Error: Encountered internal HISAT2 exception (#1)

Question

[kanchanpe]

Hello everyone! This hisat2 script is working well so far, but this time it couldn't work. And this Error came back. What should I deal with this error?

hisat2 -q -p 4 -x ~/mouse/mm10/genome -U ~/SRR5385271_trimmed.fq -S ~/SRR5385271.sam

Encountered internal HISAT2 exception (#1)
Command: /Users/myname/opt/anaconda3/bin/hisat2-align-s --wrapper basic-0 -q -p 4 -x /Users/myname/mouse/mm10/genome -S /Users/myname/SRR5385271.sam --read-lengths
134,144,122,123,138,146,142,124,128,133,143,141,139,156,140,137,153,132,125,115,136,120,154,148,131,150,145,130,155,147,151,118,129,117,107,162,159,121,127,119,157,169,167,135,164,161,160,111,165,149,126,116,113,172,158,152,112,168,166,177,171,110,179,114,170,173,182,163,99,187,181,104,108,186,109,103,97,105,176,184,175,174,106,100,95,178,101,183,79,89,180,93,195,83,82,91,85,76,190,185,73,200,198,197,193,189,96,67,194,78,30,191,102,59,55,20,98,88,61,54,52,36,24,86,66,44,19,213,206,192,80,69,63,51,209,199,196,188,94,70,41,35,27,81,48,46,26,92,77,74,64,50,38,217,72,62,58,57,53,42,39,28,18,202,87,71,68,37,203,201,90,49,29,22,214,84,65,56,32,25,21,215,34,220,210,208,60,40,33,31,216,211,204,75,43,219,23,47,212,205,45,218,230,207,229,222,226,221,228,236,234,231,244,233,232,227,225,237,223,249,247,238,235,224,250,248,240,239,263,262,257,254,246,242,258,256,253,245,243,241,280,277,274,267,265,255,252,251,301,288,285,283,271,269,266,264,260,259 -U /Users/myname/SRR5385271_trimmed.fq
(ERR): hisat2-align exited with value 1

Thank you for your cooperation.

[kanchanpe]

Thank you for your comment, genomax. This is the first time to use this website, I'm really glad everybody gives me the comment.

Answer 1

[ATpoint]

Ion-torrent reads with quite variable lengths. Maybe try and filter out very short reads, e.g. below 50bp before alignment.

Filtering Fastq Sequences Based On Lengths

[kanchanpe]

Thank you ATpoint! I did trim_galore beforehand, and removed below 20bp. After removing below 20bp, I did hisat2, but didn't work well.

[kanchanpe]

After trim_galore once again, hisat2 could work well! thank you for your advice. I really appreciate your comment!

[GenoMax]

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.

[ATpoint]

You're welcome, glad to hear it works now.