Hello! I am using samtools 1.2. When I run the index command like this:
/software/ensembl/funcgen/samtools index /lustre/scratch109/ensembl/funcgen/mn1/problem_bam/HEL9217:hist:BR2_WCE_3526_bwa_samse_1.unfiltered.bam samtools instantly terminates and generates no output. The exit code does not indicate a failure: echo $? 0 The bam file exists ls -lah /lustre/scratch109/ensembl/funcgen/mn1/problem_bam/HEL9217:hist:BR2_WCE_3526_bwa_samse_1.unfiltered.bam -rw-r--r-- 1 mn1 ebiusers 34G Nov 5 11:20 /lustre/scratch109/ensembl/funcgen/mn1/problem_bam/HEL9217:hist:BR2_WCE_3526_bwa_samse_1.unfiltered.bam and has headers and alignments in it. The bam file is generated by picard. Any idea what is going on? If the index command fails, I would expect to see an error message and a non zero exit code. Cheers, Michael. ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
