HISAT2- (ERR): hisat2-align exited with value 134

Question

[Chvatil]

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 ?

Answer 1

[MatthewP]

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.

[Chvatil]

Thank you I will try that

[Chvatil]

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

[MatthewP]

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

[Chvatil]

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