bamFilesList: ['wgEncodeUwRepliSeqK562S2AlnRep1.bam']
binLength: 50
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
genomeChunkSize: None
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 50
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000
Traceback (most recent call last):
  File "/scratch/bmijzen_B/mamba/envs/bam2bigwig/bin/bamCoverage", line 12, in <module>
    main(args)
  File "/scratch/bmijzen_B/mamba/envs/bam2bigwig/lib/python3.7/site-packages/deeptools/bamCoverage.py", line 258, in main
    format=args.outFileFormat, smoothLength=args.smoothLength)
  File "/scratch/bmijzen_B/mamba/envs/bam2bigwig/lib/python3.7/site-packages/deeptools/writeBedGraph.py", line 152, in run
    numberOfProcessors=self.numberOfProcessors)
  File "/scratch/bmijzen_B/mamba/envs/bam2bigwig/lib/python3.7/site-packages/deeptools/mapReduce.py", line 146, in mapReduce
    res = list(map(func, TASKS))
  File "/scratch/bmijzen_B/mamba/envs/bam2bigwig/lib/python3.7/site-packages/deeptools/writeBedGraph.py", line 27, in writeBedGraph_wrapper
    return WriteBedGraph.writeBedGraph_worker(*args)
  File "/scratch/bmijzen_B/mamba/envs/bam2bigwig/lib/python3.7/site-packages/deeptools/writeBedGraph.py", line 249, in writeBedGraph_worker
    value = func_to_call(tileCoverage, func_args)
KeyboardInterrupt
wgEncodeUwRepliSeqK562S2AlnRep1.bam
bamFilesList: ['wgEncodeUwRepliSeqK562S3AlnRep1.bam']
binLength: 50
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
genomeChunkSize: None
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 50
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000
The file 'wgEncodeUwRepliSeqK562S3AlnRep1.bam' does not have BAM or CRAM format 
wgEncodeUwRepliSeqK562S3AlnRep1.bam
bamFilesList: ['wgEncodeUwRepliSeqK562S4AlnRep1.bam']
binLength: 50
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
genomeChunkSize: None
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 50
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000
Traceback (most recent call last):
  File "/scratch/bmijzen_B/mamba/envs/bam2bigwig/bin/bamCoverage", line 12, in <module>
    main(args)
  File "/scratch/bmijzen_B/mamba/envs/bam2bigwig/lib/python3.7/site-packages/deeptools/bamCoverage.py", line 258, in main
    format=args.outFileFormat, smoothLength=args.smoothLength)
  File "/scratch/bmijzen_B/mamba/envs/bam2bigwig/lib/python3.7/site-packages/deeptools/writeBedGraph.py", line 152, in run
    numberOfProcessors=self.numberOfProcessors)
  File "/scratch/bmijzen_B/mamba/envs/bam2bigwig/lib/python3.7/site-packages/deeptools/mapReduce.py", line 146, in mapReduce
    res = list(map(func, TASKS))
  File "/scratch/bmijzen_B/mamba/envs/bam2bigwig/lib/python3.7/site-packages/deeptools/writeBedGraph.py", line 27, in writeBedGraph_wrapper
    return WriteBedGraph.writeBedGraph_worker(*args)
  File "/scratch/bmijzen_B/mamba/envs/bam2bigwig/lib/python3.7/site-packages/deeptools/writeBedGraph.py", line 249, in writeBedGraph_worker
    value = func_to_call(tileCoverage, func_args)
  File "/scratch/bmijzen_B/mamba/envs/bam2bigwig/lib/python3.7/site-packages/deeptools/writeBedGraph.py", line 347, in scaleCoverage
    return args['scaleFactor'] * tile_coverage[0]
KeyboardInterrupt
wgEncodeUwRepliSeqK562S4AlnRep1.bam
bamFilesList: ['wgEncodeUwRepliSeqK562S2AlnRep1.bam']
binLength: 50
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
genomeChunkSize: None
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 50
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000
wgEncodeUwRepliSeqK562S2AlnRep1.bam
bamFilesList: ['wgEncodeUwRepliSeqK562S3AlnRep1.bam']
binLength: 50
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
genomeChunkSize: None
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 50
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000
wgEncodeUwRepliSeqK562S3AlnRep1.bam
bamFilesList: ['wgEncodeUwRepliSeqK562S4AlnRep1.bam']
binLength: 50
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
genomeChunkSize: None
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 50
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000
wgEncodeUwRepliSeqK562S4AlnRep1.bam
bamFilesList: ['wgEncodeUwRepliSeqK562S2AlnRep1.bam']
binLength: 50
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
genomeChunkSize: None
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 50
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000
wgEncodeUwRepliSeqK562S2AlnRep1.bam
bamFilesList: ['wgEncodeUwRepliSeqK562S3AlnRep1.bam']
binLength: 50
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
genomeChunkSize: None
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 50
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000
wgEncodeUwRepliSeqK562S3AlnRep1.bam
bamFilesList: ['wgEncodeUwRepliSeqK562S4AlnRep1.bam']
binLength: 50
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
genomeChunkSize: None
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 50
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000
wgEncodeUwRepliSeqK562S4AlnRep1.bam
bamFilesList: ['wgEncodeUwRepliSeqK562S2AlnRep1.bam']
binLength: 50
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
genomeChunkSize: None
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 50
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000
wgEncodeUwRepliSeqK562S2AlnRep1.bam
bamFilesList: ['wgEncodeUwRepliSeqK562S3AlnRep1.bam']
binLength: 50
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
genomeChunkSize: None
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 50
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000
wgEncodeUwRepliSeqK562S3AlnRep1.bam
bamFilesList: ['wgEncodeUwRepliSeqK562S4AlnRep1.bam']
binLength: 50
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
genomeChunkSize: None
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 50
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000
wgEncodeUwRepliSeqK562S4AlnRep1.bam
bamFilesList: ['wgEncodeUwRepliSeqK562S2AlnRep1.bam']
binLength: 50
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
genomeChunkSize: None
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 50
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000
wgEncodeUwRepliSeqK562S2AlnRep1.bam
bamFilesList: ['wgEncodeUwRepliSeqK562S3AlnRep1.bam']
binLength: 50
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
genomeChunkSize: None
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 50
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000
wgEncodeUwRepliSeqK562S3AlnRep1.bam
bamFilesList: ['wgEncodeUwRepliSeqK562S4AlnRep1.bam']
binLength: 50
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
genomeChunkSize: None
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 50
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000
wgEncodeUwRepliSeqK562S4AlnRep1.bam
bamFilesList: ['wgEncodeUwRepliSeqK562S2AlnRep1.bam']
binLength: 50
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
genomeChunkSize: None
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 50
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000
wgEncodeUwRepliSeqK562S2AlnRep1.bam
bamFilesList: ['wgEncodeUwRepliSeqK562S3AlnRep1.bam']
binLength: 50
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
genomeChunkSize: None
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 50
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000
wgEncodeUwRepliSeqK562S3AlnRep1.bam
bamFilesList: ['wgEncodeUwRepliSeqK562S4AlnRep1.bam']
binLength: 50
numberOfSamples: None
blackListFileName: None
skipZeroOverZero: False
bed_and_bin: False
genomeChunkSize: None
defaultFragmentLength: read length
numberOfProcessors: 1
verbose: False
region: None
bedFile: None
minMappingQuality: None
ignoreDuplicates: False
chrsToSkip: []
stepSize: 50
center_read: False
samFlag_include: None
samFlag_exclude: None
minFragmentLength: 0
maxFragmentLength: 0
zerosToNans: False
smoothLength: None
save_data: False
out_file_for_raw_data: None
maxPairedFragmentLength: 1000
wgEncodeUwRepliSeqK562S4AlnRep1.bam