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rikuu / Gap2Seq

Gap2Seq is a gap filling and insertion genotyping tool.
GNU Affero General Public License v3.0
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Error running Gage Example #6

Closed vrohnie closed 5 years ago

vrohnie commented 5 years ago

So because I'm very new to this I tried to run the Gage example with the Example Data.

When running

python3.4 /[mybuildFolderPath]/Gap2Seq --scaffolds Assembly/SGA/genome.scf.fasta --filled Assembly/SGA/genome.scf.fill.fasta --reads Data/original/frag_1.fastq,Data/original/frag_2.fastq,Data/original/shortjump_1.fastq,Data/original/shortjump_2.fastq

I get following Ouput:

Cutting gaps Merging filled gaps and contigs Traceback (most recent call last): File "/home/schusterbauer/Programs/Gap2Seq-3.1/build/Gap2Seq", line 505, in merge_gaps(args['filled'], args['final_out']) File "/home/schusterbauer/Programs/Gap2Seq-3.1/build/Gap2Seq", line 319, in merge_gaps stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL) File "/usr/lib/python3.4/subprocess.py", line 561, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/home/schusterbauer/Programs/Gap2Seq-3.1/build/GapMerger', '-scaffolds', 'Assembly/SGA/genome.scf.fill.fasta', '-gaps', 'tmp.filled', '-contigs', 'tmp.contigs']' returned non-zero exit status 1

As this didn't mean a lot to me, but I think I tracked it down to Gap2Seq-core failing to fill any gaps and therefore creating an empty 'Assembly/SGA/genome.scf.fill.fasta' and no 'tmp.filled' file.

But the real question now is, why doesn't Gap2Seq-core work properly.

I ran it directly with:

/[mybuildFolderPath]/Gap2Seq-core -scaffolds Assembly/SGA/genome.scf.fasta -filled Assembly/SGA/genome.scf.fill.fasta -reads Data/original/frag_1.fastq,Data/original/frag_2.fastq,Data/original/shortjump_1.fastq,Data/original/shortjump_2.fastq

and it seems to do stuff but then in the end just outputs:

etc... [Graph: build branching nodes ] 97 % elapsed: 0 min 1 sec remaining: 0 min 0 s[Graph: build branching nodes ] 98 % elapsed: 0 min 1 sec remaining: 0 min 0 s[Graph: build branching nodes ] 99 % elapsed: 0 min 1 sec remaining: 0 min 0 s[Graph: build branching nodes ] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 s[Graph: nb branching found : 406997 ] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 s[Graph: nb branching found : 406997 ] 100 % elapsed: 0 min 1 sec remaining: 0 min 0 sec cpu: 719.6 % mem: [ 700, 703, 770] MB Max mem: 2684354560 Filled 0 gaps out of 0

I would appreciate any help

Sidenote: Gap2Seq 2.1 seems to run smoothly, but I was mainly excited to try the Insertion Genotyping :/

Greetings, Veronika

rikuu commented 5 years ago

I think I fixed the crash now. Thanks for reporting this! Feel free to open more issues if you have any other trouble.

vrohnie commented 5 years ago

Thanks, It does run now :)

MgLaMontagne commented 3 years ago

I received the exact same error as above (see below) when I tried to run the same Gage example. I ran the Gap2Seq 3.1, which I installed through bioconda. I have attached the package list from the conda environment. Any help would be greatly appreciated. Michael

package-list.txt

Merging filled gaps and contigs Traceback (most recent call last): File "/home/mgl111/miniconda3/envs/gap2seqEnv/bin/Gap2Seq", line 505, in merge_gaps(args['filled'], args['final_out']) File "/home/mgl111/miniconda3/envs/gap2seqEnv/bin/Gap2Seq", line 319, in merge_gaps stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL) File "/home/mgl111/miniconda3/envs/gap2seqEnv/lib/python3.7/subprocess.py", line 363, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/home/mgl111/miniconda3/envs/gap2seqEnv/bin/GapMerger', '-scaffolds', 'Assembly/SGA/genome.scf.fill.fasta', '-gaps', 'tmp.filled', '-contigs', 'tmp.contigs']' returned non-zero exit status 1.