--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/maxbin2/log_file.txt	Tue Jul 15 09:51:56 2025 +0000
@@ -0,0 +1,138 @@
+MaxBin 2.2.7
+Input contig: /shared/ifbstor1/galaxy/datasets2/9/e/8/dataset_9e8cd0b6-cb85-4c33-98e5-9372b097fa40.dat
+out header: out
+Min contig length: 1000
+Max iteration: 50
+Probability threshold: 0.5
+Thread: 10
+Located reads file [HSMA33QY.fastq]
+Running Bowtie2 on reads file [HSMA33QY.fastq]...this may take a while...
+Searching against 107 marker genes to find starting seed contigs for [/shared/ifbstor1/galaxy/datasets2/9/e/8/dataset_9e8cd0b6-cb85-4c33-98e5-9372b097fa40.dat]...
+Done data collection. Running MaxBin...
+Command: /shared/ifbstor1/galaxy/mutable-data/dependencies/_conda/envs/__maxbin2@2.2.7/opt/MaxBin-2.2.7/src/MaxBin -fasta out.contig.tmp  -abund out.contig.tmp.reads.abund1 -seed out.seed -out out -min_contig_length 1000 -max_run 50 -prob_threshold 0.5 -thread 10
+Done data collection. Running MaxBin...
+Command: /shared/ifbstor1/galaxy/mutable-data/dependencies/_conda/envs/__maxbin2@2.2.7/opt/MaxBin-2.2.7/src/MaxBin -fasta out.0002.fasta  -abund out.contig.tmp.reads.abund1 -seed out.0002.out.seed -out out.0002.out -min_contig_length 1000 -max_run 50 -prob_threshold 0.5 -thread 10
+Minimum contig length set to 1000.
+Reading seed list...
+Looking for seeds in sequences.
+	k141_16093 [13.919579]
+	k141_35827 [21.405429]
+	k141_32187 [11.332857]
+	k141_16792 [20.304843]
+	k141_10178 [11.294563]
+	k141_2436 [19.777457]
+	k141_18047 [33.333916]
+	k141_15329 [24.868185]
+	k141_34672 [9.952122]
+	k141_19156 [27.248337]
+Get 10 seeds.
+
+Start EM process.
+Iteration 1
+Iteration 2
+Iteration 3
+Iteration 4
+Iteration 5
+Iteration 6
+Iteration 7
+Iteration 8
+Iteration 9
+Iteration 10
+Iteration 11
+Iteration 12
+Iteration 13
+Iteration 14
+Iteration 15
+Iteration 16
+Iteration 17
+Iteration 18
+Iteration 19
+Iteration 20
+Iteration 21
+Iteration 22
+Iteration 23
+Iteration 24
+Iteration 25
+Iteration 26
+Iteration 27
+Iteration 28
+Iteration 29
+Iteration 30
+Iteration 31
+Iteration 32
+Iteration 33
+Iteration 34
+Iteration 35
+Iteration 36
+Iteration 37
+Iteration 38
+Iteration 39
+Iteration 40
+Iteration 41
+Iteration 42
+Iteration 43
+Iteration 44
+Iteration 45
+Iteration 46
+Iteration 47
+Iteration 48
+Iteration 49
+Iteration 50
+
+EM finishes successfully.
+
+Classifying sequences based on the EM result.
+Minimum probability for binning: 0.50
+Ignoring 0 bins without any sequences.
+Number of unclassified sequences: 156 (1.66%)
+Elapsed time:  0 days 00:00:33
+
+Minimum contig length set to 1000.
+Reading seed list...
+Looking for seeds in sequences.
+	k141_16494 [26.817735]
+	k141_29344 [22.460258]
+Get 2 seeds.
+
+Start EM process.
+Iteration 1
+Iteration 2
+Iteration 3
+Iteration 4
+Iteration 5
+Iteration 6
+Iteration 7
+Iteration 8
+Iteration 9
+Iteration 10
+
+EM finishes successfully.
+
+Classifying sequences based on the EM result.
+Minimum probability for binning: 0.50
+Ignoring 0 bins without any sequences.
+Number of unclassified sequences: 0 (0.00%)
+Elapsed time:  0 days 00:00:00
+
+Deleting intermediate files.
+
+
+========== Job finished ==========
+Yielded 11 bins for contig (scaffold) file /shared/ifbstor1/galaxy/datasets2/9/e/8/dataset_9e8cd0b6-cb85-4c33-98e5-9372b097fa40.dat
+
+Here are the output files for this run.
+Please refer to the README file for further details.
+
+Summary file: out.summary
+Marker counts: out.marker
+Marker genes for each bin: out.marker_of_each_gene.tar.gz
+Bin files: out.001.fasta - out.011.fasta
+Unbinned sequences: out.noclass
+Marker plot: out.marker.pdf
+
+Store abundance information of reads file [HSMA33QY.fastq] in [out.abund1].
+
+
+========== Elapsed Time ==========
+0 hours 7 minutes and 28 seconds.
+