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JetBrains-Research / washu

Reproducible and scalable technical pipelines for ChIP-Seq and RNA-Seq processing
https://artyomovlab.wustl.edu/aging
MIT License
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mm10 is not recognised by SICER step #64

Closed olegs closed 5 years ago

olegs commented 6 years ago 
Preprocess the raw IP5_RJ_S2_L002_3_uM_Met6_mm10 file to remove redundancy with threshold 1...
python2 /home/oshpynov/SICER_V1.1/SICER/src/remove_redundant_reads.py -s mm10 -b /tmp/4715783.mgt2.cluster//IP5_RJ_S2_L002_3_uM_Met6_mm10_F150_W200_G0_FDR0.01/IP5_RJ_S2_L002_3_uM_Met6_mm10.bed -t 1 -o /tm
p/4715783.mgt2.cluster//IP5_RJ_S2_L002_3_uM_Met6_mm10_F150_W200_G0_FDR0.01/out/IP5_RJ_S2_L002_3_uM_Met6_mm10-1-removed.bed
This species is not recognized, exiting

Preprocess the raw IP5_RJ_S2_L002_Input_1_mm10 file to remove redundancy with threshold 1...
python2 /home/oshpynov/SICER_V1.1/SICER/src/remove_redundant_reads.py -s mm10 -b /tmp/4715783.mgt2.cluster//IP5_RJ_S2_L002_3_uM_Met6_mm10_F150_W200_G0_FDR0.01/IP5_RJ_S2_L002_Input_1_mm10.bed -t 1 -o /tmp/
4715783.mgt2.cluster//IP5_RJ_S2_L002_3_uM_Met6_mm10_F150_W200_G0_FDR0.01/out/IP5_RJ_S2_L002_Input_1_mm10-1-removed.bed
This species is not recognized, exiting
olegs commented 5 years ago

Has nothing to do with our pipeline. See for details: https://biostar.usegalaxy.org/p/28442/