Assembly error in runPipeline about metamos HOT 1 CLOSED

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$

---

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#41

from metamos.