cmkobel/mspipeline1

🪆🦖 A snakemake wrapper around Nesvilab's FragPipe-CLI. In a perfect world, this pipeline was based on Sage.

mspipeline1's Issues

rule philosopher_database permissions

Config file config.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Select jobs to execute...

[Tue Jul 19 10:21:30 2022]
rule philosopher_database:
    output: output/220506_DnnT6S_carl/msfragger/philosopher_database.fas
    jobid: 0
    benchmark: output/220506_DnnT6S_carl/benchmarks/philosopher_database.tsv
    reason: Forced execution
    wildcards: config_batch=220506_DnnT6S_carl
    resources: mem_mb=1000, disk_mb=1000, tmpdir=/scratch/3973804




        >&2 echo "Catting database files ..."
        # Cat all database source files into one.
        cat  > output/220506_DnnT6S_carl/msfragger/cat_database_sources.faa


        >&2 echo "Change dir ..."
        # As philosopher can't specify output files, we need to change dir.
        mkdir -p output/220506_DnnT6S_carl/msfragger
        cd output/220506_DnnT6S_carl/msfragger

        >&2 echo "Philosopher workspace clean ..."
        /faststorage/project/gBGC/bin/philosopher_v4.1.1_linux_amd64/philosopher workspace             --nocheck             --clean 

        >&2 echo "Philosopher workspace init ..."
        /faststorage/project/gBGC/bin/philosopher_v4.1.1_linux_amd64/philosopher workspace             --nocheck             --init 

        >&2 echo "Removing previous .fas ..."
        rm *.fas || echo "nothing to delete" # Remove all previous databases if any.

        >&2 echo "Philosopher database ..."
        /faststorage/project/gBGC/bin/philosopher_v4.1.1_linux_amd64/philosopher database             --custom cat_database_sources.faa             --contam 

        >&2 echo "Move output ..."
        # Manually rename the philosopher output so we can grab it later
        mv *-decoys-contam-cat_database_sources.faa.fas philosopher_database.fas

        >&2 echo "Clean up ..."
        # clean up 
        rm cat_database_sources.faa


        
Catting database files ...
Change dir ...
Philosopher workspace clean ...
time="10:21:32" level=info msg="Executing Workspace  v4.1.1"
time="10:21:32" level=info msg="Removing workspace"
time="10:21:32" level=warning msg="Cannot read file. open .meta/meta.bin: no such file or directory"
time="10:21:32" level=info msg=Done
Philosopher workspace init ...
time="10:21:32" level=info msg="Executing Workspace  v4.1.1"
time="10:21:32" level=info msg="Creating workspace"
time="10:21:32" level=warning msg="Cannot verify local directory path. getwd: no such file or directory"
time="10:21:32" level=fatal msg="Cannot create meta directory; check folder permissions. stat .meta: no such file or directory"
[Tue Jul 19 10:21:32 2022]
Error in rule philosopher_database:
    jobid: 0
    output: output/220506_DnnT6S_carl/msfragger/philosopher_database.fas
    shell:
        


        >&2 echo "Catting database files ..."
        # Cat all database source files into one.
        cat  > output/220506_DnnT6S_carl/msfragger/cat_database_sources.faa


        >&2 echo "Change dir ..."
        # As philosopher can't specify output files, we need to change dir.
        mkdir -p output/220506_DnnT6S_carl/msfragger
        cd output/220506_DnnT6S_carl/msfragger

        >&2 echo "Philosopher workspace clean ..."
        /faststorage/project/gBGC/bin/philosopher_v4.1.1_linux_amd64/philosopher workspace             --nocheck             --clean 

        >&2 echo "Philosopher workspace init ..."
        /faststorage/project/gBGC/bin/philosopher_v4.1.1_linux_amd64/philosopher workspace             --nocheck             --init 

        >&2 echo "Removing previous .fas ..."
        rm *.fas || echo "nothing to delete" # Remove all previous databases if any.

        >&2 echo "Philosopher database ..."
        /faststorage/project/gBGC/bin/philosopher_v4.1.1_linux_amd64/philosopher database             --custom cat_database_sources.faa             --contam 

        >&2 echo "Move output ..."
        # Manually rename the philosopher output so we can grab it later
        mv *-decoys-contam-cat_database_sources.faa.fas philosopher_database.fas

        >&2 echo "Clean up ..."
        # clean up 
        rm cat_database_sources.faa


        
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

Mem change over attempts not burning through to slurm.

https://github.com/cmkobel/MS-pipeline1/blob/4bcb6b4d2a476281e4f9dbddfd17e34159fabd7c/snakefile#L125

Shows up fine in the snakemake interactive stdout. But jobinfo shows the same mem allocation for all retries.

ule link_input fails sometimes

        
Touching output file output/220506_DnnT6S_carl/msfragger/link_input.done.
Traceback (most recent call last):
  File "/home/cmkobel/faststorage/miniconda3/envs/smk785/lib/python3.10/site-packages/snakemake/__init__.py", line 726, in snakemake
    success = workflow.execute(
  File "/home/cmkobel/faststorage/miniconda3/envs/smk785/lib/python3.10/site-packages/snakemake/workflow.py", line 1133, in execute
    raise e
  File "/home/cmkobel/faststorage/miniconda3/envs/smk785/lib/python3.10/site-packages/snakemake/workflow.py", line 1129, in execute
    success = self.scheduler.schedule()
  File "/home/cmkobel/faststorage/miniconda3/envs/smk785/lib/python3.10/site-packages/snakemake/scheduler.py", line 423, in schedule
    self._finish_jobs()
  File "/home/cmkobel/faststorage/miniconda3/envs/smk785/lib/python3.10/site-packages/snakemake/scheduler.py", line 526, in _finish_jobs
    self.get_executor(job).handle_job_success(job)
  File "/home/cmkobel/faststorage/miniconda3/envs/smk785/lib/python3.10/site-packages/snakemake/executors/__init__.py", line 633, in handle_job_success
    super().handle_job_success(job)
  File "/home/cmkobel/faststorage/miniconda3/envs/smk785/lib/python3.10/site-packages/snakemake/executors/__init__.py", line 232, in handle_job_success
    job.postprocess(
  File "/home/cmkobel/faststorage/miniconda3/envs/smk785/lib/python3.10/site-packages/snakemake/jobs.py", line 1076, in postprocess
    self.dag.check_and_touch_output(
  File "/home/cmkobel/faststorage/miniconda3/envs/smk785/lib/python3.10/site-packages/snakemake/dag.py", line 594, in check_and_touch_output
    f.touch()
  File "/home/cmkobel/faststorage/miniconda3/envs/smk785/lib/python3.10/site-packages/snakemake/io.py", line 707, in touch
    raise e
  File "/home/cmkobel/faststorage/miniconda3/envs/smk785/lib/python3.10/site-packages/snakemake/io.py", line 693, in touch
    with open(file, "w"):
PermissionError: [Errno 13] Permission denied: 'output/220506_DnnT6S_carl/msfragger/20220506_C9_Slot1-33_1_1971.d/.snakemake_timestamp'```

Merge some rules together.

The temporary directories given to some of the rules, especially the ones that create workspaces should be merged together. The problem is that the temporary dirs (scratch) don't exist after the initial job ends, so, really, the only option to use the scratch directory is to have more rules merged.

temporary directories

One major bottleneck of this pipeline is that it doesn't utilize temporary directories efficiently. Currently, the snakemake temporary directory is set to somewhere on the userwork partition on saga. The problem is that stupidly, several rules need access to the same temporary directory. I guess it really goes against the definition of a temporary directory to use it for something that isn't temporary.