Hi
I am running the bedtools bamtofastq for converting bam to splitted fastq (read1 and read2) files for paired end reads with an expected wall time of 24 hours and memory of 4000mb.
The input bam file is about 140 GB whereas the output file size has reached to merely 0.3 GB. So it seems that the tools is running too slow for some reason. The following is command was used. The input file has been sorted by samtools sort by names.
bedtools bamtofastq -i X_Sorted.bam -fq X.R1.fq -fq2 X.R2.fq
Any suggestions appreciated.
I am running the bedtools bamtofastq for converting bam to splitted fastq (read1 and read2) files for paired end reads with an expected wall time of 24 hours and memory of 4000mb.
The input bam file is about 140 GB whereas the output file size has reached to merely 0.3 GB. So it seems that the tools is running too slow for some reason. The following is command was used. The input file has been sorted by samtools sort by names.
bedtools bamtofastq -i X_Sorted.bam -fq X.R1.fq -fq2 X.R2.fq
Any suggestions appreciated.
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