--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/logfile_test_4.log	Thu Sep 22 07:51:48 2022 +0000
@@ -0,0 +1,90 @@
+
+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
+