--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/groot.log	Fri Oct 18 08:19:42 2024 +0000
@@ -0,0 +1,77 @@
+2024/10/15 11:32:06 i am groot (version 1.1.2)
+2024/10/15 11:32:06 starting the index subcommand
+2024/10/15 11:32:06 checking parameters...
+2024/10/15 11:32:06 	directory containing MSA files: arg-annot.90
+2024/10/15 11:32:06 	number of MSA files: 12
+2024/10/15 11:32:06 	processors: 1
+2024/10/15 11:32:06 	k-mer size: 41
+2024/10/15 11:32:06 	sketch size: 21
+2024/10/15 11:32:06 	graph window size: 150
+2024/10/15 11:32:06 	num. partitions: 8
+2024/10/15 11:32:06 	max. K: 4
+2024/10/15 11:32:06 	max. sketch span: 30
+2024/10/15 11:32:06 initialising indexing pipeline...
+2024/10/15 11:32:06 	initialising the processes
+2024/10/15 11:32:06 	connecting data streams
+2024/10/15 11:32:06 	number of processes added to the indexing pipeline: 3
+2024/10/15 11:32:06 creating graphs, sketching traversals and indexing...
+2024/10/15 11:32:07 	number of groot graphs built: 12
+2024/10/15 11:32:07 		graphs sketched: 12
+2024/10/15 11:32:07 		graph windows processed: 35387
+2024/10/15 11:32:07 		mean approximate distinct sketches per graph: 29.20%
+2024/10/15 11:32:07 	number of sketches added to the LSH Ensemble index: 5155
+2024/10/15 11:32:07 writing index files in "grootIndex"...
+2024/10/15 11:32:07 finished in 685.70958ms
+2024/10/15 11:32:39 i am groot (version 1.1.2)
+2024/10/15 11:32:39 starting the sketch subcommand
+2024/10/15 11:32:39 checking parameters...
+2024/10/15 11:32:39 terminated
+
+ERROR --> file does not exist: argannot-150bp-10000-reads.fq.gz
+
+2024/10/15 11:33:04 i am groot (version 1.1.2)
+2024/10/15 11:33:04 starting the sketch subcommand
+2024/10/15 11:33:04 checking parameters...
+2024/10/15 11:33:04 	minimum k-mer coverage: 1
+2024/10/15 11:33:04 	processors: 1
+2024/10/15 11:33:04 	input file: argannot_light-150bp-10000-reads.fq.gz
+2024/10/15 11:33:04 loading the index information...
+2024/10/15 11:33:04 	k-mer size: 41
+2024/10/15 11:33:04 	sketch size: 21
+2024/10/15 11:33:04 	window size used in indexing: 150
+2024/10/15 11:33:04 loading the graphs...
+2024/10/15 11:33:04 	number of variation graphs: 12
+2024/10/15 11:33:04 rebuilding the LSH Ensemble...
+2024/10/15 11:33:04 	containment threshold: 0.99
+2024/10/15 11:33:04 initialising alignment pipeline...
+2024/10/15 11:33:04 	initialising the processes
+2024/10/15 11:33:04 	connecting data streams
+2024/10/15 11:33:04 	number of processes added to the alignment pipeline: 5
+2024/10/15 11:33:04 now streaming reads...
+2024/10/15 11:33:04 	number of reads received from input: 5000
+2024/10/15 11:33:04 	mean read length: 150
+2024/10/15 11:33:04 	number of reads sketched: 5000
+2024/10/15 11:33:04 	total number of unmapped reads: 4873
+2024/10/15 11:33:04 	total number of mapped reads: 127
+2024/10/15 11:33:04 		mapped to one graph: 127
+2024/10/15 11:33:04 		mapped to multiple graphs: 0
+2024/10/15 11:33:04 	total number of exact alignments: 954
+2024/10/15 11:33:04 processing graphs...
+2024/10/15 11:33:04 	total number of k-mers projected onto graphs: 10890
+2024/10/15 11:33:04 	graph 7 has 4 remaining paths after weighting and pruning
+2024/10/15 11:33:04 	- [*argannot~~~(Bla)cfxA2~~~AF504910:1-966]
+2024/10/15 11:33:04 	- [argannot~~~(Bla)cfxA4~~~AY769933:1-966]
+2024/10/15 11:33:04 	- [argannot~~~(Bla)cfxA5~~~AY769934:28-993]
+2024/10/15 11:33:04 	- [argannot~~~(Bla)cfxA~~~U38243:150-1115]
+2024/10/15 11:33:04 	total number of graphs pruned: 12
+2024/10/15 11:33:04 	total number of graphs remaining: 1
+2024/10/15 11:33:04 	total number of possible haplotypes found: 4
+2024/10/15 11:33:04 saving graphs...
+2024/10/15 11:33:04 finished in 223.277576ms
+2024/10/15 11:33:15 i am groot (version 1.1.2)
+2024/10/15 11:33:15 starting the report subcommand
+2024/10/15 11:33:15 checking parameters...
+2024/10/15 11:33:15 	BAM file: groot.bam
+2024/10/15 11:33:15 	coverage cutoff: 0.97
+2024/10/15 11:33:15 	processors: 1
+2024/10/15 11:33:15 finished