Hi all,

I am currently analyzing a pop-seq dataset and encounter some problems when trying to convert my .sam file into a .bam file.

Here is what i did so far:

1) I indexed the genome using Bowtie2 v. 2.4.2

bowtie2-build GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna philip_indexed_genome

2) I then mapped the reads using Bowtie2 v. 2.4.2

bowtie2 -x philip_indexed_genome -1 b2_HCHKKDSXY_L1_1.fq -2 b2_HCHKKDSXY_L1_2.fq -S b2_bowtie2_to_indexed_genome.sam

When looking at the output, the mapping seems to have been successful:

302546831 reads; of these:

302546831 (100.00%) were paired; of these:

31467015 (10.40%) aligned concordantly 0 times

217839984 (72.00%) aligned concordantly exactly 1 time

53239832 (17.60%) aligned concordantly >1 times

---

31467015 pairs aligned concordantly 0 times; of these:

10785696 (34.28%) aligned discordantly 1 time

---

20681319 pairs aligned 0 times concordantly or discordantly; of these:

41362638 mates make up the pairs; of these:

26239879 (63.44%) aligned 0 times

7729764 (18.69%) aligned exactly 1 time

7392995 (17.87%) aligned >1 times

95.66% overall alignment rate

3) However, when trying to convert the resulting .sam file, into a .bam file using (I used samtools 1.9)

samtools view -Sb b2_bowtie2_to_indexed_genome.sam > b2_bowtie2_to_indexed_genome.bam

I get the following message:

[W::sam_read1] Parse error at line 545655373

[main_samview] truncated file.

I tried to look at that line using

sed -n 545655372p b2_bowtie2_to_indexed_genome.sam > output_from_sam2

but the output file is empty. Besides, I counted the number of rows in the sam file using

wc -l b2_bowtie2_to_indexed_genome.sam

and got

198853022

which is less than the line flagged as problematic.

Does anybody have an idea of what's going on? Thanks a lot Philip