Inactive Modules: 1) slurm Traceback (most recent call last): File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/bin/bamCompare", line 12, in main(args) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/bamCompare.py", line 265, in main scale_factors = get_scale_factors(args, [stats1, stats2], [mapped1, mapped2]) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/bamCompare.py", line 214, in get_scale_factors bam1_mapped, _ = get_num_kept_reads(args, statsList[0]) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/getScaleFactor.py", line 197, in get_num_kept_reads blacklisted = utilities.bam_blacklisted_reads(bam_handle, args.ignoreForNormalization, File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/utilities.py", line 367, in bam_blacklisted_reads bl = GTF(blackListFileName) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptoolsintervals/parse.py", line 584, in __init__ fp = openPossiblyCompressed(fname) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptoolsintervals/parse.py", line 102, in openPossiblyCompressed with open(fname, "rb") as f: FileNotFoundError: [Errno 2] No such file or directory: '/grid/vakoc/data/Patrick/ChIP_seq/hg38.blacklit.bed' Traceback (most recent call last): File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/bin/bamCompare", line 12, in main(args) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/bamCompare.py", line 265, in main scale_factors = get_scale_factors(args, [stats1, stats2], [mapped1, mapped2]) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/bamCompare.py", line 214, in get_scale_factors bam1_mapped, _ = get_num_kept_reads(args, statsList[0]) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/getScaleFactor.py", line 197, in get_num_kept_reads blacklisted = utilities.bam_blacklisted_reads(bam_handle, args.ignoreForNormalization, File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/utilities.py", line 367, in bam_blacklisted_reads bl = GTF(blackListFileName) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptoolsintervals/parse.py", line 584, in __init__ fp = openPossiblyCompressed(fname) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptoolsintervals/parse.py", line 102, in openPossiblyCompressed with open(fname, "rb") as f: FileNotFoundError: [Errno 2] No such file or directory: '/grid/vakoc/data/Patrick/ChIP_seq/hg38.blacklit.bed' Traceback (most recent call last): File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/bin/bamCompare", line 12, in main(args) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/bamCompare.py", line 265, in main scale_factors = get_scale_factors(args, [stats1, stats2], [mapped1, mapped2]) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/bamCompare.py", line 214, in get_scale_factors bam1_mapped, _ = get_num_kept_reads(args, statsList[0]) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/getScaleFactor.py", line 197, in get_num_kept_reads blacklisted = utilities.bam_blacklisted_reads(bam_handle, args.ignoreForNormalization, File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/utilities.py", line 367, in bam_blacklisted_reads bl = GTF(blackListFileName) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptoolsintervals/parse.py", line 584, in __init__ fp = openPossiblyCompressed(fname) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptoolsintervals/parse.py", line 102, in openPossiblyCompressed with open(fname, "rb") as f: FileNotFoundError: [Errno 2] No such file or directory: '/grid/vakoc/data/Patrick/ChIP_seq/hg38.blacklit.bed' Traceback (most recent call last): File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/bin/bamCompare", line 12, in main(args) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/bamCompare.py", line 265, in main scale_factors = get_scale_factors(args, [stats1, stats2], [mapped1, mapped2]) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/bamCompare.py", line 214, in get_scale_factors bam1_mapped, _ = get_num_kept_reads(args, statsList[0]) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/getScaleFactor.py", line 197, in get_num_kept_reads blacklisted = utilities.bam_blacklisted_reads(bam_handle, args.ignoreForNormalization, File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/utilities.py", line 367, in bam_blacklisted_reads bl = GTF(blackListFileName) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptoolsintervals/parse.py", line 584, in __init__ fp = openPossiblyCompressed(fname) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptoolsintervals/parse.py", line 102, in openPossiblyCompressed with open(fname, "rb") as f: FileNotFoundError: [Errno 2] No such file or directory: '/grid/vakoc/data/Patrick/ChIP_seq/hg38.blacklit.bed' Traceback (most recent call last): File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/bin/bamCompare", line 12, in main(args) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/bamCompare.py", line 265, in main scale_factors = get_scale_factors(args, [stats1, stats2], [mapped1, mapped2]) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/bamCompare.py", line 214, in get_scale_factors bam1_mapped, _ = get_num_kept_reads(args, statsList[0]) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/getScaleFactor.py", line 197, in get_num_kept_reads blacklisted = utilities.bam_blacklisted_reads(bam_handle, args.ignoreForNormalization, File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/utilities.py", line 367, in bam_blacklisted_reads bl = GTF(blackListFileName) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptoolsintervals/parse.py", line 584, in __init__ fp = openPossiblyCompressed(fname) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptoolsintervals/parse.py", line 102, in openPossiblyCompressed with open(fname, "rb") as f: FileNotFoundError: [Errno 2] No such file or directory: '/grid/vakoc/data/Patrick/ChIP_seq/hg38.blacklit.bed' Traceback (most recent call last): File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/bin/bamCompare", line 12, in main(args) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/bamCompare.py", line 265, in main scale_factors = get_scale_factors(args, [stats1, stats2], [mapped1, mapped2]) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/bamCompare.py", line 214, in get_scale_factors bam1_mapped, _ = get_num_kept_reads(args, statsList[0]) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/getScaleFactor.py", line 197, in get_num_kept_reads blacklisted = utilities.bam_blacklisted_reads(bam_handle, args.ignoreForNormalization, File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/utilities.py", line 367, in bam_blacklisted_reads bl = GTF(blackListFileName) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptoolsintervals/parse.py", line 584, in __init__ fp = openPossiblyCompressed(fname) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptoolsintervals/parse.py", line 102, in openPossiblyCompressed with open(fname, "rb") as f: FileNotFoundError: [Errno 2] No such file or directory: '/grid/vakoc/data/Patrick/ChIP_seq/hg38.blacklit.bed' Traceback (most recent call last): File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/bin/bamCompare", line 12, in main(args) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/bamCompare.py", line 265, in main scale_factors = get_scale_factors(args, [stats1, stats2], [mapped1, mapped2]) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/bamCompare.py", line 214, in get_scale_factors bam1_mapped, _ = get_num_kept_reads(args, statsList[0]) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/getScaleFactor.py", line 197, in get_num_kept_reads blacklisted = utilities.bam_blacklisted_reads(bam_handle, args.ignoreForNormalization, File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/utilities.py", line 367, in bam_blacklisted_reads bl = GTF(blackListFileName) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptoolsintervals/parse.py", line 584, in __init__ fp = openPossiblyCompressed(fname) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptoolsintervals/parse.py", line 102, in openPossiblyCompressed with open(fname, "rb") as f: FileNotFoundError: [Errno 2] No such file or directory: '/grid/vakoc/data/Patrick/ChIP_seq/hg38.blacklit.bed' Traceback (most recent call last): File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/bin/bamCompare", line 12, in main(args) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/bamCompare.py", line 265, in main scale_factors = get_scale_factors(args, [stats1, stats2], [mapped1, mapped2]) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/bamCompare.py", line 214, in get_scale_factors bam1_mapped, _ = get_num_kept_reads(args, statsList[0]) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/getScaleFactor.py", line 197, in get_num_kept_reads blacklisted = utilities.bam_blacklisted_reads(bam_handle, args.ignoreForNormalization, File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptools/utilities.py", line 367, in bam_blacklisted_reads bl = GTF(blackListFileName) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptoolsintervals/parse.py", line 584, in __init__ fp = openPossiblyCompressed(fname) File "/grid/it/data/elzar/easybuild/software/deepTools/3.5.2-foss-2022a/lib/python3.10/site-packages/deeptoolsintervals/parse.py", line 102, in openPossiblyCompressed with open(fname, "rb") as f: FileNotFoundError: [Errno 2] No such file or directory: '/grid/vakoc/data/Patrick/ChIP_seq/hg38.blacklit.bed' usage: bamCompare -b1 treatment.bam -b2 control.bam -o log2ratio.bw bamCompare: error: unrecognized arguments: H3K27ac_hg38_sorted.bam H3K27ac_hg38_sorted.bw