[2023-06-08 09:17:38,309] [INFO] DFAST_QC pipeline started.
[2023-06-08 09:17:38,311] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 09:17:38,311] [INFO] DQC Reference Directory: /var/lib/cwl/stg771e9562-1781-48cf-87fe-c25d3a445e7a/dqc_reference
[2023-06-08 09:17:39,601] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 09:17:39,602] [INFO] Task started: Prodigal
[2023-06-08 09:17:39,603] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8727299-125b-4d1e-8514-d0d82d82fa73/GCA_947385565.1_ERR6760104_bin.42_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947385565.1_ERR6760104_bin.42_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947385565.1_ERR6760104_bin.42_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 09:17:44,111] [INFO] Task succeeded: Prodigal
[2023-06-08 09:17:44,112] [INFO] Task started: HMMsearch
[2023-06-08 09:17:44,112] [INFO] Running command: hmmsearch --tblout GCA_947385565.1_ERR6760104_bin.42_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg771e9562-1781-48cf-87fe-c25d3a445e7a/dqc_reference/reference_markers.hmm GCA_947385565.1_ERR6760104_bin.42_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 09:17:44,333] [INFO] Task succeeded: HMMsearch
[2023-06-08 09:17:44,334] [INFO] Found 6/6 markers.
[2023-06-08 09:17:44,361] [INFO] Query marker FASTA was written to GCA_947385565.1_ERR6760104_bin.42_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 09:17:44,361] [INFO] Task started: Blastn
[2023-06-08 09:17:44,361] [INFO] Running command: blastn -query GCA_947385565.1_ERR6760104_bin.42_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg771e9562-1781-48cf-87fe-c25d3a445e7a/dqc_reference/reference_markers.fasta -out GCA_947385565.1_ERR6760104_bin.42_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:17:44,937] [INFO] Task succeeded: Blastn
[2023-06-08 09:17:44,940] [INFO] Selected 12 target genomes.
[2023-06-08 09:17:44,940] [INFO] Target genome list was writen to GCA_947385565.1_ERR6760104_bin.42_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 09:17:44,941] [INFO] Task started: fastANI
[2023-06-08 09:17:44,941] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8727299-125b-4d1e-8514-d0d82d82fa73/GCA_947385565.1_ERR6760104_bin.42_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947385565.1_ERR6760104_bin.42_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947385565.1_ERR6760104_bin.42_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 09:17:50,584] [INFO] Task succeeded: fastANI
[2023-06-08 09:17:50,584] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg771e9562-1781-48cf-87fe-c25d3a445e7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 09:17:50,585] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg771e9562-1781-48cf-87fe-c25d3a445e7a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 09:17:50,597] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 09:17:50,597] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 09:17:50,597] [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
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	79.3014	210	430	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	79.285	203	430	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	78.1085	133	430	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	77.3068	111	430	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.0038	121	430	95	below_threshold
Intestinimonas butyriciproducens	strain=SRB-521-5-I	GCA_004154955.1	1297617	1297617	type	True	76.9929	126	430	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	76.9526	127	430	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	76.6967	60	430	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	76.2777	53	430	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 09:17:50,599] [INFO] DFAST Taxonomy check result was written to GCA_947385565.1_ERR6760104_bin.42_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 09:17:50,600] [INFO] ===== Taxonomy check completed =====
[2023-06-08 09:17:50,600] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 09:17:50,600] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg771e9562-1781-48cf-87fe-c25d3a445e7a/dqc_reference/checkm_data
[2023-06-08 09:17:50,602] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 09:17:50,628] [INFO] Task started: CheckM
[2023-06-08 09:17:50,629] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947385565.1_ERR6760104_bin.42_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947385565.1_ERR6760104_bin.42_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947385565.1_ERR6760104_bin.42_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 09:18:10,695] [INFO] Task succeeded: CheckM
[2023-06-08 09:18:10,696] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.56%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 09:18:10,718] [INFO] ===== Completeness check finished =====
[2023-06-08 09:18:10,718] [INFO] ===== Start GTDB Search =====
[2023-06-08 09:18:10,719] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947385565.1_ERR6760104_bin.42_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 09:18:10,719] [INFO] Task started: Blastn
[2023-06-08 09:18:10,719] [INFO] Running command: blastn -query GCA_947385565.1_ERR6760104_bin.42_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg771e9562-1781-48cf-87fe-c25d3a445e7a/dqc_reference/reference_markers_gtdb.fasta -out GCA_947385565.1_ERR6760104_bin.42_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:18:11,562] [INFO] Task succeeded: Blastn
[2023-06-08 09:18:11,568] [INFO] Selected 20 target genomes.
[2023-06-08 09:18:11,568] [INFO] Target genome list was writen to GCA_947385565.1_ERR6760104_bin.42_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 09:18:11,576] [INFO] Task started: fastANI
[2023-06-08 09:18:11,576] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8727299-125b-4d1e-8514-d0d82d82fa73/GCA_947385565.1_ERR6760104_bin.42_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947385565.1_ERR6760104_bin.42_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947385565.1_ERR6760104_bin.42_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 09:18:21,966] [INFO] Task succeeded: fastANI
[2023-06-08 09:18:21,990] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 09:18:21,991] [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
GCA_910585415.1	s__NSJ-51 sp910585415	98.7584	375	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NSJ-51	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002161215.1	s__Flavonifractor avistercoris	79.7051	217	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	96.82	96.45	0.91	0.89	7	-
GCF_000239295.1	s__Flavonifractor plautii	79.2503	203	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	98.23	97.77	0.83	0.59	43	-
GCF_002159455.1	s__Flavonifractor sp002159455	79.1805	213	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	97.17	96.82	0.76	0.75	4	-
GCF_002159265.1	s__Flavonifractor sp002159265	79.1326	190	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119335.1	s__Flavonifractor merdavium	79.0984	187	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549565.1	s__UMGS1202 sp900549565	79.0433	201	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__UMGS1202	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119165.1	s__Flavonifractor intestinigallinarum	78.8241	183	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	98.85	97.85	0.90	0.88	3	-
GCF_014287895.1	s__NSJ-51 sp900549795	78.7597	201	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__NSJ-51	95.0	99.27	99.06	0.90	0.89	3	-
GCF_002159175.1	s__An92 sp002159175	78.7325	152	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	98.91	98.91	0.91	0.91	2	-
GCF_002161085.1	s__Flavonifractor avicola	78.684	182	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	96.94	96.68	0.83	0.78	7	-
GCF_016901955.1	s__Flavonifractor phocaeensis_A	78.6105	172	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014281125.1	s__Instestinimonas_A gabonensis	78.491	166	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Instestinimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000492175.1	s__Lawsonibacter sp000492175	78.1783	140	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115785.1	s__Intestinimonas merdavium	78.0046	114	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	98.39	98.39	0.88	0.88	2	-
GCA_018715695.1	s__Galloscillospira_A stercoripullorum	77.8891	109	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Galloscillospira_A	95.0	99.04	99.04	0.82	0.82	2	-
GCA_910575265.1	s__Lawsonibacter sp910575265	77.8414	120	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585815.1	s__Lawsonibacter sp910585815	77.6396	137	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009911645.1	s__Lawsonibacter sp009911645	77.3551	122	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003612335.1	s__Lawsonibacter sp003612335	77.2692	120	430	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 09:18:21,993] [INFO] GTDB search result was written to GCA_947385565.1_ERR6760104_bin.42_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 09:18:21,993] [INFO] ===== GTDB Search completed =====
[2023-06-08 09:18:21,997] [INFO] DFAST_QC result json was written to GCA_947385565.1_ERR6760104_bin.42_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 09:18:21,997] [INFO] DFAST_QC completed!
[2023-06-08 09:18:21,997] [INFO] Total running time: 0h0m44s