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vcepeda avatar vcepeda commented on August 21, 2024

Hi Alex,
I recommend you to run the stable releases 1.1
https://github.com/marbl/MetaCompass/releases/tag/1.1
The new release will be available next the week.

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alexdthomas avatar alexdthomas commented on August 21, 2024

Thanks you for your prompt reply! I downloaded and installed the stable version. Running
python go_metacompass.py -r tutorial/Candidatus_Carsonella_ruddii_HT_Thao2000.fasta -P tutorial/thao2000.1.fq,tutorial/thao2000.2.fq -o example1_output -m 1 -t 4

the output is

confirming file containing reference genomes exists..
[OK]
checking for dependencies (Bowtie2, Blast, kmermask, Snakemake, etc)
Bowtie2--->[OK]
/home/talex/.pyenv/versions/miniconda3-latest/bin/blastn
Blast+--->[OK]
/home/talex/apps/MetaCompass-1.1/bin/kmer-mask
kmer-mask--->[OK]
/home/talex/.pyenv/versions/miniconda3-latest/bin/snakemake
Snakemake--->[OK]
Provided cores: 4
Rules claiming more threads will be scaled down.
Job counts:
        count   jobs
        1       all
        1       assemble_unmapped
        1       bam_sort
        1       bowtie2_map
        1       build_contigs
        1       create_tsv
        1       join_contigs
        1       merge_reads
        1       pilon_contigs
        1       pilon_map
        1       sam_to_bam
        11
Resources before job selection: {'_cores': 4, '_nodes': 9223372036854775807}                                                                        [53/14267]
Ready jobs (1):
        merge_reads
Selected jobs (1):
        merge_reads
Resources after job selection: {'_cores': 3, '_nodes': 9223372036854775806}
---merge fastq reads
Releasing 1 _cores (now 4).
Releasing 1 _nodes (now 9223372036854775807).
1 of 11 steps (9%) done
Resources before job selection: {'_cores': 4, '_nodes': 9223372036854775807}
Ready jobs (1):
        bowtie2_map
Selected jobs (1):
        bowtie2_map
Resources after job selection: {'_cores': 0, '_nodes': 9223372036854775806}
---Build index .
Full Traceback (most recent call last):
  File "/home/talex/.pyenv/versions/miniconda3-latest/lib/python3.5/site-packages/snakemake/executors.py", line 784, in run_wrapper
    version)
  File "/home/talex/apps/MetaCompass-1.1/snakemake/metacompass.iter0.ref.py", line 86, in __rule_bowtie2_map
  File "/home/talex/.pyenv/versions/miniconda3-latest/lib/python3.5/site-packages/snakemake/shell.py", line 74, in __new__
    raise sp.CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'bowtie2-build -o 3 --threads 4 -q tutorial/Candidatus_Carsonella_ruddii_HT_Thao2000.fasta example1_output/thao2000.0.a
ssembly.out/thao2000.index 1>> example1_output/thao2000.0.assembly.out/thao2000.index 2>&1;bowtie2 -a --end-to-end --sensitive --no-unal -p 4 -x example1_outp
ut/thao2000.0.assembly.out/thao2000.index -q -U example1_output/thao2000.merged.fq -S example1_output/thao2000.0.assembly.out/thao2000.sam.all > example1_outp
ut/thao2000.0.bowtie2map.log 2>&1; /home/talex/apps/MetaCompass-1.1/bin/best_strata.py example1_output/thao2000.0.assembly.out/thao2000.sam.all example1_outpu
t/thao2000.0.assembly.out/thao2000.sam; rm example1_output/thao2000.0.assembly.out/thao2000.sam.all' returned non-zero exit status 1

Error in job bowtie2_map while creating output files example1_output/thao2000.0.assembly.out/thao2000.index, example1_output/thao2000.0.assembly.out/thao2000.
index, example1_output/thao2000.0.assembly.out/thao2000.sam.
Full Traceback (most recent call last):
  File "/home/talex/.pyenv/versions/miniconda3-latest/lib/python3.5/site-packages/snakemake/executors.py", line 784, in run_wrapper
    version)
  File "/home/talex/apps/MetaCompass-1.1/snakemake/metacompass.iter0.ref.py", line 86, in __rule_bowtie2_map
  File "/home/talex/.pyenv/versions/miniconda3-latest/lib/python3.5/site-packages/snakemake/shell.py", line 74, in __new__
    raise sp.CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command 'bowtie2-build -o 3 --threads 4 -q tutorial/Candidatus_Carsonella_ruddii_HT_Thao2000.fasta example1_output/thao2000.0.a
ssembly.out/thao2000.index 1>> example1_output/thao2000.0.assembly.out/thao2000.index 2>&1;bowtie2 -a --end-to-end --sensitive --no-unal -p 4 -x example1_outp
ut/thao2000.0.assembly.out/thao2000.index -q -U example1_output/thao2000.merged.fq -S example1_output/thao2000.0.assembly.out/thao2000.sam.all > example1_outp
ut/thao2000.0.bowtie2map.log 2>&1; /home/talex/apps/MetaCompass-1.1/bin/best_strata.py example1_output/thao2000.0.assembly.out/thao2000.sam.all example1_outpu
t/thao2000.0.assembly.out/thao2000.sam; rm example1_output/thao2000.0.assembly.out/thao2000.sam.all' returned non-zero exit status 1

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/talex/.pyenv/versions/miniconda3-latest/lib/python3.5/site-packages/snakemake/executors.py", line 247, in _callback
    raise ex
  File "/home/talex/.pyenv/versions/miniconda3-latest/lib/python3.5/concurrent/futures/thread.py", line 55, in run
    result = self.fn(*self.args, **self.kwargs)
  File "/home/talex/.pyenv/versions/miniconda3-latest/lib/python3.5/site-packages/snakemake/executors.py", line 798, in run_wrapper
    show_traceback=True))
snakemake.exceptions.RuleException: CalledProcessError in line 50 of /home/talex/apps/MetaCompass-1.1/snakemake/metacompass.iter0.ref.py:
Command 'bowtie2-build -o 3 --threads 4 -q tutorial/Candidatus_Carsonella_ruddii_HT_Thao2000.fasta example1_output/thao2000.0.assembly.out/thao2000.index 1>>
example1_output/thao2000.0.assembly.out/thao2000.index 2>&1;bowtie2 -a --end-to-end --sensitive --no-unal -p 4 -x example1_output/thao2000.0.assembly.out/thao
2000.index -q -U example1_output/thao2000.merged.fq -S example1_output/thao2000.0.assembly.out/thao2000.sam.all > example1_output/thao2000.0.bowtie2map.log 2>
&1; /home/talex/apps/MetaCompass-1.1/bin/best_strata.py example1_output/thao2000.0.assembly.out/thao2000.sam.all example1_output/thao2000.0.assembly.out/thao2
000.sam; rm example1_output/thao2000.0.assembly.out/thao2000.sam.all' returned non-zero exit status 1
  File "/home/talex/apps/MetaCompass-1.1/snakemake/metacompass.iter0.ref.py", line 50, in __rule_bowtie2_map
RuleException:
CalledProcessError in line 50 of /home/talex/apps/MetaCompass-1.1/snakemake/metacompass.iter0.ref.py:
Command 'bowtie2-build -o 3 --threads 4 -q tutorial/Candidatus_Carsonella_ruddii_HT_Thao2000.fasta example1_output/thao2000.0.assembly.out/thao2000.index 1>>
example1_output/thao2000.0.assembly.out/thao2000.index 2>&1;bowtie2 -a --end-to-end --sensitive --no-unal -p 4 -x example1_output/thao2000.0.assembly.out/thao
2000.index -q -U example1_output/thao2000.merged.fq -S example1_output/thao2000.0.assembly.out/thao2000.sam.all > example1_output/thao2000.0.bowtie2map.log 2>
&1; /home/talex/apps/MetaCompass-1.1/bin/best_strata.py example1_output/thao2000.0.assembly.out/thao2000.sam.all example1_output/thao2000.0.assembly.out/thao2
000.sam; rm example1_output/thao2000.0.assembly.out/thao2000.sam.all' returned non-zero exit status 1
  File "/home/talex/apps/MetaCompass-1.1/snakemake/metacompass.iter0.ref.py", line 50, in __rule_bowtie2_map
  File "/home/talex/.pyenv/versions/miniconda3-latest/lib/python3.5/concurrent/futures/thread.py", line 55, in run
Removing output files of failed job bowtie2_map since they might be corrupted:
example1_output/thao2000.0.assembly.out/thao2000.index, example1_output/thao2000.0.assembly.out/thao2000.index
Releasing 4 _cores (now 4).
Releasing 1 _nodes (now 9223372036854775807).
Will exit after finishing currently running jobs.
Exiting because a job execution failed. Look above for error message
unlocking
removing lock
removing lock
removed all locks
ERROR: snakemake command failed; exiting..

the example_output dir contains
Candidatus_Carsonella_ruddii_HT_Thao2000.fasta thao2000.0.assembly.out thao2000.fasta thao2000.marker.match.1.fastq thao2000.merged.fq

I suppose I should wait until next week or so?

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alexdthomas avatar alexdthomas commented on August 21, 2024

I'm trying to run the tutorial example with the new release (https://github.com/marbl/MetaCompass/releases/tag/paper-v1.0). After checking dependencies and installing I ran
python go_metacompass.py -r tutorial/Candidatus_Carsonella_ruddii_HT_Thao2000.fasta -P tutorial/thao2000.1.fq,tutorial/thao2000.2.fq -o example1_output -m 1 -t 4. I am no longer getting these errors, instead I am getting Issue #7. I'll mark this as closed

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