sh: 1: /usr/bin/hisat2_read_statistics.py: not found - Warning or Error?

Question

[marcelolaia]

Hi, I run the hisat2 like this:

$ for f in `ls ./raw_data/*.fq.gz | sed 's/_[12].fq.gz//g' | sort -u`; do hisat2 -p 1 -x ./HiSat2/GCA_000389695.3_Cfim3.0_genomic_hisat2 -1 ${f}_1.fq.gz -2 ${f}_2.fq.gz -S ${f}.sam; done
$

and got this message:

sh: 1: /usr/bin/hisat2_read_statistics.py: not found

Is this message an error or a warning? Have I do it important? Or is it harmless?

I got an output, like this:

9719652 reads; of these:
  9719652 (100.00%) were paired; of these:
    9633706 (99.12%) aligned concordantly 0 times
    85859 (0.88%) aligned concordantly exactly 1 time
    87 (0.00%) aligned concordantly >1 times
    ----
    9633706 pairs aligned concordantly 0 times; of these:
      366 (0.00%) aligned discordantly 1 time
    ----
    9633340 pairs aligned 0 times concordantly or discordantly; of these:
      19266680 mates make up the pairs; of these:
        19244902 (99.89%) aligned 0 times
        21695 (0.11%) aligned exactly 1 time
        83 (0.00%) aligned >1 times
1.00% overall alignment rate

My system:

$ uname -a
Linux marcelo 5.6.0-2-amd64 #1 SMP Debian 5.6.14-1 (2020-05-23) x86_64 GNU/Linux
$ hisat2 --version
/usr/bin/hisat2-align-s version 2.2.0
64-bit
Built on Debian
06 May 2020
Compiler: gcc version 9.3.0 (Debian 9.3.0-11) 
Options: -O3   -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
$ python --version
Python 2.7.18
$

Thank you!

[Asaf]

It seems like you got the mapping. I would recommend using pipeline manager instead of a for loop for the execution though.