I am using MALT (version 0.4.1, built 24 May 2018) to align my DNA reads to a reference database that was created with MALT. After analyzing the alignments using MEGAN tool, I am filtering the SAM files that were created by MALT by reference and read names.
To continue my analysis, I am converting the filtered SAM files to BAM format using SAMtools. But in some files I got this error:
[E::sam_parse1] CIGAR and query sequence are of different length
[W::sam_read1] Parse error at line 493
[main_samview] truncated file.
Here is a subset of the entries that could help to replicate this problem and the options that I used for MALT:
-at SemiGlobal -ssc -m BlastN
subset_cigar.sam (409.8 KB)