Error occurred when filtering regions and sorting the BAM file

[sebel76]

Dear programmer,

I ran miR-PREFeR on sRNA from plant genomes. I test it first on B. distachyon (small genome). It ran smoothly and return results.

However, the program stoped and returned the following error when I ran it on H. vulgare (large genome) sRNA data. Please see the following message error:

2021-09-22 14:49:15,887 main: INFO ACTION is 'pipeline'. 2021-09-22 14:49:15,887 main: INFO Starting preparing data for the 'candidate' stage. 2021-09-22 14:49:15,887 main: INFO Getting genomic sequence lengths. 2021-09-22 14:49:15,888 main: INFO Converting SAM files to BAM files using samtools. 2021-09-22 14:49:15,888 main: INFO Converting ./SB2.sam 2021-09-22 14:49:22,500 main: INFO Converting ./SB4.sam 2021-09-22 14:49:28,670 main: INFO Converting ./SB5.sam 2021-09-22 14:49:34,866 main: INFO Converting ./SB8.sam 2021-09-22 14:49:40,807 main: INFO Converting ./SB9.sam 2021-09-22 14:49:46,769 main: INFO Converting ./SB10.sam 2021-09-22 14:49:50,802 main: INFO Converting ./SB11.sam 2021-09-22 14:50:01,317 main: INFO Converting ./SB13.sam 2021-09-22 14:50:09,948 main: INFO Converting ./SB15.sam 2021-09-22 14:50:17,878 main: INFO Converting ./SB96.sam 2021-09-22 14:50:24,138 main: INFO Converting ./SB98.sam 2021-09-22 14:50:29,155 main: INFO Converting ./SB100.sam 2021-09-22 14:50:50,929 main: INFO Converting ./SB101.sam 2021-09-22 14:51:10,677 main: INFO Converting ./SB102.sam 2021-09-22 14:51:34,991 main: INFO Combining multiple BAM files from multiple samples together.

[bam_sort_core] merging from 31 files and 1 in-memory blocks... [E::hts_idx_check_range] Region 536870918..536870942 cannot be stored in a bai index. Try using a csi index [E::sam_index] Read 'Hvu.pre-meiotic.rep1_r3035_x1' with ref_name='Hvu_2H', ref_length=665585731, flags=0, pos=536870919 cannot be indexed samtools index: failed to create index for "/Users/sbelanger/Documents/research/evolution.phasirna.anthers/srna/miR-PREFeR/mirna_prediction/Hvu_miRNA_miR-PREFeR_tmp/combined.filtered.sort.bam": Result too large Error occurred when filtering regions and sorting the BAM file

It seem to fail because of the BAM index with Samtools.

Any suggestion to solve the issue?

Best regard, Sébastien

[sebel76]

I solved my issue. The solution was to change the code for "samtools index -c" instead of "samtools index". Then, it work for all genome regardless the size from 0.385 Gb to 16.0 Gb.

Thanks, Sébastien