search

marbl / metAMOS

A metagenomic and isolate assembly and analysis pipeline built with AMOS
http://marbl.github.io/metAMOS
Other
93 stars 45 forks source link

Assembly error in runPipeline #41

Closed hollybik closed 12 years ago

hollybik commented 12 years ago

Hello, I am trying to run MetAMOS on our UC Davis servers, and I keep getting a persistent error as follows (error is repeatable regardless of which Illumnia dataset I try to process - seems like a broken pipe somewhere?):

-bash-3.2$ initPipeline -1 Aphelenchus_1510-KO-4_L4_1.fastq -2 Aphelenchus_1510-KO-4_L4_2.fastq -d Aphelenhcus_4Mar -i 100:600 -q Project dir /share/jumbo-0-1-scratch-2/hbik/Aphelenhcus_4Mar successfully created! Use runPipeline.py to start Pipeline -bash-3.2$ runPipeline -k 45 -d Aphelenhcus_4Mar/ Starting metAMOS pipeline Warning: Newbler is not found, some functionality will not be available Warning: FCP is not found, some functionality will not be available Warning: PHmmer is not found, some functionality will not be available

Tasks which will be run:

Task = preprocess.Preprocess Task = assemble.Assemble Task = findorfs.FindORFS Task = findreps.FindRepeats Task = annotate.Annotate Task = abundance.Abundance Task = scaffold.Scaffold Task = findscforfs.FindScaffoldORFS Task = propagate.Propagate Task = classify.Classify Task = postprocess.Postprocess

Job = [[Aphelenchus_1510-KO-4_L4_1.fastq, Aphelenchus_1510-KO-4_L4_2.fastq] -> preprocess.success] completed Completed Task = preprocess.Preprocess Running SOAPdenovo on input reads... Traceback (most recent call last): File "/home/koadman/software/metAMOS/runPipeline", line 358, in pipeline_run([preprocess.Preprocess,assemble.Assemble,findorfs.FindORFS, findreps.FindRepeats, annotate.Annotate, abundance.Abundance, scaffold.Scaffold, findscforfs.FindScaffoldORFS, propagate.Propagate, classify.Classify, postprocess.Postprocess], verbose = 1) File "/home/koadman/software/metAMOS/Utilities/ruffus/task.py", line 2680, in pipeline_run raise errt ruffus.ruffus_exceptions.RethrownJobError:

Exceptions running jobs for

'def assemble.Assemble(...):'

Original exception:

Exception #1 exceptions.ValueError(invalid literal for int() with base 10: 'ggaggdfadae]gggggcggfdfefbgggaffdcdfdffdaggggggg_ggdgggfggggffffdggf_ggggggggggg'): for assemble.Assemble.Job = [[lib1.seq] -> [proba.asm.contig]]

Traceback (most recent call last): File "/home/koadman/software/metAMOS/Utilities/ruffus/task.py", line 517, in run_pooled_job_without_exceptions return_value = job_wrapper(param, user_defined_work_func, register_cleanup, touch_files_only) File "/home/koadman/software/metAMOS/Utilities/ruffus/task.py", line 447, in job_wrapper_io_files ret_val = user_defined_work_func(*param) File "/home/koadman/software/metAMOS/src/assemble.py", line 464, in Assemble map2contig() File "/home/koadman/software/metAMOS/src/assemble.py", line 110, in map2contig epos = int(spos)+len(read_seq) ValueError: invalid literal for int() with base 10: 'ggaggdfadae]gggggcggfdfefbgggaffdcdfdffdaggggggg_ggdgggfggggffffdggf_ggggggggggg'

-bash-3.2$

treangen commented 12 years ago

hi Holly,

Thank you for sending this. This is a known issue and a recent fix should be committed and available via a "git pull" command on your local repository. This error occurs when bowtie fails to find a valid alignment of a read to one of the assembled contigs before exhausting the predefined memory limit, resulting in a bug in the bowtie output parser as the read id field is not output when this happens.

Once you update the metAMOS code base, please let me know if this fixes this error. thanks!

best,

Todd

Hello, I am trying to run MetAMOS on our UC Davis servers, and I keep getting a persistent error as follows (error is repeatable regardless of which Illumnia dataset I try to process - seems like a broken pipe somewhere?):

-bash-3.2$ initPipeline -1 Aphelenchus_1510-KO-4_L4_1.fastq -2 Aphelenchus_1510-KO-4_L4_2.fastq -d Aphelenhcus_4Mar -i 100:600 -q Project dir /share/jumbo-0-1-scratch-2/hbik/Aphelenhcus_4Mar successfully created! Use runPipeline.py to start Pipeline -bash-3.2$ runPipeline -k 45 -d Aphelenhcus_4Mar/ Starting metAMOS pipeline Warning: Newbler is not found, some functionality will not be available Warning: FCP is not found, some functionality will not be available Warning: PHmmer is not found, some functionality will not be available

Tasks which will be run:

Task = preprocess.Preprocess Task = assemble.Assemble Task = findorfs.FindORFS Task = findreps.FindRepeats Task = annotate.Annotate Task = abundance.Abundance Task = scaffold.Scaffold Task = findscforfs.FindScaffoldORFS Task = propagate.Propagate Task = classify.Classify Task = postprocess.Postprocess

Job = [[Aphelenchus_1510-KO-4_L4_1.fastq, Aphelenchus_1510-KO-4_L4_2.fastq] ->  preprocess.success] completed

Completed Task = preprocess.Preprocess Running SOAPdenovo on input reads... Traceback (most recent call last): File "/home/koadman/software/metAMOS/runPipeline", line 358, in pipeline_run([preprocess.Preprocess,assemble.Assemble,findorfs.FindORFS, findreps.FindRepeats, annotate.Annotate, abundance.Abundance, scaffold.Scaffold, findscforfs.FindScaffoldORFS, propagate.Propagate, classify.Classify, postprocess.Postprocess], verbose = 1) File "/home/koadman/software/metAMOS/Utilities/ruffus/task.py", line 2680, in pipeline_run raise errt ruffus.ruffus_exceptions.RethrownJobError:

Exceptions running jobs for

'def assemble.Assemble(...):'

Original exception:

Exception #1
exceptions.ValueError(invalid literal for int() with base 10: 'ggaggdfadae]gggggcggfdfefbgggaffdcdfdffdaggggggg_ggdgggfggggffffdggf_ggggggggggg'):
for assemble.Assemble.Job = [[lib1.seq] ->  [proba.asm.contig]]

Traceback (most recent call last):
  File "/home/koadman/software/metAMOS/Utilities/ruffus/task.py", line 517, in run_pooled_job_without_exceptions
    return_value =  job_wrapper(param, user_defined_work_func, register_cleanup, touch_files_only)
  File "/home/koadman/software/metAMOS/Utilities/ruffus/task.py", line 447, in job_wrapper_io_files
    ret_val = user_defined_work_func(*param)
  File "/home/koadman/software/metAMOS/src/assemble.py", line 464, in Assemble
    map2contig()
  File "/home/koadman/software/metAMOS/src/assemble.py", line 110, in map2contig
    epos = int(spos)+len(read_seq)
ValueError: invalid literal for int() with base 10: 'ggaggdfadae]gggggcggfdfefbgggaffdcdfdffdaggggggg_ggdgggfggggffffdggf_ggggggggggg'

-bash-3.2$

Reply to this email directly or view it on GitHub: https://github.com/treangen/metAMOS/issues/41