about the pipe from bowtie2 to samtools view

[Lv Ray]

Hi, dears.
Last night I ran the code:
nohup bowtie2 -x Ref_index -U ER172.fastq --local -D 20 -R 3 -N 1 -L 21 -i S,1,0.75 -p 15 | samtools view -bS -t Ref.fa.fai - > ER172.bam
Unfortunately，I got:
[sam_read1] reference ' 1482179 (26.27%) aligned 0 times' is recognized as '*'.Parse error at line 5645986: invalid CIGAR character

I tried to view the line 5645986 from fastq, but I failed to find the reason. Maybe I need to view it from .sam file, but I used the pipe with no .sam file.
Can you help me ?

[sphil]

from bowtie manual:
Alignment summmary

When Bowtie 2 finishes running, it prints messages summarizing what happened. These messages are printed to the "standard error" ("stderr") filehandle. For datasets consisting of unpaired reads, the summary might look like this:

20000 reads; of these:
20000 (100.00%) were unpaired; of these:
1247 (6.24%) aligned 0 times
18739 (93.69%) aligned exactly 1 time
14 (0.07%) aligned >1 times
93.77% overall alignment rate

For datasets consisting of pairs, the summary might look like this:

10000 reads; of these:
10000 (100.00%) were paired; of these:
650 (6.50%) aligned concordantly 0 times
8823 (88.23%) aligned concordantly exactly 1 time
527 (5.27%) aligned concordantly >1 times
----
650 pairs aligned concordantly 0 times; of these:
34 (5.23%) aligned discordantly 1 time
----
616 pairs aligned 0 times concordantly or discordantly; of these:
1232 mates make up the pairs; of these:
660 (53.57%) aligned 0 times
571 (46.35%) aligned exactly 1 time
1 (0.08%) aligned >1 times
96.70% overall alignment rate

The indentation indicates how subtotals relate to totals.

---

I guess you are capturing this because of the nohup command....

[Lv Ray]

Thanks,sphil.
how about the error :.Parse error at line 5645986: invalid CIGAR character

[dpryan]

The error is caused by redirecting stderr to samtools. Don't do that.

[Lv Ray]

Thank you！
maybe it's best to me that I will not use the pipe.