HISAT2 Empty summary file


I’ve tried to use HISAT2 on some of my Cutadapt output files, however the summary files from HISAT2 are always empty for my 48 files (i.e. 0 lines). I tried re-uploading my data and starting the analysis again, re-running HISAT2 multiple times, and even trying the files on the main galaxy site (which didn’t work either). Strangely, I got a ‘normal’ summary file just once after re-running HISAT2 on one file, but I deleted it thinking the problem had been solved to re-run the tool on all the samples again.

The genome file I’m aligning to has been successfully used in previous analyses, and the bam file from HISAT2 is fine for downstream analyses. Can anyone give me some insight on what I can do to fix this?

The stderr output is:
Output files: "genome..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:
Reading reference sizes
Time reading reference sizes: 00:00:03
Calculating joined length
Writing header
Reserving space for joined string
Joining reference sequences
Time to join reference sequences: 00:00:01
Time to read SNPs and splice sites: 00:00:00
Using parameters --bmax 48513222 --dcv 1024
Doing ahead-of-time memory usage test
Passed! Constructing with these parameters: --bmax 48513222 --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]: 72099572
fchr[G]: 129346882
fchr[T]: 186624101
fchr[$]: 258737183
Exiting GFM::buildToDisk()
Returning from initFromVector
Wrote 90670663 bytes to primary GFM file: genome.1.ht2
Wrote 64684300 bytes to secondary GFM file: genome.2.ht2
Re-opening _in1 and _in2 as input streams
Returning from GFM constructor
Returning from initFromVector
Wrote 117491317 bytes to primary GFM file: genome.5.ht2
Wrote 65856150 bytes to secondary GFM file: genome.6.ht2
Re-opening _in5 and _in5 as input streams
Returning from HierEbwt constructor
len: 258737183
gbwtLen: 258737184
nodes: 258737184
sz: 64684296
gbwtSz: 64684297
lineRate: 6
offRate: 4
offMask: 0xfffffff0
ftabChars: 10
eftabLen: 0
eftabSz: 0
ftabLen: 1048577
ftabSz: 4194308
offsLen: 16171074
offsSz: 64684296
lineSz: 64
sideSz: 64
sideGbwtSz: 48
sideGbwtLen: 192
numSides: 1347590
numLines: 1347590
gbwtTotLen: 86245760
gbwtTotSz: 86245760
reverse: 0
linearFM: Yes
Total time for call to driver() for forward index: 00:01:50
Error, fewer reads in file specified with -1 than in file specified with -2
terminate called after throwing an instance of ‘int’
(ERR): hisat2-align died with signal 6 (ABRT)
[bam_sort_core] merging from 40 files and 1 in-memory blocks…