--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/logfile_test_1.log	Thu Sep 22 07:51:48 2022 +0000
@@ -0,0 +1,80 @@
+
+Starting Polypolish (2022-09-14 14:05:31)
+    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:
+  /tmp/tmpacfaqf7s/files/0/e/6/dataset_0e63b923-512f-4f9b-b6fa-8c6ead4a29db.dat
+
+Settings:
+  --fraction_invalid 0.2
+  --fraction_valid 0.5
+  --max_errors 10
+  --min_depth 5
+  --debug /tmp/tmpacfaqf7s/job_working_directory/000/3/outputs/galaxy_dataset_0fff3b6a-ddab-4999-b6a2-78a6dff1a4bc.dat
+
+
+Loading assembly (2022-09-14 14:05:31)
+contig00001 (5,513 bp)
+contig00002 (3,532 bp)
+contig00003 (3,227 bp)
+contig00004 (3,138 bp)
+
+
+Loading alignments (2022-09-14 14:05:31)
+/tmp/tmpacfaqf7s/files/0/e/6/dataset_0e63b923-512f-4f9b-b6fa-8c6ead4a29db.dat: 75 alignments from 72 reads
+
+Filtering for high-quality end-to-end alignments:
+  25 alignments kept
+  50 alignments discarded
+
+
+Polishing assembly sequences (2022-09-14 14:05:31)
+    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: 1.0x
+  2,496 bp have a depth of zero (54.7252% coverage)
+  0 positions changed (0.0000% of total positions)
+  estimated pre-polishing sequence accuracy: 100.0000%
+
+Polishing contig00002 (3,532 bp):
+  mean read depth: 0.3x
+  2,629 bp have a depth of zero (25.5663% coverage)
+  0 positions changed (0.0000% of total positions)
+  estimated pre-polishing sequence accuracy: 100.0000%
+
+Polishing contig00003 (3,227 bp):
+  mean read depth: 0.2x
+  2,818 bp have a depth of zero (12.6743% coverage)
+  0 positions changed (0.0000% of total positions)
+  estimated pre-polishing sequence accuracy: 100.0000%
+
+Polishing contig00004 (3,138 bp):
+  mean read depth: 0.1x
+  2,842 bp have a depth of zero (9.4328% coverage)
+  0 positions changed (0.0000% of total positions)
+  estimated pre-polishing sequence accuracy: 100.0000%
+
+
+Finished! (2022-09-14 14:05:31)
+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/000/3/outputs/galaxy_dataset_0fff3b6a-ddab-4999-b6a2-78a6dff1a4bc.dat
+Time to run: 0:00:00.029839
+