valeu
commented
6 years ago Please remove or comment:
step=1
=>
#step=1
And run again.
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window=1000
Open deepalivasoya opened 6 years ago
valeu
commented
6 years ago Please remove or comment:
step=1
=>
#step=1
And run again.
You can also comment
window=1000
### With this config file: [general]
BedGraphOutput=TRUE chrFiles=/exports/cmvm/eddie/eb/groups/CTLGH_GCRF/WGS_sheep/test_temp/Fasta chrLenFile=/exports/cmvm/eddie/eb/groups/CTLGH_GCRF/WGS_sheep/test_temp/Bams/Ovis_aries.Oar_v3.1.dna.toplevel.len maxThreads=4 outputDir=/exports/cmvm/eddie/eb/groups/CTLGH_GCRF/WGS_sheep/test_temp/Control-freec/WA1343 ploidy=2 window=1000 step=1
[sample] mateFile=/exports/cmvm/eddie/eb/groups/CTLGH_GCRF/WGS_sheep/test_temp/Bams/Washera/batch_X16081_WA1343_reheaded_mkdups_rg.bam inputFormat=BAM mateOrientation=FR
[control]
I had this error:
Control-FREEC v11.4 : a method for automatic detection of copy number alterations, subclones and for accurate estimation of contamination and main ploidy using deep-sequencing data Multi-threading mode using 4 threads ..Breakpoint threshold for segmentation of copy number profiles is 0.8 ..telocenromeric set to 50000 ..FREEC is not going to adjust profiles for a possible contamination by normal cells ..Window = 1000 was set ..Step: 1 ..Output directory: /exports/cmvm/eddie/eb/groups/CTLGH_GCRF/WGS_sheep/test_temp/Control-freec/WA1343 ..Directory with files containing chromosome sequences: /exports/cmvm/eddie/eb/groups/CTLGH_GCRF/WGS_sheep/test_temp/Fasta ..Sample file: /exports/cmvm/eddie/eb/groups/CTLGH_GCRF/WGS_sheep/test_temp/Bams/Washera/batch_X16081_WA1343_reheaded_mkdups_rg.bam ..Sample input format: BAM ..will use this instance of samtools: 'samtools' to read BAM files ..minimal expected GC-content (general parameter "minExpectedGC") was set to 0.35 ..maximal expected GC-content (general parameter "maxExpectedGC") was set to 0.55 ..Polynomial degree for "ReadCount ~ GC-content" normalization is 3 or 4: will try both ..Minimal CNA length (in windows) is 1 ..File with chromosome lengths: /exports/cmvm/eddie/eb/groups/CTLGH_GCRF/WGS_sheep/test_temp/Bams/Ovis_aries.Oar_v3.1.dna.toplevel.len ..Using the default minimal mappability value of 0.85 ..uniqueMatch = FALSE ..average ploidy set to 2 ..break-point type set to 2 ..noisyData set to 0 ..Control-FREEC will not look for subclones ..File /exports/cmvm/eddie/eb/groups/CTLGH_GCRF/WGS_sheep/test_temp/Bams/Ovis_aries.Oar_v3.1.dna.toplevel.len was read ..Starting reading /exports/cmvm/eddie/eb/groups/CTLGH_GCRF/WGS_sheep/test_temp/Bams/Washera/batch_X16081_WA1343_reheaded_mkdups_rg.bam ..samtools should be installed to be able to read BAM files; will use the following command for samtools: samtools view /exports/cmvm/eddie/eb/groups/CTLGH_GCRF/WGS_sheep/test_temp/Bams/Washera/batch_X16081_WA1343_reheaded_mkdups_rg.bam ..finished reading /exports/cmvm/eddie/eb/groups/CTLGH_GCRF/WGS_sheep/test_temp/Bams/Washera/batch_X16081_WA1343_reheaded_mkdups_rg.bam PROFILING [tid=47201871498240]: /exports/cmvm/eddie/eb/groups/CTLGH_GCRF/WGS_sheep/test_temp/Bams/Washera/batch_X16081_WA1343_reheaded_mkdups_rg.bam read in 4168 seconds [fillMyHash] 776139194 lines read.. 697836260 reads used to compute copy number profile printing counts into /exports/cmvm/eddie/eb/groups/CTLGH_GCRF/WGS_sheep/test_temp/Control-freec/WA1343/batch_X16081_WA1343_reheaded_mkdups_rg.bam_sample.cpn ..Window size: 1000 ..using GC-content to normalize copy number profiles CG-content printed into /exports/cmvm/eddie/eb/groups/CTLGH_GCRF/WGS_sheep/test_temp/Control-freec/WA1343/GC_profile.1000bp.cnp ..Running FREEC with ploidy set to 2 ERROR: there was a problem in the initial guess of the polynomial. Please contact the support team of change your input parameters. Exit.
It would be great if you can help me with it.
Thank you