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cnobles / iGUIDE

Bioinformatic pipeline for identifying dsDNA breaks by marker based incorporation, such as breaks induced by designer nucleases like Cas9.
https://iguide.readthedocs.io/en/latest/
GNU General Public License v3.0
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align errors #76

Closed magic2077 closed 3 years ago

magic2077 commented 3 years ago

Hi Chris,

Iguide data analysis pipeline is very useful for us. Thanks a lot for posting the pipeline in github!

I ran the simulation test but got error information as follows:

[Wed Oct 14 07:08:55 2020] Error in rule align: jobid: 109 output: /home/ubuntu/iGUIDE/analysis/simulation/process_data/align/iGXA.R1.bin2.psl log: /home/ubuntu/iGUIDE/analysis/simulation/logs/iGXA.R1.bin2.blat.log (check log file(s) for error message) shell:

if [[ $(cat /home/ubuntu/iGUIDE/analysis/simulation/process_data/consol/iGXA.R1.bin2.consol.fasta | wc -l) -eq 0 ]]
    then
        touch /home/ubuntu/iGUIDE/analysis/simulation/process_data/align/iGXA.R1.bin2.psl
        echo 'Empty input sequences for /home/ubuntu/iGUIDE/analysis/simulation/process_data/consol/iGXA.R1.bin2.consol.fasta.' > /home/ubuntu/iGUIDE/analysis/simulation/logs/iGXA.R1.bin2.blat.log 2>&1
    else
        blat /home/ubuntu/iGUIDE/genomes/hg38.2bit /home/ubuntu/iGUIDE/analysis/simulation/process_data/consol/iGXA.R1.bin2.consol.fasta /home/ubuntu/iGUIDE/analysis/simulation/process_data/align/iGXA.R1.bin2.psl                 -tileSize=11 -stepSize=9 -minIdentity=85 -maxIntron=5 -minScore=27 -dots=1000 -out=psl -noHead > /home/ubuntu/iGUIDE/analysis/simulation/logs/iGXA.R1.bin2.blat.log 2>&1
fi

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

Removing output files of failed job align since they might be corrupted: /home/ubuntu/iGUIDE/analysis/simulation/process_data/align/iGXA.R1.bin2.psl [Wed Oct 14 07:10:11 2020] Finished job 116. 50 of 125 steps (40%) done

Could you please help me solve the problem?

Thanks a lot!

magic2077 commented 3 years ago

Hi Chris,

After reinstall iGUIDE the simulation data worked. However when I run iguide using my real data (ALT iguide, library prep by simple protocol) I got errors:

$ iguide run configs/run2.config.yml ValueError in line 89 of /home/ubuntu/iGUIDE/Snakefile: 'sampleName' is not in list File "/home/ubuntu/iGUIDE/Snakefile", line 89, in File "/home/ubuntu/miniconda3/envs/iguide/lib/python3.6/site-packages/iguidelib/init.py", line 12, in import_sample_info

Any idea?

Thanks a lot! Lijie

cnobles commented 3 years ago

Hi Lijie,

This looks like this could be a sample info file issue, formatting anyways. Would you mind pasting the first two lines of your sampleInfo file here? Additionally, the first part of the config could be helpful is figuring out the issue (just down to the dashed line is enough).

Best, Chris

magic2077 commented 3 years ago

Hi Chris,

The problem was solved. I used your sample information format and just changed the details by my project and it worked. Thanks a lot!

Lijie

Sent from my iPhone

On Jan 24, 2021, at 5:16 AM, Chris Nobles notifications@github.com wrote:

 Hi Lijie,

This looks like this could be a sample info file issue, formatting anyways. Would you mind pasting the first two lines of your sampleInfo file here? Additionally, the first part of the config could be helpful is figuring out the issue (just down to the dashed line is enough).

Best, Chris

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