Question: HISAT2- (ERR): hisat2-align exited with value 134
0
gravatar for Chvatil
4 weeks ago by
Chvatil50
Chvatil50 wrote:

Hello I'm using hisat2 version 2-2.1.0

I use hisat2 in order to map fastq reads into my assembly.fa file.

here is the command I use :

#build index
$HISAT2/hisat2-build assembly.fa mapping_index

#mapping
$HISAT2/hisat2 -k 1  -x mapping_index -1 $READS1a,$READS1b,$READS1c,$READS1d -2 $READS2a,$READS2b,$READS2c,$READS2d | $SAMTOOLS/samtools view -o mapping_assembly.bam

So the index files seems to be wrote correctly but the mapping process raise an error message at the end, ( it runs and fil a .bam file till I get this error message )

Settings:
  Output files: "mapping_index.*.ht2"
  Line rate: 6 (line is 64 bytes)
  Lines per side: 1 (side is 64 bytes)
  Offset rate: 4 (one in 16)
  FTable chars: 10
  Strings: unpacked
  Local offset rate: 3 (one in 8)
  Local fTable chars: 6
  Local sequence length: 57344
  Local sequence overlap between two consecutive indexes: 1024
  Endianness: little
  Actual local endianness: little
  Sanity checking: disabled
  Assertions: disabled
  Random seed: 0
  Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
  Assembly.fa
Reading reference sizes
  Time reading reference sizes: 00:00:50
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
  Time to join reference sequences: 00:00:08
  Time to read SNPs and splice sites: 00:00:01
Using parameters --bmax 67648278 --dcv 1024
  Doing ahead-of-time memory usage test
  Passed!  Constructing with these parameters: --bmax 67648278 --dcv 1024
Constructing suffix-array element generator
Converting suffix-array elements to index image
Allocating ftab, absorbFtab
Entering GFM loop
Exited GFM loop
fchr[A]: 0
fchr[C]: 110541071
fchr[G]: 181767611
fchr[T]: 252795800
fchr[$]: 360790813
Exiting GFM::buildToDisk()
Returning from initFromVector
Wrote 144743723 bytes to primary GFM file: mapping_index.1.ht2
Wrote 90197708 bytes to secondary GFM file: mapping_index.2.ht2
Re-opening _in1 and _in2 as input streams
Returning from GFM constructor
Returning from initFromVector
Wrote 5392736659 bytes to primary GFM file: mapping_index.5.ht2
Wrote 90996464 bytes to secondary GFM file: mapping_index.6.ht2
Re-opening _in5 and _in5 as input streams
Returning from HierEbwt constructor
Headers:
    len: 360790813
    gbwtLen: 360790814
    nodes: 360790814
    sz: 90197704
    gbwtSz: 90197704
    lineRate: 6
    offRate: 4
    offMask: 0xfffffff0
    ftabChars: 10
    eftabLen: 0
    eftabSz: 0
    ftabLen: 1048577
    ftabSz: 4194308
    offsLen: 22549426
    offsSz: 90197704
    lineSz: 64
    sideSz: 64
    sideGbwtSz: 48
    sideGbwtLen: 192
    numSides: 1879119
    numLines: 1879119
    gbwtTotLen: 120263616
    gbwtTotSz: 120263616
    reverse: 0
    linearFM: Yes
Total time for call to driver() for forward index: 00:22:47
Saw ASCII character -8 but expected 33-based Phred qual.
terminate called after throwing an instance of 'int'
Aborted
(ERR): hisat2-align exited with value 134

My disk space is not full, so it cannot come from that.

Does someone have an idea ?

mapping hisat • 136 views
ADD COMMENTlink modified 4 weeks ago by MatthewP780 • written 4 weeks ago by Chvatil50
2
gravatar for MatthewP
4 weeks ago by
MatthewP780
China
MatthewP780 wrote:

Hello, the error message "Saw ASCII character -8 but expected 33-based Phred qual" indicates the problem may relative to fastq quality system(Phred+33 or Phred+64). The default value of hisat2 is Phred+33, you can use --phred64 to set to Phred+64, this may solve your problem.

ADD COMMENTlink written 4 weeks ago by MatthewP780

Thank you I will try that

ADD REPLYlink written 4 weeks ago by Chvatil50

Well I changed it and got the following message now ...

Saw ASCII character 35 but expected 64-based Phred qual.
Try not specifying --solexa1.3-quals/--phred64-quals.
terminate called after throwing an instance of 'int'
Aborted
(ERR): hisat2-align exited with value 134
ADD REPLYlink written 4 weeks ago by Chvatil50

Can you post first record(4 lines) of your fastq file?

ADD REPLYlink written 4 weeks ago by MatthewP780

OK I found the issue, it came from the fact that some fastq.gz files had .1 extension after the .gz.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by Chvatil50
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 996 users visited in the last hour