faa
|2014-11-28 11:19:05| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.faa /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindRepeats/in/proba.faa
|2014-11-28 11:19:05| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/in/proba.fna
|2014-11-28 11:19:05| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.fna /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/in/proba.fna
|2014-11-28 11:19:05| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/in/proba.faa
|2014-11-28 11:19:05| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindORFS/out/proba.faa /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/in/proba.faa
|2014-11-28 11:19:05| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.lib1.badmates
|2014-11-28 11:19:05| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.lib1.badmates /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.lib1.badmates
|2014-11-28 11:19:05| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.lib1.hdr
|2014-11-28 11:19:05| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.lib1.hdr /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.lib1.hdr
|2014-11-28 11:19:05| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.lib1.mappedmates
|2014-11-28 11:19:05| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.lib1.mappedmates /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.lib1.mappedmates
|2014-11-28 11:19:05| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.lib1.mates_in_diff_contigs
|2014-11-28 11:19:05| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.lib1.mates_in_diff_contigs /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.lib1.mates_in_diff_contigs
|2014-11-28 11:19:05| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.lib1contig.reads
|2014-11-28 11:19:05| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.lib1contig.reads /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.lib1contig.reads
|2014-11-28 11:19:05| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/lib1.unaligned.fasta
|2014-11-28 11:19:05| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.lib1.unaligned.fasta /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/lib1.unaligned.fasta
|2014-11-28 11:19:05| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/lib1.unaligned.fastq
|2014-11-28 11:19:06|# [FINDREPEATS]
|2014-11-28 11:19:06| touch /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Logs/findrepeats.skip
|2014-11-28 11:19:07|# [ANNOTATE]
|2014-11-28 11:19:07| touch /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/out/proba.annots
|2014-11-28 11:19:07| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/in/proba.asm.contig
|2014-11-28 11:19:07| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.asm.contig /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/in/proba.asm.contig
|2014-11-28 11:19:07| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/out/proba.hits
|2014-11-28 11:19:07| rm -f /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/out/*.hits
|2014-11-28 11:19:07| rm -f /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/out/*.epsilon-nb_results.txt
|2014-11-28 11:19:07| rm -f /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/out/*.phymm.out
|2014-11-28 11:19:48| /home/surette-1/software/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/kraken/bin/kraken --threads 15 -db /home/surette-1/software/metAMOS-1.5rc3/Utilities/DB//kraken /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/in/proba.asm.contig --preload   | kraken-filter --db /home/surette-1/software/metAMOS-1.5rc3/Utilities/DB//kraken --threshold 0.05 > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/out/proba.hits
|2014-11-28 11:19:51| perl /home/surette-1/software/metAMOS-1.5rc3/Utilities/perl/ImportKraken.pl  -c -i -f /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/in/proba.asm.contig /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/out/proba.hits:/home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.contig.cnt:class
|2014-11-28 11:19:51| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Postprocess/in/proba.hits
|2014-11-28 11:19:51| unlink /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Postprocess/out/proba.hits
|2014-11-28 11:19:51| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/out/proba.hits /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Postprocess/in/proba.hits
|2014-11-28 11:19:51| ln /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Annotate/out/proba.hits /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Postprocess/out/proba.hits
|2014-11-28 11:19:52|# [FUNCTIONALANNOTATION]
|2014-11-28 11:19:52| touch /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Logs/functionalannotation.skip
|2014-11-28 11:19:52| touch /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FunctionalAnnotation/out/blast.out
|2014-11-28 11:19:53|# [SCAFFOLD]
|2014-11-28 11:19:53| rm -rf /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk
|2014-11-28 11:19:55| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/toAmos_new -s /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.seq -m /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.lib1.mappedmates -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk 
|2014-11-28 11:19:55| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/toAmos_new -c /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.asm.tigr -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk 
|2014-11-28 11:19:56| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/asmQC -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk -scaff -recompute -update -numsd 2 
|2014-11-28 11:19:56| perl /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/bank-unlock /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk
|2014-11-28 11:19:57| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/clk -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk
|2014-11-28 11:19:57| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/Bundler -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk
|2014-11-28 11:19:57| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/MarkRepeats -redundancy 50  -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.reps
|2014-11-28 11:19:58| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/OrientContigs -minRedundancy 5 -all  -redundancy 10  -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk -repeats /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.reps 
|2014-11-28 11:19:58| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/bank2fasta -eid  -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/out/proba.contigs
|2014-11-28 11:19:58| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/OutputMotifs -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/out/proba.motifs
|2014-11-28 11:19:58| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/OutputScaffolds -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/out/proba.scaffolds.final
|2014-11-28 11:19:58| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/Linearize -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk
|2014-11-28 11:19:58| /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/OutputScaffolds -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk > /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/out/proba.linearize.scaffolds.final
|2014-11-28 11:19:59|# [FINDSCAFFOLDORFS]
|2014-11-28 11:19:59| /home/surette-1/software/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/FragGeneScan -s /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/out/proba.linearize.scaffolds.final -o /home/surette-1/software/metAMOS-1.5rc3/Test/test1/FindScaffoldORFS/out/proba.orfs -w 0 -t complete

Logs/ASSEMBLE.log:


Version 1.05: released on July 29th, 2010

In /home/surette-1/software/metAMOS-1.5rc3/Test/test1/soapconfig.txt, 1 libs, max seq len 250, max name len 256

15 thread created
read from file:
 /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.1.fastq
read from file:
 /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.2.fastq
time spent on hash reads: 1s, 100000 reads processed
[LIB] 0, avg_ins 2000, reverse 0 
1104848 nodes allocated, 2600000 kmer in reads, 2600000 kmer processed
1003405 linear nodes
time spent on marking linear nodes 0s
time spent on pre-graph construction: 1s

deLowKmer 0, deLowEdge 1
Start to remove tips of single frequency kmers short than 110
52179 tips off
15 thread created
26445 linear nodes
Start to remove tips which don't contribute the most links
kmer set 0 done
kmer set 1 done
kmer set 2 done
kmer set 3 done
kmer set 4 done
kmer set 5 done
kmer set 6 done
kmer set 7 done
kmer set 8 done
kmer set 9 done
kmer set 10 done
kmer set 11 done
kmer set 12 done
kmer set 13 done
kmer set 14 done
1215 tips off
15 thread created
0 linear nodes
time spent on cutTipe: 0s

20 (10) edges 1 extra nodes
time spent on making edges: 0s

In file: /home/surette-1/software/metAMOS-1.5rc3/Test/test1/soapconfig.txt, max seq len 250, max name len 256

15 thread created
read from file:
 /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.1.fastq
read from file:
 /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Preprocess/out/lib1.2.fastq
100000 reads processed
time 0,0,0,0,0,0,0
3 markers outputed
3 markers counted
done mapping reads, 42115 reads deleted, 8 arcs created
[LIB] 0, avg_ins 2000, reverse 0 
time spent on mapping reads: 0s

13 vertex outputed
overall time for lightgraph: 0m

Version 1.05: released on July 29th, 2010

there're 13 kmers in vertex file
there're 20 edge in edge file
done sort
input 20 edges
12 pre-arcs loaded
6 markers overall
6 markers loaded
0 repeats solvable, 0 more edges
0 dead arcs removed
time spent on solving repeat: 0s
start to pinch bubbles, cutoff 0.100000, MAX NODE NUM 30, MAX DIFF 10
8 startingPoints, 2 dheap nodes
0 pairs found, 0 pairs of paths compared, 0 pairs merged
sequenc compare failure: 0 0 0 0
DFibHeap: 1 Nodes allocated
a linear concatenation lap, 0 concatenated
20 edges in graph
time spent on bubblePinch: 0s
1 weak inner edges destroyed
2 dead arcs removed
Remove low coverage(1): 0 inner edges destroyed
0 dead arcs removed
a linear concatenation lap, 2 concatenated
a linear concatenation lap, 0 concatenated
14 edges in graph
there're 20 edges
after compacting 14 edges left
strict 0, cutLen 110
a cutTipsInGraph lap, 3 tips cut
a cutTipsInGraph lap, 0 tips cut
1 dead arcs removed
a linear concatenation lap, 1 concatenated
a linear concatenation lap, 0 concatenated
6 edges in graph
there're 14 edges
after compacting 6 edges left
3 ctgs longer than 100, sum up 159795bp, with average length 53265
the longest is 92399bp, contig N50 is 92399 bp,contig N90 is 65703 bp
3 contigs longer than 56 output
time elapsed: 0m

Processing file /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Assemble/out/soapdenovo.55.asm.contigWIUPAC.fa

Logs/SCAFFOLD.log (abberviated):

Read Bank doesn't exist; creating
frag Bank doesn't exist; creating
lib Bank doesn't exist; creating
parsing fasta file
Closing frag stream/bank
Closing read stream/bank
Contig Bank doesn't exist; creating
Read bank exists; opening
frag bank exists; opening
lib bank exists; opening
Closing frag stream/bank
Closing read stream/bank
Handling contigs
Contig stream closed.
Invocation: /home/surette-1/software/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin/asmQC -b /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk -scaff -recompute -update -numsd 2 

Will update libraries in bank
Will not write features in bank
Mates within 2 standard deviations from mean considered good
Reporting regions with less than 0 good mate coverage
Will recompute library sizes
Libraries whose mean changes by less than 50
and whose std. dev. changes by less than 10 are considered to not have changed
Minimum number of observations required to change library size: 100
Reporting regions with more than 2 short mate coverage
Reporting regions with more than 2 long mate coverage
Reporting regions with more than 3 coverage by mates oriented the same way
Reporting regions with more than 3 coverage by outie mates
Reporting regions with more than 3 coverage by outie mates
Reporting regions with more than 3 coverage by linking mates
Reporting regions with more than 3 coverage by singleton mates

Reporting results by scaffold.  In this mode linking clones connect different scaffolds.

Library 1 recomputed as mean = 2000 SD = 200

>Contig_1 1 1693 bases
Regions of 0X clone coverage
0   131
1606    1693

Regions of 2X or more short mate coverage
184 1620

Regions of 3X or more linking coverage
0   1691

>Contig_2 3 65703 bases
Regions of 0X clone coverage
0   79
65622   65703

Regions of 2X or more short mate coverage
318 65115

Regions of 2X or more long mate coverage
176 65515

Regions of 3X or more linking coverage
10  2173
63473   63546
63559   65698

>Contig_3 5 92399 bases
Regions of 0X clone coverage
0   78
92314   92399

Regions of 2X or more short mate coverage
57  92329

Regions of 2X or more long mate coverage
137 92179

Regions of 3X or more linking coverage
12  2131
2143    2293
90141   92391

No scaffold account found in bank /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk
ignoring -scaff option
>Contig_1 1 1693 bases
>Contig_2 3 65703 bases
>Contig_3 5 92399 bases

IFOs found: 4
File locks: 0
Bank locks: 0

Entering '/home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk'
Found CTG bank
Found FRG bank
Found LIB bank
Found RED bank
Adding link 1
Adding link 2
Adding link 3
Adding link 4
Adding link 5
Adding link 6
Adding link 7
Adding link 8
Adding link 9
Adding link 10
…
Adding link 1581
Adding link 1582
Adding link 1583
Adding link 1584
Adding link 1585
Doing contig pair (2, 1)
NORMALS: 0 ANTINORMALS: 0 INNIES: 0 OUTIES: 449
Doing 449 links of type O
 Found 449 links 
 Begins has 449 elements
 Ends has 449 elements
best coord is -1223
best coord is -1147
best coord is -1104
best coord is -1098
best coord is -1089
best coord is -1085
best coord is -1076
best coord is -1072
best coord is -1069
…
best coord is -205
best coord is -204
best coord is -157
best coord is -99
link 7, 1207 did not surround -99
link 114, 1314 did not surround -99
nbest is 447
best has 447 records 
Clique range = -99, 1101
Clique range = -99, 1043
Clique range = -99, 996
Clique range = -99, 995
Clique range = -99, 995
Clique range = -99, 988
Clique range = -99, 987
Clique range = -99, 962
Clique range = -99, 960
Clique range = -99, 948
Clique range = -99, 939
…
Clique range = -99, 111
Clique range = -99, 102
Clique range = -99, 96
Clique range = -99, 53
Clique range = -99, -23
Link 680 (714, 200) is too long ( > -23)
Link 1017 (607, 200) is too long ( > -23)
new NORMALS: 0 ANTINORMALS: 0 INNIES: 0 OUTIES: 447
Writing edge link with it 1
Doing contig pair (3, 1)
NORMALS: 0 ANTINORMALS: 0 INNIES: 502 OUTIES: 0
Doing 502 links of type I
 Found 502 links 
 Begins has 502 elements
 Ends has 502 elements
best coord is -1322
best coord is -1318
best coord is -1304
best coord is -1250
best coord is -1231
best coord is -1177
…
best coord is -269
best coord is -248
best coord is -209
best coord is -206
best coord is -187
best coord is -149
link -66, 1134 did not surround -149
link -2, 1198 did not surround -149
link 2, 1202 did not surround -149
nbest is 499
best has 499 records 
Clique range = -149, 1051
Clique range = -149, 1013
Clique range = -149, 994
Clique range = -149, 991
Clique range = -149, 952
Clique range = -149, 931
Clique range = -149, 928
Clique range = -149, 925
Clique range = -149, 922
…
Clique range = -149, 105
Clique range = -149, 100
Clique range = -149, 98
Clique range = -149, 73
Clique range = -149, 62
Clique range = -149, 48
Clique range = -149, 23
Clique range = -149, -31
Clique range = -149, -50
Clique range = -149, -104
Clique range = -149, -118
Clique range = -149, -122
Link 28 (602, 200) is too long ( > -122)
Link 897 (598, 200) is too long ( > -122)
Link 1435 (534, 200) is too long ( > -122)
new NORMALS: 0 ANTINORMALS: 0 INNIES: 499 OUTIES: 0
Writing edge link with it 2
Doing contig pair (3, 2)
NORMALS: 76 ANTINORMALS: 558 INNIES: 0 OUTIES: 0
Doing 558 links of type A
 Found 558 links 
 Begins has 558 elements
 Ends has 558 elements
best coord is -1212
best coord is -1210
best coord is -1207
best coord is -1200
best coord is -1184
best coord is -1153
best coord is -1132
best coord is -1131
best coord is -1128
..
best coord is -293
best coord is -288
best coord is -285
best coord is -255
best coord is -255
best coord is -247
best coord is -242
best coord is -240
best coord is -229
best coord is -212
best coord is -181
best coord is -169
best coord is -72
nbest is 558
best has 558 records 
Clique range = -72, 1128
Clique range = -72, 1031
Clique range = -72, 1019
Clique range = -72, 988
Clique range = -72, 971
Clique range = -72, 960
Clique range = -72, 958
Clique range = -72, 953
..
Clique range = -72, 16
Clique range = -72, 0
Clique range = -72, -7
Clique range = -72, -10
Clique range = -72, -12
Doing 76 links of type N
 Found 76 links 
 Begins has 76 elements
 Ends has 76 elements
best coord is 458
best coord is 554
best coord is 598
best coord is 636
best coord is 654
best coord is 682
best coord is 687
best coord is 720
..
best coord is 1106
best coord is 1111
best coord is 1112
best coord is 1169
best coord is 1199
nbest is 76
best has 76 records 
Clique range = 1199, 2399
Clique range = 1199, 2369
Clique range = 1199, 2312
Clique range = 1199, 2311
Clique range = 1199, 2306
Clique range = 1199, 2304
Clique range = 1199, 2265
Clique range = 1199, 2264
Clique range = 1199, 2263
…
Clique range = 1199, 1887
Clique range = 1199, 1882
Clique range = 1199, 1854
Clique range = 1199, 1836
Clique range = 1199, 1798
Clique range = 1199, 1754
Clique range = 1199, 1658
new NORMALS: 76 ANTINORMALS: 558 INNIES: 0 OUTIES: 0
Writing edge link with it 3
Writing edge link with it 4
Elapsed time threaded is 1e-05
The number of components is 1
Options summary:
Bank =  /home/surette-1/software/metAMOS-1.5rc3/Test/test1/Scaffold/in/proba.bnk
Redundancy =    10
InitAll =   1
Compress =  1
AgressiveScf =  0
Max Overlap =   -1
PROCESSING EDGE WITH ID 3 BETWEEN CONTIGS 3 AND 2 WEIGHT 558 LAST WEIGHT WAS 558 AND INT VERSION OF LAST IS 140
BAD DST EDGE: 4 between 3 and 2 with dist 1471 and std 22 and the orientation is N
WE HIT UNINITIALIZED NODE 1 using edge 1 (2, 1) AND IM BACKPEDALING TO NODE 2 THIS NODE IS 52 WORSE THAN BEST UNINITIALIZED
PROCESSING EDGE WITH ID 1 BETWEEN CONTIGS 2 AND 1 WEIGHT 447 LAST WEIGHT WAS 558 AND INT VERSION OF LAST IS 140
BAD DST EDGE: 1 between 2 and 1 with dist -49 and std 9 and the orientation is O
PROCESSING EDGE WITH ID 2 BETWEEN CONTIGS 3 AND 1 WEIGHT 499 LAST WEIGHT WAS 558 AND INT VERSION OF LAST IS 140
PROCESSING EDGE WITH ID 4 BETWEEN CONTIGS 3 AND 2 WEIGHT 76 LAST WEIGHT WAS 558 AND INT VERSION OF LAST IS 140
SKIPPING EDGE 4
BEGIN COMPRESSION
VISITING NODE 2 USING EDGE ID 4194967297 WITH SIZE 0
VISITING NODE 3 USING EDGE ID 3 WITH SIZE -66
VISITING NODE 1 USING EDGE ID 2 WITH SIZE -58
FOR SKIPPED EDGE 4 SET EDGE STATUS TO BE 6
BEGINNING PATH ITERATION #1
PROCESSING SCAFFOLD 1
PROCESSING CONTIG 2
TESTING LINEAR PATH : 1 2 3 
COLLAPSING LINEAR PATH : 
CREATED COPY OF EDGE 3 WITH ID 6 FROM 4
CREATED COPY OF EDGE 1 WITH ID 7 FROM 4
CREATED COPY OF EDGE 2 WITH ID 8 FROM 4
CREATED COPY OF EDGE 4 WITH ID 9 FROM 4
PROCESSING CONTIG 4
TESTING LINEAR PATH : 4 
BEGINNING COMPRESSION ITERATION #2
PROCESSING SCAFFOLD 1
PROCESSING CONTIG 4
END COMPRESSION ITERATION #2 UPDATED: 0
DONE COMPRESSION
Finished! Had 2 Good links and 2 bad ones.

AMOS/Linux-x86_64/bin/toAmos_new -h:

$ ./toAmos_new -h

.USAGE.  toAmos_new (-m mates|-f frg)
         (-c contig|-s fasta|-q qual|-Q fastq)
         -t fastqQualtyType [SCUFL]
.DESCRIPTION.
 toAmos_new is designed as a replacement for the current perl script.
 It does not cover all of the formats but will encompass the main ones.
 It inserts the output of an assembly program into the AMOS bank.

 If you simply need a program to generate assembly inputs for one the
 AMOS-based assemblers (e.g. minimus or AMOS-cmp) use tarchive2amos.

 toAmos reads the inputs specified on the command line and stores  the
 information directly into the AMOS Bank.  The following types of
 information can be provided to toAmos:
   -> Sequence and quality data (options -f, -s, -q, -Q)
   -> Fastq data (options -Q, -t)
   -> Library and mate-pair data (options -m, or -f)
   -> Contig  data (options -c, -a)
   -> Scaffold data (option -a)
 *NEW* If using interleaved fastq file no need to specify mates files,
       these can be extract by specifying the following:
   -> Interleaved flag (-i)
   -> Sequence data (-Q)
   -> Library name/Identifier (-I)
   -> Library min (-N)
   -> Library max (-X)
.OPTIONS.
  -m <matefile> - library and mate-pair information in Bambus format
     in Trace Archive format (not compatible with -i option)
  -b <bank> - The location where the AMOS bank will be stored.
  -S - include the surrogate unitigs in the .asm file as AMOS contigs.
  -C - include the contigs in the .asm file as AMOS contigs.
  -U - include the unitigs in the .asm file as AMOS contigs (implies -S and turns off -C
).
  -F - include the surrogate unitigs as reads in the tilling for a contig. Without this 
option the contig may have 0-coverage regions of coverage.
  -L - output only the layout, not the consensus sequence for contigs. Will not output c
ontig links or scaffolds. Implies -F.
  -i - fastq file is interleaved, parse mates from this file (mutually exclusive with -m
 option)
  -I - lib Identifier
  -N - min insert length
  -X - max insert length
  -t - fastq quality type. The currently supported types are ILLUMINA SANGER. The default is SANGER
.KEYWORDS.
  converter, amos format
 ...

Thanks for you help!

skoren commented 9 years ago

Hi,

We've seen some instability in FragGeneScan on some systems. First, double check that you have the Scaffold/out/proba.linearize.scaffolds.final file and it is non-empty. If that is the case, you can either skip Scaffold ORF calling (-n FindScaffoldORFS) or try installing/using metagenemark instead (-g metagenemark).