[2023-06-08 02:20:22,088] [INFO] DFAST_QC pipeline started.
[2023-06-08 02:20:22,090] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 02:20:22,090] [INFO] DQC Reference Directory: /var/lib/cwl/stga35592d6-02fe-47e7-b7c0-dae2caf81251/dqc_reference
[2023-06-08 02:20:23,743] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 02:20:23,744] [INFO] Task started: Prodigal
[2023-06-08 02:20:23,744] [INFO] Running command: gunzip -c /var/lib/cwl/stg7c09725f-c45d-4cac-b44c-29a8c5b10474/GCA_947074205.1_SRR7610136_bin.1_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947074205.1_SRR7610136_bin.1_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_947074205.1_SRR7610136_bin.1_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 02:20:39,215] [INFO] Task succeeded: Prodigal
[2023-06-08 02:20:39,216] [INFO] Task started: HMMsearch
[2023-06-08 02:20:39,216] [INFO] Running command: hmmsearch --tblout GCA_947074205.1_SRR7610136_bin.1_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga35592d6-02fe-47e7-b7c0-dae2caf81251/dqc_reference/reference_markers.hmm GCA_947074205.1_SRR7610136_bin.1_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 02:20:39,485] [INFO] Task succeeded: HMMsearch
[2023-06-08 02:20:39,487] [INFO] Found 6/6 markers.
[2023-06-08 02:20:39,525] [INFO] Query marker FASTA was written to GCA_947074205.1_SRR7610136_bin.1_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 02:20:39,525] [INFO] Task started: Blastn
[2023-06-08 02:20:39,525] [INFO] Running command: blastn -query GCA_947074205.1_SRR7610136_bin.1_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga35592d6-02fe-47e7-b7c0-dae2caf81251/dqc_reference/reference_markers.fasta -out GCA_947074205.1_SRR7610136_bin.1_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 02:20:40,130] [INFO] Task succeeded: Blastn
[2023-06-08 02:20:40,134] [INFO] Selected 24 target genomes.
[2023-06-08 02:20:40,134] [INFO] Target genome list was writen to GCA_947074205.1_SRR7610136_bin.1_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 02:20:40,139] [INFO] Task started: fastANI
[2023-06-08 02:20:40,140] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c09725f-c45d-4cac-b44c-29a8c5b10474/GCA_947074205.1_SRR7610136_bin.1_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947074205.1_SRR7610136_bin.1_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947074205.1_SRR7610136_bin.1_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 02:20:56,258] [INFO] Task succeeded: fastANI
[2023-06-08 02:20:56,258] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga35592d6-02fe-47e7-b7c0-dae2caf81251/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 02:20:56,259] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga35592d6-02fe-47e7-b7c0-dae2caf81251/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 02:20:56,280] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 02:20:56,280] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 02:20:56,280] [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
Bacteroides caccae	strain=FDAARGOS_1097	GCA_016726305.1	47678	47678	suspected-type	True	76.9684	88	1057	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_002221665.1	1796613	1796613	type	True	76.9441	83	1057	95	below_threshold
Bacteroides finegoldii	strain=DSM 17565	GCA_000156195.1	338188	338188	suspected-type	True	76.9364	86	1057	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	76.8883	87	1057	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_001688725.2	1796613	1796613	type	True	76.8861	85	1057	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_016697125.1	1796613	1796613	type	True	76.8623	86	1057	95	below_threshold
Bacteroides faecichinchillae	strain=JCM 17102	GCA_000614145.1	871325	871325	type	True	76.7823	69	1057	95	below_threshold
Bacteroides faecichinchillae	strain=DSM 26883	GCA_900129065.1	871325	871325	type	True	76.7459	69	1057	95	below_threshold
Bacteroides fragilis	strain=ATCC 25285	GCA_001997325.1	817	817	type	True	76.7421	92	1057	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI-5482	GCA_020179495.1	818	818	type	True	76.7157	89	1057	95	below_threshold
Bacteroides thetaiotaomicron	strain=NCTC10582	GCA_900445595.1	818	818	type	True	76.7154	89	1057	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	76.7146	91	1057	95	below_threshold
Bacteroides faecalis	strain=KCTC 15687	GCA_003865075.1	2447885	2447885	type	True	76.6979	78	1057	95	below_threshold
Bacteroides bouchesdurhonensis	strain=Marseille-P2653	GCA_900155865.1	1841855	1841855	type	True	76.6783	78	1057	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_002959635.1	28116	28116	suspected-type	True	76.6761	112	1057	95	below_threshold
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	76.6584	113	1057	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_001314995.1	28116	28116	suspected-type	True	76.6323	112	1057	95	below_threshold
Bacteroides ovatus	strain=DSM 1896	GCA_900107475.1	28116	28116	suspected-type	True	76.6287	112	1057	95	below_threshold
Bacteroides xylanisolvens	strain=XB1A	GCA_000210075.1	371601	371601	suspected-type	True	76.5714	100	1057	95	below_threshold
Bacteroides salyersiae	strain=DSM 18765	GCA_000381365.1	291644	291644	type	True	76.5584	95	1057	95	below_threshold
Bacteroides ovatus	strain=NCTC11153	GCA_900445505.1	28116	28116	suspected-type	True	76.5484	110	1057	95	below_threshold
Bacteroides neonati	strain=MS4	GCA_000499785.1	1347393	1347393	type	True	76.4596	108	1057	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 02:20:56,282] [INFO] DFAST Taxonomy check result was written to GCA_947074205.1_SRR7610136_bin.1_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 02:20:56,283] [INFO] ===== Taxonomy check completed =====
[2023-06-08 02:20:56,283] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 02:20:56,283] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga35592d6-02fe-47e7-b7c0-dae2caf81251/dqc_reference/checkm_data
[2023-06-08 02:20:56,284] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 02:20:56,322] [INFO] Task started: CheckM
[2023-06-08 02:20:56,323] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947074205.1_SRR7610136_bin.1_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947074205.1_SRR7610136_bin.1_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_947074205.1_SRR7610136_bin.1_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 02:21:42,280] [INFO] Task succeeded: CheckM
[2023-06-08 02:21:42,281] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 02:21:42,304] [INFO] ===== Completeness check finished =====
[2023-06-08 02:21:42,304] [INFO] ===== Start GTDB Search =====
[2023-06-08 02:21:42,304] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947074205.1_SRR7610136_bin.1_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 02:21:42,305] [INFO] Task started: Blastn
[2023-06-08 02:21:42,305] [INFO] Running command: blastn -query GCA_947074205.1_SRR7610136_bin.1_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga35592d6-02fe-47e7-b7c0-dae2caf81251/dqc_reference/reference_markers_gtdb.fasta -out GCA_947074205.1_SRR7610136_bin.1_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 02:21:43,145] [INFO] Task succeeded: Blastn
[2023-06-08 02:21:43,151] [INFO] Selected 27 target genomes.
[2023-06-08 02:21:43,151] [INFO] Target genome list was writen to GCA_947074205.1_SRR7610136_bin.1_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 02:21:43,162] [INFO] Task started: fastANI
[2023-06-08 02:21:43,162] [INFO] Running command: fastANI --query /var/lib/cwl/stg7c09725f-c45d-4cac-b44c-29a8c5b10474/GCA_947074205.1_SRR7610136_bin.1_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947074205.1_SRR7610136_bin.1_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947074205.1_SRR7610136_bin.1_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 02:22:00,748] [INFO] Task succeeded: fastANI
[2023-06-08 02:22:00,771] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 02:22:00,771] [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_002471185.1	s__Bacteroides sp002471185	77.7186	106	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002471195.1	s__Bacteroides sp002471195	77.4639	104	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903181435.1	s__Bacteroides sp900765785	77.211	74	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.28	97.12	0.65	0.59	3	-
GCF_002222615.2	s__Bacteroides caccae	76.9542	87	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.30	98.91	0.88	0.81	77	-
GCF_000156195.1	s__Bacteroides finegoldii	76.8727	84	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.8579	98.84	97.86	0.83	0.75	21	-
GCA_900547205.1	s__Bacteroides sp900547205	76.8287	87	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.99	99.99	0.95	0.95	2	-
GCF_001688725.2	s__Bacteroides caecimuris	76.8204	83	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.14	95.76	0.86	0.68	7	-
GCA_000613385.1	s__Bacteroides acidifaciens	76.8173	78	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.33	97.99	0.81	0.75	18	-
GCF_014334015.1	s__Bacteroides intestinigallinarum	76.7124	104	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.71	95.47	0.80	0.53	8	-
GCF_902364365.1	s__Bacteroides sp900556215	76.6711	85	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.2143	99.84	99.69	0.91	0.82	3	-
GCF_000614145.1	s__Bacteroides faecichinchillae	76.6665	68	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.89	99.80	0.96	0.92	3	-
GCF_000011065.1	s__Bacteroides thetaiotaomicron	76.6649	87	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.45	97.24	0.84	0.75	121	-
GCF_900155865.1	s__Bacteroides bouchesdurhonensis	76.6248	76	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.60	98.60	0.88	0.88	2	-
GCF_000428105.1	s__Bacteroides pyogenes	76.6203	64	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.76	98.45	0.87	0.82	21	-
GCF_003865075.1	s__Bacteroides faecalis	76.6134	75	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001314995.1	s__Bacteroides ovatus	76.5781	110	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.48	95.28	0.79	0.72	126	-
GCF_000381365.1	s__Bacteroides salyersiae	76.5584	95	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.03	96.77	0.88	0.58	55	-
GCF_014196225.1	s__Bacteroides pyogenes_A	76.5235	51	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.74	99.26	0.97	0.91	4	-
GCF_000210075.1	s__Bacteroides xylanisolvens	76.5094	98	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	96.81	0.77	0.68	125	-
GCF_900130125.1	s__Bacteroides congonensis	76.4991	95	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.81	97.60	0.79	0.75	6	-
GCF_000499785.1	s__Bacteroides neonati	76.4358	107	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	100.00	100.00	1.00	1.00	2	-
GCA_910578895.1	s__Bacteroides sp910578895	76.1503	69	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108345.1	s__Bacteroides ndongoniae	76.0491	63	1057	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.52	97.32	0.85	0.83	4	-
--------------------------------------------------------------------------------
[2023-06-08 02:22:00,773] [INFO] GTDB search result was written to GCA_947074205.1_SRR7610136_bin.1_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 02:22:00,774] [INFO] ===== GTDB Search completed =====
[2023-06-08 02:22:00,779] [INFO] DFAST_QC result json was written to GCA_947074205.1_SRR7610136_bin.1_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 02:22:00,779] [INFO] DFAST_QC completed!
[2023-06-08 02:22:00,779] [INFO] Total running time: 0h1m39s