[2023-06-29 13:29:25,883] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:29:25,885] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:29:25,885] [INFO] DQC Reference Directory: /var/lib/cwl/stgea08ea59-48ff-4df0-879e-ca36132a7e9c/dqc_reference
[2023-06-29 13:29:27,110] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:29:27,111] [INFO] Task started: Prodigal
[2023-06-29 13:29:27,111] [INFO] Running command: gunzip -c /var/lib/cwl/stg56ecafed-5db6-4016-9720-47c0bd9f1968/GCA_937877705.1_ERR598965_bin.146_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937877705.1_ERR598965_bin.146_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937877705.1_ERR598965_bin.146_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:29:32,711] [INFO] Task succeeded: Prodigal
[2023-06-29 13:29:32,711] [INFO] Task started: HMMsearch
[2023-06-29 13:29:32,711] [INFO] Running command: hmmsearch --tblout GCA_937877705.1_ERR598965_bin.146_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea08ea59-48ff-4df0-879e-ca36132a7e9c/dqc_reference/reference_markers.hmm GCA_937877705.1_ERR598965_bin.146_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:29:32,951] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:29:32,953] [INFO] Found 6/6 markers.
[2023-06-29 13:29:32,984] [INFO] Query marker FASTA was written to GCA_937877705.1_ERR598965_bin.146_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 13:29:32,984] [INFO] Task started: Blastn
[2023-06-29 13:29:32,984] [INFO] Running command: blastn -query GCA_937877705.1_ERR598965_bin.146_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgea08ea59-48ff-4df0-879e-ca36132a7e9c/dqc_reference/reference_markers.fasta -out GCA_937877705.1_ERR598965_bin.146_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:29:33,644] [INFO] Task succeeded: Blastn
[2023-06-29 13:29:33,648] [INFO] Selected 18 target genomes.
[2023-06-29 13:29:33,649] [INFO] Target genome list was writen to GCA_937877705.1_ERR598965_bin.146_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 13:29:33,653] [INFO] Task started: fastANI
[2023-06-29 13:29:33,654] [INFO] Running command: fastANI --query /var/lib/cwl/stg56ecafed-5db6-4016-9720-47c0bd9f1968/GCA_937877705.1_ERR598965_bin.146_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937877705.1_ERR598965_bin.146_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937877705.1_ERR598965_bin.146_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:29:43,560] [INFO] Task succeeded: fastANI
[2023-06-29 13:29:43,561] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea08ea59-48ff-4df0-879e-ca36132a7e9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:29:43,561] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea08ea59-48ff-4df0-879e-ca36132a7e9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:29:43,573] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2023-06-29 13:29:43,573] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 13:29:43,573] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Idiomarina loihiensis	strain=L2TR	GCA_000008465.1	135577	135577	type	True	96.9431	751	808	95	conclusive
Idiomarina ramblicola	strain=R22	GCA_003987255.1	263724	263724	type	True	84.7138	600	808	95	below_threshold
Idiomarina abyssalis	strain=KMM 227	GCA_001294685.1	86102	86102	type	True	84.4543	580	808	95	below_threshold
Idiomarina abyssalis	strain=KMM 227	GCA_900116625.1	86102	86102	type	True	84.3017	596	808	95	below_threshold
Idiomarina zobellii	strain=KMM 231	GCA_001294745.1	86103	86103	type	True	80.1171	358	808	95	below_threshold
Idiomarina zobellii	strain=KMM 231	GCA_900100855.1	86103	86103	type	True	80.072	357	808	95	below_threshold
Idiomarina piscisalsi	strain=TPS4-2	GCA_003987095.1	1096243	1096243	type	True	79.5084	348	808	95	below_threshold
Pseudidiomarina planktonica	strain=CGMCC 1.12458	GCA_900177775.1	1323738	1323738	type	True	77.1462	98	808	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 13:29:43,575] [INFO] DFAST Taxonomy check result was written to GCA_937877705.1_ERR598965_bin.146_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 13:29:43,576] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:29:43,576] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:29:43,576] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea08ea59-48ff-4df0-879e-ca36132a7e9c/dqc_reference/checkm_data
[2023-06-29 13:29:43,577] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:29:43,604] [INFO] Task started: CheckM
[2023-06-29 13:29:43,604] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937877705.1_ERR598965_bin.146_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937877705.1_ERR598965_bin.146_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937877705.1_ERR598965_bin.146_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 13:30:07,048] [INFO] Task succeeded: CheckM
[2023-06-29 13:30:07,050] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.82%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 13:30:07,072] [INFO] ===== Completeness check finished =====
[2023-06-29 13:30:07,073] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:30:07,073] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937877705.1_ERR598965_bin.146_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 13:30:07,074] [INFO] Task started: Blastn
[2023-06-29 13:30:07,074] [INFO] Running command: blastn -query GCA_937877705.1_ERR598965_bin.146_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgea08ea59-48ff-4df0-879e-ca36132a7e9c/dqc_reference/reference_markers_gtdb.fasta -out GCA_937877705.1_ERR598965_bin.146_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:30:08,082] [INFO] Task succeeded: Blastn
[2023-06-29 13:30:08,087] [INFO] Selected 15 target genomes.
[2023-06-29 13:30:08,087] [INFO] Target genome list was writen to GCA_937877705.1_ERR598965_bin.146_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:30:08,104] [INFO] Task started: fastANI
[2023-06-29 13:30:08,104] [INFO] Running command: fastANI --query /var/lib/cwl/stg56ecafed-5db6-4016-9720-47c0bd9f1968/GCA_937877705.1_ERR598965_bin.146_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937877705.1_ERR598965_bin.146_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937877705.1_ERR598965_bin.146_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:30:16,777] [INFO] Task succeeded: fastANI
[2023-06-29 13:30:16,791] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 13:30:16,791] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000008465.1	s__Idiomarina loihiensis	96.9431	751	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.95	95.80	0.91	0.86	17	conclusive
GCF_003987255.1	s__Idiomarina ramblicola	84.7138	600	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116625.1	s__Idiomarina abyssalis	84.3017	596	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.70	97.34	0.91	0.79	25	-
GCF_900100855.1	s__Idiomarina zobellii	80.072	357	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	96.93	96.27	0.89	0.85	9	-
GCF_003987095.1	s__Idiomarina piscisalsi	79.5084	348	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002211765.1	s__Idiomarina piscisalsi_A	79.2758	360	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	97.69	97.69	0.90	0.90	2	-
GCF_003987185.1	s__Idiomarina aquatica	77.7226	181	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Idiomarina	95.0	99.08	99.08	0.91	0.91	2	-
GCF_900177775.1	s__Pseudidiomarina planktonica	77.1462	98	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018222985.1	s__Pseudidiomarina sp018222985	76.5929	75	808	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 13:30:16,793] [INFO] GTDB search result was written to GCA_937877705.1_ERR598965_bin.146_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 13:30:16,794] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:30:16,797] [INFO] DFAST_QC result json was written to GCA_937877705.1_ERR598965_bin.146_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 13:30:16,798] [INFO] DFAST_QC completed!
[2023-06-29 13:30:16,798] [INFO] Total running time: 0h0m51s