How to get polished reads after Pilon has run?

[tayabsoomro]

Hi,

I ran Pilon using the following command:

pilon --genome $RUN7/all_contigs.fasta --bam $COMBINED/run7_raw.sorted.bam -Xmx1000G --output ./pilon.output --threads

The --genome option contains the draft assembly and the --bam option contains the alignment of nanopore reads with draft assembly.

I get the following output, but other than that, no other file/output is generated.

Pilon version 1.23 Mon Nov 26 16:04:05 2018 -0500
Genome: /.../all_contigs.fasta
Fixing snps, indels, gaps, local
Input genome size: 25498843
Scanning BAMs
/.../run7_raw.sorted.bam: 4327647 reads, 602982 filtered, 3329073 mapped, 0 proper, 0 stray, Unpaired 100% 6667+/-6403, max 25876 unpaired
Processing contig_11:1-1551425
Processing contig_16:1-892121
Processing contig_9:1-648972
Processing contig_18:1-3591697
Processing contig_6:1-724032
Processing contig_4:1-1278240
Processing contig_36:1-2675
Processing contig_14:1-741276
Processing contig_1:1-1124412
Processing contig_34:1-2175
contig_34:1-2175 log:
unpaired /.../run7_raw.sorted.bam: coverage 1
Total Reads: 2, Coverage: 1, minDepth: 5
Confirmed 0 of 2175 bases (0.00%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 0 small deletions totaling 0 bases
Finished processing contig_34:1-2175
Processing contig_3:1-1441884
contig_36:1-2675 log:
unpaired /.../run7_raw.sorted.bam: coverage 311
Total Reads: 547, Coverage: 311, minDepth: 31
Confirmed 28 of 2675 bases (1.05%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 1 small deletions totaling 1 bases
Finished processing contig_36:1-2675
Processing contig_17:1-1315789
contig_9:1-648972 log:
unpaired /.../run7_raw.sorted.bam: coverage 805
Total Reads: 81079, Coverage: 805, minDepth: 81
Confirmed 52 of 648972 bases (0.01%)
Corrected 2 snps; 1 ambiguous bases; corrected 0 small insertions totaling 0 bases, 730 small deletions totaling 1013 bases
# Attempting to fix local continuity breaks
# fix break: contig_9:6057 0 -0 +0 NoSolution
# fix break: contig_9:6625 0 -0 +0 NoSolution
# fix break: contig_9:16049 0 -0 +0 NoSolution
.
.
.
Finished processing contig_9:1-648972
Processing contig_29:1-924357
contig_14:1-741276 log:
unpaired /.../run7_raw.sorted.bam: coverage 825
Total Reads: 92429, Coverage: 825, minDepth: 83
Confirmed 32 of 741276 bases (0.00%)
Corrected 1 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 803 small deletions totaling 1097 bases
Large collapsed region: contig_14:729831-741025 size 11195
# Attempting to fix local continuity breaks
# fix break: contig_14:4736 0 -0 +0 NoSolution
# fix break: contig_14:7772 0 -0 +0 NoSolution
.
.
.
.Finished processing contig_14:1-741276
Processing contig_5:1-7396
contig_5:1-7396 log:
unpaired /.../run7_raw.sorted.bam: coverage 10
Total Reads: 97, Coverage: 10, minDepth: 5
Confirmed 2807 of 7396 bases (37.95%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 1 small deletions totaling 2 bases
# Attempting to fix local continuity breaks
# fix break: contig_5:1945 0 -0 +0 NoSolution
# fix break: contig_5:2353-3047 0 -0 +0 NoSolution
# fix break: contig_5:3796-3805 0 -0 +0 NoSolution
# fix break: contig_5:4226-4853 0 -0 +0 NoSolution
# fix break: contig_5:5105-5333 0 -0 +0 NoSolution
# fix break: contig_5:5944 0 -0 +0 NoSolution
.
.
.
Finished processing contig_16:1-892121
Processing contig_33:1-9973
contig_33:1-9973 log:
unpaired /.../run7_raw.sorted.bam: coverage 156
Total Reads: 640, Coverage: 156, minDepth: 16
Confirmed 402 of 9973 bases (4.03%)
Corrected 0 snps; 0 ambiguous bases; corrected 0 small insertions totaling 0 bases, 3 small deletions totaling 5 bases
# Attempting to fix local continuity breaks
# fix break: contig_33:4363 0 -0 +0 NoSolution
Finished processing contig_33:1-9973
Processing contig_2:1-1372629
Job done

How do I know if the command ran successfully. If so, where do I get the polished assembly?

[hughcross]

I have the same problem. No output was generated.

[sadikmu]

Hi @tayabsoomro and @hughcross

I am having the same problem too. Any suggestion please if you've got it resolved?

[XuhangWu]

I am also facing the same problem. Has anyone found out how to solve it?