Core dumped issue

[yterrat]

First thanks for the nice program you provide to the scientific community. I have a bug while running Nonpareil :./nonpareil -s 20_1M.fastq -f fastq -t 12 -R 20000 -b test Nonpareil v2.2 [ 0.0] Counting sequences [ 0.0] The file 20_1M.fastq.enve-seq.18514 was just created [ 0.0] Longest sequence has 150 characters [ 0.0] Average read length is 150.000000 bp [ 0.0] Reading file with 250000 sequences [ 0.0] Sequences to store in 19997.909180Mb free: 137054208 (54821.683200%) [ 0.0] Querying library with 0.004000 times the total size (1000 seqs) [ 0.0] Building query set at 20_1M.fastq.enve-seq.18514.subsample.18514 [ 0.0] Query set built with 1004 sequences [ 0.0] Designing the blocks scheme for 250000 sequences [ 0.0] Qry blocks:1, seqs/block:1004 [ 0.0] Sbj blocks:1, seqs/block:250000 [ 0.0] Mating sequences in 1 by 1 blocks [ 0.0] Allocating ~0 Mib in RAM for block qry:1 [ 0.0] Allocating ~35 Mib in RAM for block sbj:1 [ 0.0] Computing block 1/1 [ 0.0] Launching parallel comparisons to 12 threads [ 110.8] Thread 0 completed 84 comparisons, joining results
[ 111.4] Thread 1 completed 84 comparisons, joining results
[ 111.5] Thread 4 completed 84 comparisons, joining results
[ 112.6] Thread 3 completed 84 comparisons, joining results
[ 113.2] Thread 2 completed 84 comparisons, joining results
[ 113.7] Thread 5 completed 84 comparisons, joining results
[ 117.7] Thread 11 completed 80 comparisons, joining results
[ 119.4] Thread 8 completed 84 comparisons, joining results
[ 119.6] Thread 6 completed 84 comparisons, joining results
[ 119.7] Thread 10 completed 84 comparisons, joining results
[ 119.7] Thread 7 completed 84 comparisons, joining results
[ 119.8] Thread 9 completed 84 comparisons, joining results
[ 119.8] Sub-sampling library Erreur de segmentation (core dumped)0%

Any ideas of what could be wrong ?

All the best from Montréal,

Y.

[lmrodriguezr]

Salut Y ! There is a number of glitches that I corrected in v2.3 and v2.3r2. I would like to look into your particular problem more in detail, but please try first updating to the latest version (git pull; rm nonpareil; make && make install) and testing again. I suspect there is a wild bug I didn't catch yet, but first I want to make sure it's not one of the previously solved issues.

On a side note: I see that the maximum read length is equal to the average read length in your test. Although that's possible (with an exceptionally good run), I suspect you didn't trim/filter your reads beforehand. Check out preprocessing reads in the documentation.

Best, Miguel

[yterrat]

Many thanks for your really fast answer. I did not trimmed the sequences as it was just a trial but I will follow your instructions. I will try to download the last version first. I was sure it was the last update... All the best from Montréal !

[lmrodriguezr]

I'm sure the no-trimming won't affect in this way (I'll just cause unreliable estimations).

[lmrodriguezr]

This error was reproduced by @lhor, I'm investigating.

[lhor]

that's correct @lmrodriguezr, let me know if you need more details (although, I get the exact same error reported here).

[yterrat]

Make a new run with the v2.302 version and get the same final error after the "sub-sampling library" step : Sub-sampling library Erreur de segmentation (core dumped)0%

Thank you for your kind attention !

[lmrodriguezr]

@lhor @BinfYT please test v2.303 in your machines. The segmentation error I reproduced was solved, but I want to confirm it was the only problem around there.

Thanks!

[yterrat]

It works perfectly. Thanks for your responsiveness !