[2023-06-07 20:25:37,822] [INFO] DFAST_QC pipeline started.
[2023-06-07 20:25:37,824] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 20:25:37,825] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d6be203-cedc-4ac1-a7d8-c055470c6581/dqc_reference
[2023-06-07 20:25:40,280] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 20:25:40,281] [INFO] Task started: Prodigal
[2023-06-07 20:25:40,282] [INFO] Running command: gunzip -c /var/lib/cwl/stg3e2f5208-c0ea-4e65-a367-840e1c6510b2/GCA_945948385.1_SRR11489751_bin.3_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945948385.1_SRR11489751_bin.3_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945948385.1_SRR11489751_bin.3_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 20:25:46,223] [INFO] Task succeeded: Prodigal
[2023-06-07 20:25:46,224] [INFO] Task started: HMMsearch
[2023-06-07 20:25:46,224] [INFO] Running command: hmmsearch --tblout GCA_945948385.1_SRR11489751_bin.3_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d6be203-cedc-4ac1-a7d8-c055470c6581/dqc_reference/reference_markers.hmm GCA_945948385.1_SRR11489751_bin.3_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-07 20:25:46,458] [INFO] Task succeeded: HMMsearch
[2023-06-07 20:25:46,460] [INFO] Found 6/6 markers.
[2023-06-07 20:25:46,483] [INFO] Query marker FASTA was written to GCA_945948385.1_SRR11489751_bin.3_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-07 20:25:46,483] [INFO] Task started: Blastn
[2023-06-07 20:25:46,483] [INFO] Running command: blastn -query GCA_945948385.1_SRR11489751_bin.3_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d6be203-cedc-4ac1-a7d8-c055470c6581/dqc_reference/reference_markers.fasta -out GCA_945948385.1_SRR11489751_bin.3_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:25:47,455] [INFO] Task succeeded: Blastn
[2023-06-07 20:25:47,459] [INFO] Selected 24 target genomes.
[2023-06-07 20:25:47,459] [INFO] Target genome list was writen to GCA_945948385.1_SRR11489751_bin.3_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-07 20:25:47,484] [INFO] Task started: fastANI
[2023-06-07 20:25:47,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e2f5208-c0ea-4e65-a367-840e1c6510b2/GCA_945948385.1_SRR11489751_bin.3_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945948385.1_SRR11489751_bin.3_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945948385.1_SRR11489751_bin.3_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 20:25:57,867] [INFO] Task succeeded: fastANI
[2023-06-07 20:25:57,868] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d6be203-cedc-4ac1-a7d8-c055470c6581/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 20:25:57,869] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d6be203-cedc-4ac1-a7d8-c055470c6581/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 20:25:57,891] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2023-06-07 20:25:57,891] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-07 20:25:57,892] [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 phoceense	strain=MC1	GCA_900092335.1	1686286	1686286	type	True	95.3251	548	611	95	conclusive
Corynebacterium striatum	strain=ATCC 6940	GCA_000159135.1	43770	43770	type	True	80.3219	290	611	95	below_threshold
Corynebacterium striatum	strain=FDAARGOS_1054	GCA_016403285.1	43770	43770	type	True	80.2004	284	611	95	below_threshold
Corynebacterium striatum	strain=NCTC764	GCA_900447675.1	43770	43770	type	True	80.187	291	611	95	below_threshold
Corynebacterium striatum	strain=NBRC 15291	GCA_006538485.1	43770	43770	type	True	80.1653	288	611	95	below_threshold
Corynebacterium aurimucosum	strain=FDAARGOS_1109	GCA_016728705.1	169292	169292	suspected-type	True	79.0327	253	611	95	below_threshold
Corynebacterium tuberculostearicum	strain=FDAARGOS_1117	GCA_016728365.1	38304	38304	type	True	79.0131	224	611	95	below_threshold
Corynebacterium aurimucosum	strain=DSM 44532	GCA_024138775.1	169292	169292	suspected-type	True	78.996	256	611	95	below_threshold
Corynebacterium tuberculostearicum	strain=DSM 44922	GCA_013408445.1	38304	38304	type	True	78.9494	228	611	95	below_threshold
Corynebacterium camporealensis	strain=DSM 44610	GCA_000980815.1	161896	161896	type	True	78.7588	251	611	95	below_threshold
Corynebacterium humireducens	strain=DSM 45392	GCA_000819445.1	1223514	1223514	type	True	78.7371	249	611	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	78.7181	247	611	95	below_threshold
Corynebacterium massiliense	strain=DSM 45435	GCA_000420605.1	441501	441501	type	True	78.6894	208	611	95	below_threshold
Corynebacterium halotolerans	strain=DSM 44683	GCA_000688435.1	225326	225326	type	True	78.5567	261	611	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	78.5037	258	611	95	below_threshold
Corynebacterium marinum	strain=CGMCC 1.6998	GCA_014645275.1	349751	349751	type	True	78.3883	229	611	95	below_threshold
Corynebacterium frankenforstense	strain=ST18	GCA_001941485.1	1230998	1230998	type	True	78.3416	235	611	95	below_threshold
Corynebacterium senegalense	strain=Marseille-P4329	GCA_900411315.1	2080750	2080750	type	True	78.0939	212	611	95	below_threshold
Corynebacterium freneyi	strain=DSM 44506	GCA_017876455.1	134034	134034	type	True	77.7499	148	611	95	below_threshold
Corynebacterium freneyi	strain=FDAARGOS 1426	GCA_019047805.1	134034	134034	type	True	77.6891	153	611	95	below_threshold
Corynebacterium xerosis	strain=NBRC 16721	GCA_001552415.1	1725	1725	suspected-type	True	77.6283	160	611	95	below_threshold
Corynebacterium bovis	strain=DSM 20582	GCA_014191555.1	36808	36808	type	True	77.2755	124	611	95	below_threshold
Corynebacterium bovis	strain=FDAARGOS_1052	GCA_016128075.1	36808	36808	type	True	77.2196	126	611	95	below_threshold
Corynebacterium sphenisci	strain=DSM 44792	GCA_001941505.1	191493	191493	type	True	76.727	119	611	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 20:25:57,895] [INFO] DFAST Taxonomy check result was written to GCA_945948385.1_SRR11489751_bin.3_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-07 20:25:57,896] [INFO] ===== Taxonomy check completed =====
[2023-06-07 20:25:57,896] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 20:25:57,896] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d6be203-cedc-4ac1-a7d8-c055470c6581/dqc_reference/checkm_data
[2023-06-07 20:25:57,898] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 20:25:57,928] [INFO] Task started: CheckM
[2023-06-07 20:25:57,928] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945948385.1_SRR11489751_bin.3_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945948385.1_SRR11489751_bin.3_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945948385.1_SRR11489751_bin.3_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-07 20:26:21,557] [INFO] Task succeeded: CheckM
[2023-06-07 20:26:21,559] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 4.63%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 20:26:21,582] [INFO] ===== Completeness check finished =====
[2023-06-07 20:26:21,582] [INFO] ===== Start GTDB Search =====
[2023-06-07 20:26:21,582] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945948385.1_SRR11489751_bin.3_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-07 20:26:21,583] [INFO] Task started: Blastn
[2023-06-07 20:26:21,583] [INFO] Running command: blastn -query GCA_945948385.1_SRR11489751_bin.3_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d6be203-cedc-4ac1-a7d8-c055470c6581/dqc_reference/reference_markers_gtdb.fasta -out GCA_945948385.1_SRR11489751_bin.3_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:26:23,000] [INFO] Task succeeded: Blastn
[2023-06-07 20:26:23,004] [INFO] Selected 23 target genomes.
[2023-06-07 20:26:23,004] [INFO] Target genome list was writen to GCA_945948385.1_SRR11489751_bin.3_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 20:26:23,053] [INFO] Task started: fastANI
[2023-06-07 20:26:23,054] [INFO] Running command: fastANI --query /var/lib/cwl/stg3e2f5208-c0ea-4e65-a367-840e1c6510b2/GCA_945948385.1_SRR11489751_bin.3_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945948385.1_SRR11489751_bin.3_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945948385.1_SRR11489751_bin.3_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 20:26:34,583] [INFO] Task succeeded: fastANI
[2023-06-07 20:26:34,615] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 20:26:34,615] [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_900092335.1	s__Corynebacterium phoceense	95.3251	548	611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.96	96.08	0.95	0.92	11	conclusive
GCF_000159135.1	s__Corynebacterium striatum	80.3421	289	611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.44	95.19	0.92	0.85	41	-
GCF_002861385.1	s__Corynebacterium aurimucosum_C	79.4558	266	611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.04	96.50	0.91	0.89	28	-
GCF_001815935.1	s__Corynebacterium sp001815935	79.3438	294	611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001586215.1	s__Corynebacterium simulans	79.1008	258	611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.78	97.47	0.94	0.92	11	-
GCF_016889765.1	s__Corynebacterium minutissimum_B	79.0788	236	611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.10	96.19	0.95	0.91	3	-
GCF_000988205.1	s__Corynebacterium minutissimum_A	79.0611	278	611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.53	96.09	0.91	0.89	16	-
GCF_001812805.1	s__Corynebacterium sp001812805	78.9756	246	611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408445.1	s__Corynebacterium tuberculostearicum	78.9494	228	611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	96.3332	98.29	96.59	0.96	0.92	3	-
GCF_000175635.1	s__Corynebacterium tuberculostearicum_C	78.8365	223	611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	96.3332	96.71	96.71	0.91	0.91	2	-
GCF_000819445.1	s__Corynebacterium humireducens	78.7037	251	611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.80	97.60	0.97	0.93	3	-
GCF_000478175.1	s__Corynebacterium sp000478175	78.6066	196	611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.95	99.95	0.99	0.98	3	-
GCF_000341345.1	s__Corynebacterium halotolerans	78.5193	257	611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000835165.1	s__Corynebacterium marinum	78.413	235	611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.21	98.42	0.97	0.94	3	-
GCF_900411315.1	s__Corynebacterium senegalense	78.0939	212	611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012838985.1	s__Corynebacterium sp012838985	78.0728	209	611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876455.1	s__Corynebacterium freneyi	77.7277	149	611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.50	96.48	0.94	0.86	4	-
GCF_001056295.1	s__Corynebacterium halotolerans_A	77.6422	170	611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552415.1	s__Corynebacterium xerosis	77.628	160	611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.07	95.54	0.95	0.90	8	-
GCA_012837295.1	s__Corynebacterium sp012837295	77.503	138	611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000183325.1	s__Corynebacterium bovis	77.4757	104	611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.01	98.42	0.92	0.83	23	-
GCA_012838715.1	s__Corynebacterium sp012838715	77.399	122	611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862095.1	s__Actinoplanes cyaneus	74.9973	71	611	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 20:26:34,617] [INFO] GTDB search result was written to GCA_945948385.1_SRR11489751_bin.3_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-07 20:26:34,617] [INFO] ===== GTDB Search completed =====
[2023-06-07 20:26:34,623] [INFO] DFAST_QC result json was written to GCA_945948385.1_SRR11489751_bin.3_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-07 20:26:34,623] [INFO] DFAST_QC completed!
[2023-06-07 20:26:34,623] [INFO] Total running time: 0h0m57s