empty alignments_sorted.txt file while generating .hic file

[gitcruz]

Dear Marbl Team,

I've ran SALSA2 "successfully" on a genome assembly and scaffold N50 increased from 12Mb to 16Mb. In principle, everything looks good to me, except to what I considered a few warnings.

However, when I run the converter script to obtain the .hic file I am getting this error: "alignments_sorted.txt does not exist or does not contain any reads". I realized that the expected input file for converter.sh (i.e. alignment_iteration_1.bed) is actually empty. In fact, the .bed files for the three iterations are empty.

Do you know what could be the reason for this error? I would love to fix it without re-running SALSA2...

Cheers, F

[ghuryejay]

Did you run it with -m yes option? If not, then you can use the bed file that you provided to SALSA as an input to the .hic file creation script.

[gitcruz]

Hi Jay,

I certainly used the -m option to detect misassemblies with Arima Hi-C data. However, I made a mistake and I passed it twice (-m 1000 instead of -c 1000!!!)...but the program did not complain. I think I should re-run the scaffolding and compare the results. Please let me know your opinion on this.

Below the commandline used: python /home/devel/fcruz/SALSA2_Scaffolder/SALSA/run_pipeline.py -s 1340000000 -m 1000 -i 3 -a base_assembly.fa -l base_assembly.fa.fai -b Arima.1_2.hicup.bed -e GATC,GANTC -o out -m yes

Thanks, F

[sheinasim]

I'm experiencing this same issue. all my .bed files are empty so an alignments.txt is not written.