samtools error caused by ncurses version information

[imogen-foote]

Thanks for your efforts putting this tool together. I previously had the workflow running using the following command nextflow run hoelzer/clean --input_type nano --input /path/to/file.fastq.gz --host eco --control dcs --output /path/to/fastq/clean_output -profile singularity

However I then tried to run it on the same fastq file adding in human as a host nextflow run hoelzer/clean --input_type nano --input /path/to/file.fastq.gz --host eco,hsa --control dcs --output /path/to/fastq/clean_output -profile singularity Ever since then I've had issues running the workflow regardless of whether I specify --host eco, --host eco,hsa or even just remove this line entirely (really all I want to do is remove the ONT DNA control sequence). I have also tried running on a different fastq file and get the same issue. The issues all seem to relate to samtools and the below message:

samtools: /opt/conda/bin/../lib/libtinfow.so.6: no version information available (required by samtools) samtools: /opt/conda/bin/../lib/libncursesw.so.6: no version information available (required by samtools) samtools: /opt/conda/bin/../lib/libncursesw.so.6: no version information available (required by samtools)

Is this an issue with the container image, or more likely something with my system? Thanks heaps in advance!

[hoelzer]

Hey @imogen-foote thanks for using the pipeline!

Can you please try using a latest release version of CLEAN? E.g.

nextflow pull hoelzer/clean
nextflow run hoelzer/clean -r v1.0.0-beta ...

If this still fails, please let us know which process is failing. Yes, maybe there is a problem with the samtools version in the container. Also, if you can provide the .nextflow.{log,err} information from the working directory of the failed process that usually helps to solve the problem.

thanks!

[imogen-foote]

Thanks for your response!

I tried running the latest version, but am still getting the error. The process that's failing is 'clean:minimap2'. There were no files in the working directory named .nextflow.{log,err} but I have pasted the contents of .command.log below (the contents of .command.err were identical to this as well). Hopefully this is the information that you're after.

[M::mm_idx_gen::0.005*2.75] collected minimizers
[M::mm_idx_gen::0.006*2.57] sorted minimizers
[M::main::0.006*2.57] loaded/built the index for 1 target sequence(s)
[M::mm_mapopt_update::0.006*2.53] mid_occ = 10
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 1
[M::mm_idx_stat::0.006*2.51] distinct minimizers: 663 (99.25% are singletons); average occurrences: 1.008; average spacing: 5.370; total length: 3587
samtools: /opt/conda/bin/../lib/libtinfow.so.6: no version information available (required by samtools)
samtools: /opt/conda/bin/../lib/libncursesw.so.6: no version information available (required by samtools)
samtools: /opt/conda/bin/../lib/libncursesw.so.6: no version information available (required by samtools)
[M::worker_pipeline::48.706*1.00] mapped 67360 sequences
[M::worker_pipeline::98.420*1.00] mapped 70975 sequences
[M::worker_pipeline::147.669*1.00] mapped 68596 sequences
[M::worker_pipeline::197.191*1.00] mapped 67851 sequences
[M::worker_pipeline::245.776*1.00] mapped 69128 sequences
[M::worker_pipeline::294.519*1.00] mapped 68707 sequences
[M::worker_pipeline::345.825*1.00] mapped 70063 sequences
[M::worker_pipeline::394.619*1.00] mapped 68582 sequences
[M::worker_pipeline::448.032*1.00] mapped 77205 sequences
[M::worker_pipeline::465.817*1.00] mapped 24624 sequences
[M::worker_pipeline::495.401*0.98] mapped 67360 sequences
[M::worker_pipeline::516.764*0.96] mapped 70975 sequences
[M::worker_pipeline::538.277*0.94] mapped 68596 sequences
[M::worker_pipeline::560.460*0.92] mapped 67851 sequences
samtools view: writing to standard output failed
samtools view: error closing standard output: -1

Please let me know if there's any other information you need!

[hoelzer]

Hey, thanks! I think we identified the problem and need to switch to another container for minimap2: nanozoo/minimap2:2.26--d9ef6b6

We will let you know when there is a new version for testing.

[MarieLataretu]

HI @imogen-foote ,

I changed the minimap2 container (same version, but includes ncurses) - this should solve the problem!

The change is active in -r master or -r v1.0.0-beta.1. For v1.0.0-beta.1, please have a look at the changelog.

[imogen-foote]

Perfect, this is working for me now! Thank you