[2023-06-17 18:46:38,212] [INFO] DFAST_QC pipeline started.
[2023-06-17 18:46:38,214] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 18:46:38,214] [INFO] DQC Reference Directory: /var/lib/cwl/stge4e861d6-2c54-44b2-84a7-a637a7c47fef/dqc_reference
[2023-06-17 18:46:39,529] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 18:46:39,530] [INFO] Task started: Prodigal
[2023-06-17 18:46:39,531] [INFO] Running command: gunzip -c /var/lib/cwl/stg8e80d3a3-4ebb-4b8c-a9a1-d2bf479d9564/GCA_905201455.1_ERR321346-mag-bin.16_genomic.fna.gz | prodigal -d GCA_905201455.1_ERR321346-mag-bin.16_genomic.fna/cds.fna -a GCA_905201455.1_ERR321346-mag-bin.16_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 18:46:56,146] [INFO] Task succeeded: Prodigal
[2023-06-17 18:46:56,146] [INFO] Task started: HMMsearch
[2023-06-17 18:46:56,147] [INFO] Running command: hmmsearch --tblout GCA_905201455.1_ERR321346-mag-bin.16_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4e861d6-2c54-44b2-84a7-a637a7c47fef/dqc_reference/reference_markers.hmm GCA_905201455.1_ERR321346-mag-bin.16_genomic.fna/protein.faa > /dev/null
[2023-06-17 18:46:56,443] [INFO] Task succeeded: HMMsearch
[2023-06-17 18:46:56,445] [INFO] Found 6/6 markers.
[2023-06-17 18:46:56,480] [INFO] Query marker FASTA was written to GCA_905201455.1_ERR321346-mag-bin.16_genomic.fna/markers.fasta
[2023-06-17 18:46:56,481] [INFO] Task started: Blastn
[2023-06-17 18:46:56,481] [INFO] Running command: blastn -query GCA_905201455.1_ERR321346-mag-bin.16_genomic.fna/markers.fasta -db /var/lib/cwl/stge4e861d6-2c54-44b2-84a7-a637a7c47fef/dqc_reference/reference_markers.fasta -out GCA_905201455.1_ERR321346-mag-bin.16_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 18:46:57,097] [INFO] Task succeeded: Blastn
[2023-06-17 18:46:57,103] [INFO] Selected 22 target genomes.
[2023-06-17 18:46:57,103] [INFO] Target genome list was writen to GCA_905201455.1_ERR321346-mag-bin.16_genomic.fna/target_genomes.txt
[2023-06-17 18:46:57,108] [INFO] Task started: fastANI
[2023-06-17 18:46:57,108] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e80d3a3-4ebb-4b8c-a9a1-d2bf479d9564/GCA_905201455.1_ERR321346-mag-bin.16_genomic.fna.gz --refList GCA_905201455.1_ERR321346-mag-bin.16_genomic.fna/target_genomes.txt --output GCA_905201455.1_ERR321346-mag-bin.16_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 18:47:12,804] [INFO] Task succeeded: fastANI
[2023-06-17 18:47:12,805] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4e861d6-2c54-44b2-84a7-a637a7c47fef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 18:47:12,805] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4e861d6-2c54-44b2-84a7-a637a7c47fef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 18:47:12,827] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 18:47:12,827] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 18:47:12,827] [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
Phocaeicola coprocola	strain=DSM 17136	GCA_000154845.1	310298	310298	suspected-type	True	82.7675	725	1133	95	below_threshold
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	80.2663	360	1133	95	below_threshold
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	80.1242	347	1133	95	below_threshold
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	79.3545	337	1133	95	below_threshold
Phocaeicola barnesiae	strain=JCM 13652	GCA_000613645.1	376804	376804	type	True	79.2907	338	1133	95	below_threshold
Phocaeicola intestinalis	strain=Sa1CVN1	GCA_014837065.1	2762212	2762212	type	True	79.2873	254	1133	95	below_threshold
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	79.0336	300	1133	95	below_threshold
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	79.0181	302	1133	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	78.5763	121	1133	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	78.5205	163	1133	95	below_threshold
Phocaeicola faecium	strain=Sa1YUN3	GCA_014837055.1	2762213	2762213	type	True	78.4378	246	1133	95	below_threshold
Phocaeicola sartorii	strain=DSM 21941	GCA_024622025.1	671267	671267	type	True	77.8019	195	1133	95	below_threshold
Bacteroides intestinalis	strain=DSM 17393	GCA_000172175.1	329854	329854	type	True	77.7033	140	1133	95	below_threshold
Phocaeicola massiliensis	strain=DSM 17679	GCA_000382445.1	204516	204516	suspected-type	True	77.6813	196	1133	95	below_threshold
Bacteroides faecis	strain=MAJ27	GCA_900106755.1	674529	674529	type	True	77.5653	157	1133	95	below_threshold
Phocaeicola massiliensis	strain=DSM 17679	GCA_000373085.1	204516	204516	type	True	77.4969	194	1133	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	77.4432	146	1133	95	below_threshold
Bacteroides faecis	strain=MAJ27	GCA_000226135.2	674529	674529	type	True	77.4374	156	1133	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	77.2549	143	1133	95	below_threshold
Bacteroides heparinolyticus	strain=DSM 23917	GCA_004342845.1	28113	28113	type	True	76.4277	92	1133	95	below_threshold
Bacteroides graminisolvens	strain=JCM 15093	GCA_000613825.1	477666	477666	type	True	76.2731	68	1133	95	below_threshold
Bacteroides graminisolvens	strain=DSM 19988	GCA_000428125.1	477666	477666	type	True	76.1591	67	1133	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 18:47:12,830] [INFO] DFAST Taxonomy check result was written to GCA_905201455.1_ERR321346-mag-bin.16_genomic.fna/tc_result.tsv
[2023-06-17 18:47:12,830] [INFO] ===== Taxonomy check completed =====
[2023-06-17 18:47:12,830] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 18:47:12,831] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4e861d6-2c54-44b2-84a7-a637a7c47fef/dqc_reference/checkm_data
[2023-06-17 18:47:12,832] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 18:47:12,873] [INFO] Task started: CheckM
[2023-06-17 18:47:12,873] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905201455.1_ERR321346-mag-bin.16_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905201455.1_ERR321346-mag-bin.16_genomic.fna/checkm_input GCA_905201455.1_ERR321346-mag-bin.16_genomic.fna/checkm_result
[2023-06-17 18:48:02,873] [INFO] Task succeeded: CheckM
[2023-06-17 18:48:02,875] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.23%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 18:48:02,895] [INFO] ===== Completeness check finished =====
[2023-06-17 18:48:02,896] [INFO] ===== Start GTDB Search =====
[2023-06-17 18:48:02,896] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905201455.1_ERR321346-mag-bin.16_genomic.fna/markers.fasta)
[2023-06-17 18:48:02,896] [INFO] Task started: Blastn
[2023-06-17 18:48:02,896] [INFO] Running command: blastn -query GCA_905201455.1_ERR321346-mag-bin.16_genomic.fna/markers.fasta -db /var/lib/cwl/stge4e861d6-2c54-44b2-84a7-a637a7c47fef/dqc_reference/reference_markers_gtdb.fasta -out GCA_905201455.1_ERR321346-mag-bin.16_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 18:48:03,830] [INFO] Task succeeded: Blastn
[2023-06-17 18:48:03,835] [INFO] Selected 15 target genomes.
[2023-06-17 18:48:03,836] [INFO] Target genome list was writen to GCA_905201455.1_ERR321346-mag-bin.16_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 18:48:03,845] [INFO] Task started: fastANI
[2023-06-17 18:48:03,846] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e80d3a3-4ebb-4b8c-a9a1-d2bf479d9564/GCA_905201455.1_ERR321346-mag-bin.16_genomic.fna.gz --refList GCA_905201455.1_ERR321346-mag-bin.16_genomic.fna/target_genomes_gtdb.txt --output GCA_905201455.1_ERR321346-mag-bin.16_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 18:48:13,527] [INFO] Task succeeded: fastANI
[2023-06-17 18:48:13,544] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 18:48:13,544] [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_000432735.1	s__Phocaeicola sp000432735	98.4471	921	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.41	98.37	0.86	0.85	3	conclusive
GCA_000436795.1	s__Phocaeicola sp000436795	88.1103	656	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.87	99.87	0.96	0.96	3	-
GCF_000154845.1	s__Phocaeicola coprocola	82.779	724	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.02	97.39	0.78	0.65	17	-
GCF_013618865.1	s__Phocaeicola sp900541515	80.2727	359	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.28	99.22	0.94	0.91	4	-
GCF_000187895.1	s__Phocaeicola plebeius	80.124	347	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.22	96.70	0.79	0.55	12	-
GCA_902362595.1	s__Phocaeicola merdigallinarum	79.8506	344	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.33	96.40	0.87	0.80	6	-
GCF_900128495.1	s__Phocaeicola ilei	79.6675	340	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.42	98.42	0.92	0.92	2	-
GCF_003437535.1	s__Phocaeicola plebeius_A	79.424	335	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.72	95.85	0.84	0.73	27	-
GCF_000374585.1	s__Phocaeicola barnesiae	79.3545	337	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.58	98.10	0.88	0.84	8	-
GCA_900552075.1	s__Phocaeicola sp900552075	79.1627	243	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553185.1	s__Phocaeicola sp900553185	79.1015	232	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.97	99.95	0.91	0.85	3	-
GCA_900542985.1	s__Phocaeicola sp900542985	79.0253	285	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.63	98.57	0.79	0.72	3	-
GCF_016900695.1	s__Phocaeicola sp900540105	78.8313	251	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.97	98.76	0.92	0.88	6	-
GCA_905198575.1	s__Phocaeicola sp905198575	77.6628	181	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004558305.1	s__Phocaeicola plebeius_B	77.2112	143	1133	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 18:48:13,546] [INFO] GTDB search result was written to GCA_905201455.1_ERR321346-mag-bin.16_genomic.fna/result_gtdb.tsv
[2023-06-17 18:48:13,547] [INFO] ===== GTDB Search completed =====
[2023-06-17 18:48:13,555] [INFO] DFAST_QC result json was written to GCA_905201455.1_ERR321346-mag-bin.16_genomic.fna/dqc_result.json
[2023-06-17 18:48:13,555] [INFO] DFAST_QC completed!
[2023-06-17 18:48:13,555] [INFO] Total running time: 0h1m35s