[2023-06-13 15:27:03,376] [INFO] DFAST_QC pipeline started.
[2023-06-13 15:27:03,378] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 15:27:03,378] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1249f43-cb5a-437b-8a36-3916cb7a58aa/dqc_reference
[2023-06-13 15:27:05,160] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 15:27:05,161] [INFO] Task started: Prodigal
[2023-06-13 15:27:05,161] [INFO] Running command: gunzip -c /var/lib/cwl/stgda73f404-d1cf-428c-9f52-73008a62e230/GCA_930989755.1_ERR3414582_bin.14_metaWRAP_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_930989755.1_ERR3414582_bin.14_metaWRAP_v1.1_MAG_genomic.fna/cds.fna -a GCA_930989755.1_ERR3414582_bin.14_metaWRAP_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 15:27:11,279] [INFO] Task succeeded: Prodigal
[2023-06-13 15:27:11,279] [INFO] Task started: HMMsearch
[2023-06-13 15:27:11,279] [INFO] Running command: hmmsearch --tblout GCA_930989755.1_ERR3414582_bin.14_metaWRAP_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1249f43-cb5a-437b-8a36-3916cb7a58aa/dqc_reference/reference_markers.hmm GCA_930989755.1_ERR3414582_bin.14_metaWRAP_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 15:27:11,447] [INFO] Task succeeded: HMMsearch
[2023-06-13 15:27:11,448] [INFO] Found 6/6 markers.
[2023-06-13 15:27:11,470] [INFO] Query marker FASTA was written to GCA_930989755.1_ERR3414582_bin.14_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 15:27:11,470] [INFO] Task started: Blastn
[2023-06-13 15:27:11,470] [INFO] Running command: blastn -query GCA_930989755.1_ERR3414582_bin.14_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1249f43-cb5a-437b-8a36-3916cb7a58aa/dqc_reference/reference_markers.fasta -out GCA_930989755.1_ERR3414582_bin.14_metaWRAP_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:27:12,156] [INFO] Task succeeded: Blastn
[2023-06-13 15:27:12,159] [INFO] Selected 9 target genomes.
[2023-06-13 15:27:12,160] [INFO] Target genome list was writen to GCA_930989755.1_ERR3414582_bin.14_metaWRAP_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 15:27:12,161] [INFO] Task started: fastANI
[2023-06-13 15:27:12,161] [INFO] Running command: fastANI --query /var/lib/cwl/stgda73f404-d1cf-428c-9f52-73008a62e230/GCA_930989755.1_ERR3414582_bin.14_metaWRAP_v1.1_MAG_genomic.fna.gz --refList GCA_930989755.1_ERR3414582_bin.14_metaWRAP_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_930989755.1_ERR3414582_bin.14_metaWRAP_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 15:27:16,698] [INFO] Task succeeded: fastANI
[2023-06-13 15:27:16,698] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1249f43-cb5a-437b-8a36-3916cb7a58aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 15:27:16,699] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1249f43-cb5a-437b-8a36-3916cb7a58aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 15:27:16,707] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2023-06-13 15:27:16,708] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 15:27:16,708] [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
Corynebacterium stationis	strain=622=DSM 20302	GCA_001941345.1	1705	1705	type	True	97.8324	628	666	95	conclusive
Corynebacterium casei	strain=LMG S-19264	GCA_000550785.1	160386	160386	type	True	82.8759	518	666	95	below_threshold
Corynebacterium ammoniagenes	strain=DSM 20306	GCA_000164115.1	1697	1697	type	True	82.4794	525	666	95	below_threshold
Corynebacterium ammoniagenes	strain=DSM 20306 = 9.6	GCA_001941425.1	1697	1697	type	True	82.4163	529	666	95	below_threshold
Corynebacterium striatum	strain=FDAARGOS_1054	GCA_016403285.1	43770	43770	type	True	78.128	139	666	95	below_threshold
Corynebacterium camporealensis	strain=CIP 105508	GCA_000766885.2	161896	161896	type	True	77.9889	180	666	95	below_threshold
Corynebacterium camporealensis	strain=DSM 44610	GCA_000980815.1	161896	161896	type	True	77.9687	183	666	95	below_threshold
Corynebacterium tuberculostearicum	strain=FDAARGOS_1117	GCA_016728365.1	38304	38304	type	True	77.7939	127	666	95	below_threshold
Corynebacterium aurimucosum	strain=FDAARGOS_1109	GCA_016728705.1	169292	169292	suspected-type	True	77.42	139	666	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 15:27:16,710] [INFO] DFAST Taxonomy check result was written to GCA_930989755.1_ERR3414582_bin.14_metaWRAP_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 15:27:16,710] [INFO] ===== Taxonomy check completed =====
[2023-06-13 15:27:16,710] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 15:27:16,711] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1249f43-cb5a-437b-8a36-3916cb7a58aa/dqc_reference/checkm_data
[2023-06-13 15:27:16,712] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 15:27:16,736] [INFO] Task started: CheckM
[2023-06-13 15:27:16,736] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_930989755.1_ERR3414582_bin.14_metaWRAP_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_930989755.1_ERR3414582_bin.14_metaWRAP_v1.1_MAG_genomic.fna/checkm_input GCA_930989755.1_ERR3414582_bin.14_metaWRAP_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 15:27:40,093] [INFO] Task succeeded: CheckM
[2023-06-13 15:27:40,094] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 15:27:40,113] [INFO] ===== Completeness check finished =====
[2023-06-13 15:27:40,113] [INFO] ===== Start GTDB Search =====
[2023-06-13 15:27:40,114] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_930989755.1_ERR3414582_bin.14_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 15:27:40,114] [INFO] Task started: Blastn
[2023-06-13 15:27:40,114] [INFO] Running command: blastn -query GCA_930989755.1_ERR3414582_bin.14_metaWRAP_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1249f43-cb5a-437b-8a36-3916cb7a58aa/dqc_reference/reference_markers_gtdb.fasta -out GCA_930989755.1_ERR3414582_bin.14_metaWRAP_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:27:41,038] [INFO] Task succeeded: Blastn
[2023-06-13 15:27:41,042] [INFO] Selected 9 target genomes.
[2023-06-13 15:27:41,042] [INFO] Target genome list was writen to GCA_930989755.1_ERR3414582_bin.14_metaWRAP_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 15:27:41,043] [INFO] Task started: fastANI
[2023-06-13 15:27:41,043] [INFO] Running command: fastANI --query /var/lib/cwl/stgda73f404-d1cf-428c-9f52-73008a62e230/GCA_930989755.1_ERR3414582_bin.14_metaWRAP_v1.1_MAG_genomic.fna.gz --refList GCA_930989755.1_ERR3414582_bin.14_metaWRAP_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_930989755.1_ERR3414582_bin.14_metaWRAP_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 15:27:45,456] [INFO] Task succeeded: fastANI
[2023-06-13 15:27:45,465] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 15:27:45,466] [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_001941345.1	s__Corynebacterium stationis	97.8324	628	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.83	97.14	0.93	0.87	11	conclusive
GCF_002967075.1	s__Corynebacterium sp002967075	94.8885	628	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000550785.1	s__Corynebacterium casei	82.8759	518	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.58	0.94	0.92	5	-
GCF_001941425.1	s__Corynebacterium ammoniagenes	82.4063	530	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.70	98.81	0.99	0.95	5	-
GCF_000159135.1	s__Corynebacterium striatum	78.2665	137	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.44	95.19	0.92	0.85	41	-
GCF_000980815.1	s__Corynebacterium camporealensis	77.9687	183	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.96	99.96	1.00	1.00	2	-
GCF_001812805.1	s__Corynebacterium sp001812805	77.8391	132	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016894265.1	s__Corynebacterium tuberculostearicum_D	77.8093	120	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.1108	N/A	N/A	N/A	N/A	1	-
GCA_019114925.1	s__Corynebacterium faecipullorum	76.7265	102	666	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 15:27:45,467] [INFO] GTDB search result was written to GCA_930989755.1_ERR3414582_bin.14_metaWRAP_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 15:27:45,468] [INFO] ===== GTDB Search completed =====
[2023-06-13 15:27:45,471] [INFO] DFAST_QC result json was written to GCA_930989755.1_ERR3414582_bin.14_metaWRAP_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 15:27:45,471] [INFO] DFAST_QC completed!
[2023-06-13 15:27:45,472] [INFO] Total running time: 0h0m42s