Joining output blocks errors

[augustkx]

Hi developers,

diamond version 2.1.11

Command:

diamond blastx  -d psc.dmnd -q sample.fasta \
-o sample.hits.txt -F 15 --range-culling -k1 --range-cover 5 --iterate --id 80 --subject-cover 80 --masking 0 \
--outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore full_sseq qseq_translated --ext banded-slow --threads 30 

Processing query block 1, query iteration 4, reference block 19/19, shape 2/2, index chunk 2/4. Building reference seed array... [1.357s] Building query seed array... [0.003s] Computing hash join... [0.173s] Masking low complexity seeds... [0.001s] Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, query iteration 4, reference block 19/19, shape 2/2, index chunk 3/4. Building reference seed array... [1.313s] Building query seed array... [0.005s] Computing hash join... [0.177s] Masking low complexity seeds... [0.001s] Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, query iteration 4, reference block 19/19, shape 2/2, index chunk 4/4. Building reference seed array... [1.106s] Building query seed array... [0.003s] Computing hash join... [0.177s] Masking low complexity seeds... [0.001s] Searching alignments... [0.002s] Deallocating memory... [0s] Deallocating buffers... [0.005s] Clearing query masking... [0.008s] Opening temporary output file... [0.003s] Computing alignments... [0.136s] Deallocating reference... [0.007s] Loading reference sequences... [0s] Deallocating buffers... [0s] Aligned 4/4863 queries in this iteration, 4762/4863 total. Joining output blocks... Joining output blocks... Error:

I checked the memory is enough on the PC. Besides, I extracted a few contigs out of the metagenomic sample, then it runs without error on that newly created sample. I would appreciate it very much if you could help figure the issue out!

[bbuchfink]

There seems to be an incompatibility between frameshift alignment mode and --iterate. I will look into fixing this, for now you need to run without --iterate.

[augustkx]

Hi, Thanks for the quick response! But, when I removed the --iterate, there is the same error. I am attaching the problematic contig. For other contigs, the command works! Would appreciate it if you could help have a look!

[augustkx]

For a command without --iterate, the errors are similar, but with some extra information

Joining output blocks... Joining output blocks... Error: Error: free(): corrupted unsorted chunks

[aldertzomer]

I observe the same error in v 2.1.8 but not in v 2.0.15

Error: Sequence set index out of bounds.Error: Sequence set index out of bounds.

*** Error in `diamond': corrupted double-linked list: 0x000000000383df50 *** Error: Error: Error: Sequence set index out of bounds. Error: Error: Sequence set index out of bounds. Error: Sequence set index out of bounds. Error: Sequence set index out of bounds.

[aldertzomer]

2.1.11 gives no error in a simple test

[augustkx]

Update:

contig_1150.zip contig_3152.zip

Diamond Version 2.1.11: do work without "-- iterate" on contig_1150, but do not work with "-- iterate". do not work with or without "-- iterate" on contig_3152

Diamond Version v2.0.15.153: Works with "-- iterate" on both contig_3152 and contig_1150