adlyabdalla commented 1 year ago

I tried to use the tsggapcloser with pacbio and illumina reads with the following run

tgsgapcloser --scaff /work/CPB/PacBio_sequence/lordec_results/SPAdea_assembly_indo2/scaffolds.fasta --reads /work/CPB/PacBio_sequence/lordec_results/IPCL_S2M_pacbio-corrected_unclassified.fasta --output /home/adly/Desktop/TGS_gapcloser/output_tgsgaplcoser_S2M --ngs /work/CPB/NG-28892_CPB_20211126_lib548024_7771_2__1_trimmed_unclassified.fastq --ngs /work/CPB/NG-28892_CPB_20211126_lib548024_7771_2__2_trimmed_unclassified.fastq --pilon /usr/bin/pilon --samtools /usr/bin/samtools --java /usr/bin/java --tgstype pb --thread 24 --pilon_mem 500G --p_round 10

However I noticed that the final expected files are not found and the file is empty. I had a look on the tgsgapcloser sceript and found that the following step was failed

===================================== print_info_line " - iteration $round chunk $i - run pilon ... " $JAVA -Xmx$PILON_MEM -jar $PILON --fix all \ --genome $OUT_PREFIX.ont.$curr_tag.fasta --bam $OUT_PREFIX.sort.bam \ --output $OUT_PREFIX.ont.$curr_tag.pilon --outdir ./ \ --diploid --threads $THREAD >$OUT_PREFIX.$curr_tag.pilon.log 2>$OUT_PREFIX.pilon.$curr_tag.err || exit 1

remove used bam

                rm $OUT_PREFIX.sort.bam

            done
            print_info_line "   -   iteration $round end. "
        done
        date >>'done_step_3.B.1_tag'

==========================================

Can you kindly advise on how to fix this issue Best regards Adly

adlyabdalla commented 1 year ago

These mainly are the files produced by the run adly@bioanntu:~/Desktop/TGS_29082023$ ls -rtl total 17220107 -rw-rw-r-- 1 adly adly 196 Aug 29 11:39 output_tgs_S2M.seq_split.log -rw-rw-r-- 1 adly adly 1062685678 Aug 29 11:40 output_tgs_S2M.contig -rw-rw-r-- 1 adly adly 249636153 Aug 29 11:40 output_tgs_S2M.orignial_scaff_infos -rw-rw-r-- 1 adly adly 251671378 Aug 29 11:40 output_tgs_S2M.name_map -rw-rw-r-- 1 adly adly 81238 Aug 29 11:43 output_tgs_S2M.minimap2.01.log -rw-rw-r-- 1 adly adly 68521657 Aug 29 11:44 output_tgs_S2M.ont.fasta -rw-rw-r-- 1 adly adly 10852 Aug 29 11:44 output_tgs_S2M.cand.log -rw-rw-r-- 1 adly adly 22877708 Aug 29 11:44 output_tgs_S2M.ont.0.0.fasta -rw-rw-r-- 1 adly adly 22929229 Aug 29 11:44 output_tgs_S2M.ont.0.1.fasta -rw-rw-r-- 1 adly adly 22714720 Aug 29 11:44 output_tgs_S2M.ont.0.2.fasta -rw-rw-r-- 1 adly adly 71031236 Aug 29 11:44 output_tgs_S2M.mmi -rw-rw-r-- 1 adly adly 632 Aug 29 11:44 output_tgs_S2M.minimap2.02.0.0.log -rw-rw-r-- 1 adly adly 6183 Aug 29 11:57 output_tgs_S2M.minimap2.03.0.0.log -rw-rw-r-- 1 adly adly 0 Aug 29 12:01 output_tgs_S2M.samtool_01.0.0.log -rw-rw-r-- 1 adly adly 64 Aug 29 12:06 output_tgs_S2M.samtool_02.0.0.log -rw-rw-r-- 1 adly adly 15854624299 Aug 29 12:11 output_tgs_S2M.sort.bam -rw-rw-r-- 1 adly adly 0 Aug 29 12:11 output_tgs_S2M.samtool_03.0.0.log -rw-rw-r-- 1 adly adly 525216 Aug 29 12:12 output_tgs_S2M.sort.bam.bai -rw-rw-r-- 1 adly adly 49 Aug 29 12:12 output_tgs_S2M.pilon.0.0.err -rw-rw-r-- 1 adly adly 0 Aug 29 12:12 output_tgs_S2M.0.0.pilon.log -rw-rw-r-- 1 adly adly 0 Aug 29 13:34 output_tgs_S2M.ont.0.2.pilon.log -rw-rw-r-- 1 adly adly 140 Aug 29 13:34 output_tgs_S2M.ont.0.2.pilon.err

cchd0001 commented 1 year ago

Could you please provide the content of file output_tgs_S2M.ont.0.2.pilon.err ?

BGI-Qingdao / TGS-GapCloser

Pilon does not work within tgsgapclpser #69

remove used bam