diff test-data/4/out.log @ 6:2bc40bfbcfb4 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e0e4e512a0858295ce3d445b9413de2b5bcfcd78

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/4/out.log	Mon Oct 16 07:46:13 2023 +0000
@@ -0,0 +1,64 @@
+MaxBin 2.2.7
+Input contig: /tmp/tmpc9eyur_0/files/f/d/a/dataset_fda5399c-97b7-4ad2-bbe6-0f90e5e51369.dat
+out header: out
+Min contig length: 1000
+Max iteration: 50
+Probability threshold: 0.5
+Thread: 1
+Located reads file [test4_reads.fastqsanger_0]
+Located reads file [test4_reads.fastqsanger_1]
+Running Bowtie2 on reads file [test4_reads.fastqsanger_0]...this may take a while...
+Running Bowtie2 on reads file [test4_reads.fastqsanger_1]...this may take a while...
+Searching against 107 marker genes to find starting seed contigs for [/tmp/tmpc9eyur_0/files/f/d/a/dataset_fda5399c-97b7-4ad2-bbe6-0f90e5e51369.dat]...
+Try harder to dig out marker genes from contigs.
+Done data collection. Running MaxBin...
+Command: /home/gitpod/miniconda3/envs/__maxbin2@2.2.7/opt/MaxBin-2.2.7/src/MaxBin -fasta out.contig.tmp  -abund out.contig.tmp.reads.abund1 -abund2 out.contig.tmp.reads.abund2 -seed out.seed -out out -min_contig_length 1000 -max_run 50 -prob_threshold 0.5 
+Minimum contig length set to 1000.
+Reading seed list...
+Looking for seeds in sequences.
+	k141_99 [0.017288] [0.017288]
+	k141_239 [0.015466] [0.015466]
+Get 2 seeds.
+
+Start EM process.
+Iteration 1
+Iteration 2
+Iteration 3
+Iteration 4
+Iteration 5
+Iteration 6
+Iteration 7
+Iteration 8
+
+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 00:00:01
+
+Deleting intermediate files.
+
+
+========== Job finished ==========
+Yielded 2 bins for contig (scaffold) file /tmp/tmpc9eyur_0/files/f/d/a/dataset_fda5399c-97b7-4ad2-bbe6-0f90e5e51369.dat
+
+Here are the output files for this run.
+Please refer to the README file for further details.
+
+Summary file: out.summary
+Genome abundance info file: out.abundance
+Marker counts: out.marker
+Marker genes for each bin: out.marker_of_each_gene.tar.gz
+Bin files: out.001.fasta - out.002.fasta
+Unbinned sequences: out.noclass
+Marker plot: out.marker.pdf
+
+Store abundance information of reads file [test4_reads.fastqsanger_0] in [out.abund1].
+Store abundance information of reads file [test4_reads.fastqsanger_1] in [out.abund2].
+
+
+========== Elapsed Time ==========
+0 hours 0 minutes and 3 seconds.
+