abundance | samtools view: failed to add PG line to the header

[kunaljaani]

Hi! Francisco While running the -t abundance I am running into a problem with the sam to bam conversation due to a duplicate header. When I checked the grep "NODE_1753_length_683_cov_1.602310" FDSGM6.sam -c I found more than one occurrence.

Converting SAM to BAM with samtools view ... [W::sam_hdr_create] Duplicated sequence "NODE_1753_length_683_cov_1.602310" in file "FDSGM6.sam" [E::sam_hrecs_update_hashes] Duplicate entry "NODE_1753_length_683_cov_1.602310" in sam header samtools view: failed to add PG line to the header

I am also surprised to see that 2 of 35 samples ran fine. and if there was some issue it would have created problems for all the samples. So I am not able to figure out the issue. Could you please suggest a solution?

Thank you Kunal