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Missing matrix.txt file #6

Open foxandrewd opened 7 years ago

foxandrewd commented 7 years ago

Hi I am trying to run rose2 on some test data but keep getting the following 2 errors:

  1. Exception: /config/binaries/bamliquidator/c2c4865/pipeline/bamliquidator_internal/bamliquidator_regions failed with exit code 127 /config/binaries/rose2/1.0.5/lib/python2.7/site-packages/rose2 (although this is after a 'Liquidation completed' log message, so may not be an issue)

  2. OPERATION TIMED OUT. FILE example/mappedGFF/HG18_MM1S_MED1_12KB_STITCHED_TSS_DISTAL_MM1S_MED1.hg18.bwt.sorted.bam_MAPPED/matrix.txt NOT FOUND

The full rose2 output log is attached to this issue. Please advise of any resolution to these issues. Thanks. rose2_out.log

GryderArt commented 6 years ago

I'm seeing problem/error #2 also: The log file reads:

MAPPING TO THE FOLLOWING BAMS: ['/data/khanlab/projects/ChIP_seq/DATA/H3K27ac_024_C_HLFMLBGX3.bam', '/data/khanlab/projects/ChIP_seq/DATA/input_026_C_H7FGKBGX5.bam'] OPERATION TIMED OUT. FILE /data/khanlab/projects/ChIP_seq/DATA/ROSE_out_12500/mappedGFF/Sample_KG1a_H3K27ac_024_C_HLFMLBGX3_peaks_0KB_STITCHED_TSS_DISTAL_H3K27ac_024_C_HLFMLBGX3.bam_MAPPED/matrix.txt NOT FOUND

Has anyone solved this yet? I'm running ROSE2 on a cluster node with --mem=121g --cpus-per-task=4

GryderArt commented 6 years ago

Might think about version control for bamliqidator; similar issue resolved here: https://github.com/BradnerLab/pipeline/issues/62