search

dib-lab / kProcessor

kProcessor: kmers processing framework.
https://kprocessor.readthedocs.io
BSD 3-Clause "New" or "Revised" License
11 stars 1 forks source link

kDifferentialExpression usecase isn't working #88

Open mr-eyes opened 3 years ago

mr-eyes commented 3 years ago

I followed all the steps in the usecase directory to run the snakemake but it's failing.

./downloadData.sh: 7: Syntax error: "(" unexpected

snakemake -j2 --use-conda
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 2
Rules claiming more threads will be scaled down.
Job stats:
job                       count    min threads    max threads
----------------------  -------  -------------  -------------
all                           1              1              1
kDifferntialExpression        1              1              1
kmc                           2              2              2
total                         4              1              2

Select jobs to execute...

[Tue Aug 31 04:21:50 2021]
rule kmc:
    input: inputData/HBR_Rep1_ERCC-Mix2_Build37-ErccTranscripts-chr22.read1.fastq.gz, inputData/HBR_Rep1_ERCC-Mix2_Build37-ErccTranscripts-chr22.read2.fastq.gz, inputData/HBR_Rep2_ERCC-Mix2_Build37-ErccTranscripts-chr22.read1.fastq.gz, inputData/HBR_Rep2_ERCC-Mix2_Build37-ErccTranscripts-chr22.read2.fastq.gz, inputData/HBR_Rep3_ERCC-Mix2_Build37-ErccTranscripts-chr22.read1.fastq.gz, inputData/HBR_Rep3_ERCC-Mix2_Build37-ErccTranscripts-chr22.read2.fastq.gz
    output: sample.kmc_pre, sample.kmc_suf, sample.kmc.time
    log: sample.kmc.log
    jobid: 2
    wildcards: experiment=sample
    threads: 2
    resources: tmpdir=/tmp

Activating conda environment: /home/mabuelanin/dib-dev/kProcessor_wrapper/build/usecases/kDifferentialExpression/.snakemake/conda/cb6edb19c50825bf280817fbb4ac06b5
[Tue Aug 31 04:21:50 2021]
Error in rule kmc:
    jobid: 2
    output: sample.kmc_pre, sample.kmc_suf, sample.kmc.time
    log: sample.kmc.log (check log file(s) for error message)
    conda-env: /home/mabuelanin/dib-dev/kProcessor_wrapper/build/usecases/kDifferentialExpression/.snakemake/conda/cb6edb19c50825bf280817fbb4ac06b5
    shell:

        echo inputData/HBR_Rep1_ERCC-Mix2_Build37-ErccTranscripts-chr22.read1.fastq.gz inputData/HBR_Rep1_ERCC-Mix2_Build37-ErccTranscripts-chr22.read2.fastq.gz inputData/HBR_Rep2_ERCC-Mix2_Build37-ErccTranscripts-chr22.read1.fastq.gz inputData/HBR_Rep2_ERCC-Mix2_Build37-ErccTranscripts-chr22.read2.fastq.gz inputData/HBR_Rep3_ERCC-Mix2_Build37-ErccTranscripts-chr22.read1.fastq.gz inputData/HBR_Rep3_ERCC-Mix2_Build37-ErccTranscripts-chr22.read2.fastq.gz |tr -s ' ' $'
' > sample.lst
        /usr/bin/time -v -o sample.kmc.time kmc -ci1 -t2 -k31 -m2  @sample.lst sample  ./ &> sample.kmc.log

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

Removing output files of failed job kmc since they might be corrupted:
sample.kmc.time
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /home/mabuelanin/dib-dev/kProcessor_wrapper/build/usecases/kDifferentialExpression/.snakemake/log/2021-08-31T042149.582856.snakemake.log

Full Log


Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 10
Rules claiming more threads will be scaled down.
Conda environments: ignored
Job stats:
job                       count    min threads    max threads
----------------------  -------  -------------  -------------
all                           1              1              1
kDifferntialExpression        1              1              1
kmc                           2              4              4
total                         4              1              4

Select jobs to execute...

[Tue Aug 31 04:00:51 2021]
rule kmc:
    input: inputData/UHR_Rep1_ERCC-Mix1_Build37-ErccTranscripts-chr22.read1.fastq.gz, inputData/UHR_Rep1_ERCC-Mix1_Build37-ErccTranscripts-chr22.read2.fastq.gz, inputData/UHR_Rep2_ERCC-Mix1_Build37-ErccTranscripts-chr22.read1.fastq.gz, inputData/UHR_Rep2_ERCC-Mix1_Build37-ErccTranscripts-chr22.read2.fastq.gz, inputData/UHR_Rep3_ERCC-Mix1_Build37-ErccTranscripts-chr22.read1.fastq.gz, inputData/UHR_Rep3_ERCC-Mix1_Build37-ErccTranscripts-chr22.read2.fastq.gz
    output: control.kmc_pre, control.kmc_suf, control.kmc.time
    log: control.kmc.log
    jobid: 3
    wildcards: experiment=control
    threads: 4
    resources: tmpdir=/tmp

[Tue Aug 31 04:00:51 2021]
rule kmc:
    input: inputData/HBR_Rep1_ERCC-Mix2_Build37-ErccTranscripts-chr22.read1.fastq.gz, inputData/HBR_Rep1_ERCC-Mix2_Build37-ErccTranscripts-chr22.read2.fastq.gz, inputData/HBR_Rep2_ERCC-Mix2_Build37-ErccTranscripts-chr22.read1.fastq.gz, inputData/HBR_Rep2_ERCC-Mix2_Build37-ErccTranscripts-chr22.read2.fastq.gz, inputData/HBR_Rep3_ERCC-Mix2_Build37-ErccTranscripts-chr22.read1.fastq.gz, inputData/HBR_Rep3_ERCC-Mix2_Build37-ErccTranscripts-chr22.read2.fastq.gz
    output: sample.kmc_pre, sample.kmc_suf, sample.kmc.time
    log: sample.kmc.log
    jobid: 2
    wildcards: experiment=sample
    threads: 4
    resources: tmpdir=/tmp

[Tue Aug 31 04:00:51 2021]
Error in rule kmc:
    jobid: 3
    output: control.kmc_pre, control.kmc_suf, control.kmc.time
    log: control.kmc.log (check log file(s) for error message)
    shell:

    echo inputData/UHR_Rep1_ERCC-Mix1_Build37-ErccTranscripts-chr22.read1.fastq.gz inputData/UHR_Rep1_ERCC-Mix1_Build37-ErccTranscripts-chr22.read2.fastq.gz inputData/UHR_Rep2_ERCC-Mix1_Build37-ErccTranscripts-chr22.read1.fastq.gz inputData/UHR_Rep2_ERCC-Mix1_Build37-ErccTranscripts-chr22.read2.fastq.gz inputData/UHR_Rep3_ERCC-Mix1_Build37-ErccTranscripts-chr22.read1.fastq.gz inputData/UHR_Rep3_ERCC-Mix1_Build37-ErccTranscripts-chr22.read2.fastq.gz |tr -s ' ' $'
' > control.lst
    /usr/bin/time -v -o control.kmc.time kmc -ci1 -t4 -k31 -m2  @control.lst control  ./ &> control.kmc.log

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

Removing output files of failed job kmc since they might be corrupted:
control.kmc.time
[Tue Aug 31 04:00:51 2021]
Error in rule kmc:
    jobid: 2
    output: sample.kmc_pre, sample.kmc_suf, sample.kmc.time
    log: sample.kmc.log (check log file(s) for error message)
    shell:

    echo inputData/HBR_Rep1_ERCC-Mix2_Build37-ErccTranscripts-chr22.read1.fastq.gz inputData/HBR_Rep1_ERCC-Mix2_Build37-ErccTranscripts-chr22.read2.fastq.gz inputData/HBR_Rep2_ERCC-Mix2_Build37-ErccTranscripts-chr22.read1.fastq.gz inputData/HBR_Rep2_ERCC-Mix2_Build37-ErccTranscripts-chr22.read2.fastq.gz inputData/HBR_Rep3_ERCC-Mix2_Build37-ErccTranscripts-chr22.read1.fastq.gz inputData/HBR_Rep3_ERCC-Mix2_Build37-ErccTranscripts-chr22.read2.fastq.gz |tr -s ' ' $'
' > sample.lst
    /usr/bin/time -v -o sample.kmc.time kmc -ci1 -t4 -k31 -m2  @sample.lst sample  ./ &> sample.kmc.log

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

Removing output files of failed job kmc since they might be corrupted:
sample.kmc.time
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: /home/mabuelanin/dib-dev/kProcessor_wrapper/build/usecases/kDifferentialExpression/.snakemake/log/2021-08-31T040051.177052.snakemake.log
shokrof commented 3 years ago

it is working on the server. Please make sure that the download script works correctly on your computer before running the snakemake