Starting Polypolish (2022-09-14 14:06:52)
    Polypolish is a tool for polishing genome assemblies with short reads.
Unlike other tools in this category, Polypolish uses SAM files where each read
has been aligned to all possible locations (not just a single best location).
This allows it to repair errors in repeat regions that other alignment-based
polishers cannot fix.

Polypolish version: 0.5.0

Input assembly:
  input_data

Input short-read alignments:
  paired_collection/forward_input0forward_filtered.sam
  paired_collection/forward_input1forward_filtered.sam
  paired_collection/forward_input2forward_filtered.sam
  paired_collection/reverse_input0reverse_filtered.sam
  paired_collection/reverse_input1reverse_filtered.sam
  paired_collection/reverse_input2reverse_filtered.sam

Settings:
  --fraction_invalid 0.2
  --fraction_valid 0.5
  --max_errors 10
  --min_depth 5
  --debug /tmp/tmpacfaqf7s/job_working_directory/000/20/outputs/galaxy_dataset_a267d150-242f-43e2-b91d-3a230d92a70f.dat


Loading assembly (2022-09-14 14:06:52)
contig00001 (5,513 bp)
contig00002 (3,532 bp)
contig00003 (3,227 bp)
contig00004 (3,138 bp)


Loading alignments (2022-09-14 14:06:52)
paired_collection/forward_input0forward_filtered.sam: 75 alignments from 72 reads
paired_collection/forward_input1forward_filtered.sam: 75 alignments from 72 reads
paired_collection/forward_input2forward_filtered.sam: 75 alignments from 72 reads
paired_collection/reverse_input0reverse_filtered.sam: 64 alignments from 62 reads
paired_collection/reverse_input1reverse_filtered.sam: 64 alignments from 62 reads
paired_collection/reverse_input2reverse_filtered.sam: 64 alignments from 62 reads

Filtering for high-quality end-to-end alignments:
  144 alignments kept
  273 alignments discarded


Polishing assembly sequences (2022-09-14 14:06:52)
    For each position in the assembly, Polypolish determines the read depth
at that position and collects all aligned bases. It then polishes the assembly
by looking for positions where the pileup unambiguously supports a different
sequence than the assembly.

Polishing contig00001 (5,513 bp):
  mean read depth: 5.7x
  1,751 bp have a depth of zero (68.2387% coverage)
  0 positions changed (0.0000% of total positions)
  estimated pre-polishing sequence accuracy: 100.0000%

Polishing contig00002 (3,532 bp):
  mean read depth: 2.0x
  2,280 bp have a depth of zero (35.4473% coverage)
  0 positions changed (0.0000% of total positions)
  estimated pre-polishing sequence accuracy: 100.0000%

Polishing contig00003 (3,227 bp):
  mean read depth: 0.8x
  2,652 bp have a depth of zero (17.8184% coverage)
  0 positions changed (0.0000% of total positions)
  estimated pre-polishing sequence accuracy: 100.0000%

Polishing contig00004 (3,138 bp):
  mean read depth: 0.6x
  2,699 bp have a depth of zero (13.9898% coverage)
  0 positions changed (0.0000% of total positions)
  estimated pre-polishing sequence accuracy: 100.0000%


Finished! (2022-09-14 14:06:52)
Polished sequence (to stdout):
  contig00001_polypolish (5,513 bp)
  contig00002_polypolish (3,532 bp)
  contig00003_polypolish (3,227 bp)
  contig00004_polypolish (3,138 bp)

Per-base debugging info written to /tmp/tmpacfaqf7s/job_working_directory/000/20/outputs/galaxy_dataset_a267d150-242f-43e2-b91d-3a230d92a70f.dat
Time to run: 0:00:00.024238