No output files

[daisykuma22]

Dear developers,

Thank you for designing this excellent software. I have a question when running nonpareil. It seems everthing goes fine, but there is no output files. My code is 'nonpareil -b ./output-S11-0/ -s ./S11-0_1.fasta -f fasta -t 6 -R 400000 -T alignment'. The log is as below: Nonpareil v3.401 [ 0.0] Counting sequences [ 8.6] The file ./S11-0_1.fasta.enve-seq.37400 was just created [ 8.6] Longest sequence has 150 characters [ 8.6] Average read length is 149.336299 bp [ 8.6] Reading file with 90305189 sequences [ 8.6] Counting query sequences [ 8.6] Sequences to store in 399997.955078Mb free: -1553606656 (3035.662369%) [ 8.6] Querying library with 0.000011 times the total size (1000 seqs) [ 8.6] Building query set at ./S11-0_1.fasta.enve-seq.37400.subsample.37400 [ 8.9] Query set built with 989 sequences [ 8.9] Designing the blocks scheme for 90305189 sequences [ 8.9] Qry blocks:1, seqs/block:989 [ 8.9] Sbj blocks:1, seqs/block:90305189 [ 8.9] Mating sequences in 1 by 1 blocks [ 8.9] Allocating ~0 Mib in RAM for block qry:1 [ 8.9] Allocating ~12918 Mib in RAM for block sbj:1 [ 9.5] Computing block 1/1 [ 9.5] Launching parallel comparisons to 6 threads [ 17008.4] Thread 5 completed 164 comparisons, joining results
[ 17037.6] Thread 1 completed 165 comparisons, joining results
[ 17046.0] Thread 4 completed 165 comparisons, joining results
[ 17052.9] Thread 0 completed 165 comparisons, joining results
[ 17054.4] Thread 2 completed 165 comparisons, joining results
[ 17057.5] Thread 3 completed 165 comparisons, joining results
[ 17057.7] Sub-sampling library [ 17057.7] Evaluating consistency
[ 17057.7] Everything seems correct

Thanks for helping this out. Daisy

[lmrodriguezr]

Dear Daisy, thank you for your report.

Please note that the -b option serves to specify the base path of the output files, not just the directory. Since your value ends in /, the system will simply append the extensions (e.g., .npl and .npo) to that base path, creating hidden files within that directory. I suspect your files do exist, but they're hidden (because they start with .). You can check with less output-S11-0/.npo or ls -A output-S11-0/.

To solve the issue more generally, you can simply modify the command, for example using -b output-S11-0/np-out or something similar.

Please let us know if that solves the issue.

Best wishes, Miguel.

[daisykuma22]

Thank you, Miguel. Yes, all results exist in the form of hidden files. And the problem has been solved by using the suggested command.