Bismark Bug v0.14.4 --remove_spaces in bismark_methylation_extractor.
I think there is some bugs in the option of --remove_spaces in bismark_methylation_extractor.
bismark_methylation_extractor --single-end --bedGraph --counts --ignore 3 --buffer_size 10G --remove_spaces --zero_based --comprehensive --output ../methyfreq ../bam/ENCFF000LWO_trimmed.fq_bismark_bt2.bam
The error is as the following:
Changed directory to /media/LTS_33T/SG_LTS33T/monod/haib/methyfreq/
Now replacing whitespaces in the sequence ID field of the Bismark methylation extractor output /media/LTS_33T/SG_LTS33T/monod/haib/methyfreq/CpG_context_ENCFF000LWP_trimmed.fq_bismark_bt2.txt prior to bedGraph conversion
Couldn't write to file /media/LTS_33T/SG_LTS33T/monod/haib/methyfreq/CpG_context_ENCFF000LWP_trimmed.fq_bismark_bt2.txt.spaces_removed.txt: No such file or directory
Finished BedGraph conversion ...
bismark_methylation_extractor --single-end --bedGraph --counts --ignore 3 --buffer_size 10G --remove_spaces --zero_based --comprehensive --output ../methyfreq ../bam/ENCFF000LWO_trimmed.fq_bismark_bt2.bam
The error is as the following:
Changed directory to /media/LTS_33T/SG_LTS33T/monod/haib/methyfreq/
Now replacing whitespaces in the sequence ID field of the Bismark methylation extractor output /media/LTS_33T/SG_LTS33T/monod/haib/methyfreq/CpG_context_ENCFF000LWP_trimmed.fq_bismark_bt2.txt prior to bedGraph conversion
Couldn't write to file /media/LTS_33T/SG_LTS33T/monod/haib/methyfreq/CpG_context_ENCFF000LWP_trimmed.fq_bismark_bt2.txt.spaces_removed.txt: No such file or directory
Finished BedGraph conversion ...