I am using opossum for pre-processing my rna-seq bam files for variant calling and I got some errors as below, could you please help me with what the error means and how to fix it.
ERROR: [E::hts_idx_push] Region 536872898..536872913 cannot be stored in a bai index. Try using a csi index with min_shift = 14, n_lvls >= 6 Traceback (most recent call last): File "/apps/opossum/0.2/Opossum.py", line 2074, in <module> main() File "/apps/opossum/0.2/Opossum.py", line 482, in main pysam.index(outputfile) File "/apps/python/2.7.13/lib/python2.7/site-packages/pysam/utils.py", line 75, in __call__ stderr)) pysam.utils.SamtoolsError: 'samtools returned with error 1: stdout=, stderr=samtools index: failed to create index for "A_genome_mapping_sample_1_secondroundAligned.opossum.output.bam": Numerical result out of rangen'
I am using opossum/0.2
Working on wheat samples with SE reads
Script used : Opossum.py --BamFile=calm.out.bam --SoftClipsExist=True --ProperlyPaired=False --OutFile=A_genome_mapping_sample_1_secondroundAligned.opossum.output.bam LOG.OUT is: Executing command [Opossum.py --BamFile=calm.out.bam --SoftClipsExist=True --ProperlyPaired=False --OutFile=A_genome_mapping_sample_1_secondroundAligned.opossum.output.bam]... 1A 2A 3A 4A 5A 6A 7A Number of discarded secondary reads: 251942224 Number of discarded unmapped reads: 0 Number of reads whose mate is unmapped: 0 Number of discarded reads whose mate has been mapped to a different chromosome: 0 Number of discarded reads whose mate has been mapped to junk: 0 Number of discarded read pairs that are pointing outwards: 0 Number of discarded reads where read and its mate have been mapped in the same direction: 0 Number of duplicate reads that have been merged into their non-duplicate counterpart: 0 Number of duplicate single reads that have been merged to their non-duplicate counterpart: 52426493 Number of discarded reads containing hard clips: 0 Number of discarded read pairs with base mismatch: 0 Number of discarded read pairs that are not aligned to same exons: 0 Number of discarded reads / read pairs having too low mapping quality (threshold 40): 47340861 Number of merged read pairs: 0 Number of split merged read pairs: 0 Number of independently treated read pairs: 0 Number of individual reads: 8059082 Number of leftover reads: 0 0 0 0 0 0 0 ...completed
Thanks in advance