diff test-data/3/out.log @ 0:35aa0df55a62 draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/maxbin2 commit 8e118a4d24047e2c62912b962e854f789d6ff559-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/3/out.log	Thu Jun 28 08:49:29 2018 -0400
@@ -0,0 +1,72 @@
+MaxBin 2.2.4
+Input contig: /tmp/tmpES_iZn/files/000/dataset_1.dat
+out header: out
+Reassembly: 1
+Located reads file [/tmp/tmpES_iZn/files/000/dataset_2.dat]
+Running Bowtie2 on reads file [/tmp/tmpES_iZn/files/000/dataset_2.dat]...this may take a while...
+Searching against 107 marker genes to find starting seed contigs for [/tmp/tmpES_iZn/files/000/dataset_1.dat]...
+Try harder to dig out marker genes from contigs.
+Done data collection. Running MaxBin...
+Command: /home/berntm/miniconda3/envs/__maxbin2@2.2.4/opt/MaxBin-2.2.4/src/MaxBin -fasta out.contig.tmp  -abund out.contig.tmp.reads.abund1 -seed out.seed -out out -min_contig_length 1000 
+Minimum contig length set to 1000.
+Reading seed list...
+Looking for seeds in sequences.
+	contig-201_2 [11.293216]
+	contig-201_100 [10.048304]
+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
+Iteration 11
+Iteration 12
+Iteration 13
+Iteration 14
+
+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
+
+Performing reassembly. Reads file found.
+Separating reads according to the bins...
+Reassembling bin 001
+Command: idba_ud -r out.reads.001 -o out.tmp --pre_correction --num_threads 1 1>out.idba.out 2>out.idba.err
+Placing reassembled contigs into out.reassem
+cp out.tmp/scaffold.fa out.reassem/out.001.fasta
+Reassembling bin 002
+Command: idba_ud -r out.reads.002 -o out.tmp --pre_correction --num_threads 1 1>out.idba.out 2>out.idba.err
+Placing reassembled contigs into out.reassem
+cp out.tmp/scaffold.fa out.reassem/out.002.fasta
+Deleting intermediate files.
+
+
+========== Job finished ==========
+Yielded 2 bins for contig (scaffold) file /tmp/tmpES_iZn/files/000/dataset_1.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.002.fasta
+Unbinned sequences: out.noclass
+
+Store abundance information of reads file [/tmp/tmpES_iZn/files/000/dataset_2.dat] in [out.abund1].
+
+
+========== Elapsed Time ==========
+0 hours 2 minutes and 34 seconds.
+