[2023-06-28 22:10:18,175] [INFO] DFAST_QC pipeline started.
[2023-06-28 22:10:18,178] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 22:10:18,178] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e52bf4e-fefb-4e5f-845c-e7c50513913f/dqc_reference
[2023-06-28 22:10:19,496] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 22:10:19,496] [INFO] Task started: Prodigal
[2023-06-28 22:10:19,497] [INFO] Running command: gunzip -c /var/lib/cwl/stgd890e53b-d466-4dc6-aab8-1f75653c4a84/GCA_944320545.1_BRZ_BF_bin132_genomic.fna.gz | prodigal -d GCA_944320545.1_BRZ_BF_bin132_genomic.fna/cds.fna -a GCA_944320545.1_BRZ_BF_bin132_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 22:10:33,926] [INFO] Task succeeded: Prodigal
[2023-06-28 22:10:33,926] [INFO] Task started: HMMsearch
[2023-06-28 22:10:33,926] [INFO] Running command: hmmsearch --tblout GCA_944320545.1_BRZ_BF_bin132_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e52bf4e-fefb-4e5f-845c-e7c50513913f/dqc_reference/reference_markers.hmm GCA_944320545.1_BRZ_BF_bin132_genomic.fna/protein.faa > /dev/null
[2023-06-28 22:10:34,198] [INFO] Task succeeded: HMMsearch
[2023-06-28 22:10:34,200] [INFO] Found 6/6 markers.
[2023-06-28 22:10:34,238] [INFO] Query marker FASTA was written to GCA_944320545.1_BRZ_BF_bin132_genomic.fna/markers.fasta
[2023-06-28 22:10:34,238] [INFO] Task started: Blastn
[2023-06-28 22:10:34,238] [INFO] Running command: blastn -query GCA_944320545.1_BRZ_BF_bin132_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e52bf4e-fefb-4e5f-845c-e7c50513913f/dqc_reference/reference_markers.fasta -out GCA_944320545.1_BRZ_BF_bin132_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:10:34,906] [INFO] Task succeeded: Blastn
[2023-06-28 22:10:34,910] [INFO] Selected 18 target genomes.
[2023-06-28 22:10:34,910] [INFO] Target genome list was writen to GCA_944320545.1_BRZ_BF_bin132_genomic.fna/target_genomes.txt
[2023-06-28 22:10:34,915] [INFO] Task started: fastANI
[2023-06-28 22:10:34,915] [INFO] Running command: fastANI --query /var/lib/cwl/stgd890e53b-d466-4dc6-aab8-1f75653c4a84/GCA_944320545.1_BRZ_BF_bin132_genomic.fna.gz --refList GCA_944320545.1_BRZ_BF_bin132_genomic.fna/target_genomes.txt --output GCA_944320545.1_BRZ_BF_bin132_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 22:10:47,414] [INFO] Task succeeded: fastANI
[2023-06-28 22:10:47,414] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e52bf4e-fefb-4e5f-845c-e7c50513913f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 22:10:47,415] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e52bf4e-fefb-4e5f-845c-e7c50513913f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 22:10:47,429] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2023-06-28 22:10:47,429] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 22:10:47,429] [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	97.8896	871	1053	95	conclusive
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	79.1247	304	1053	95	below_threshold
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	78.9506	297	1053	95	below_threshold
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	78.7246	261	1053	95	below_threshold
Phocaeicola barnesiae	strain=JCM 13652	GCA_000613645.1	376804	376804	type	True	78.6911	260	1053	95	below_threshold
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	78.5414	261	1053	95	below_threshold
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	78.4624	269	1053	95	below_threshold
Phocaeicola faecium	strain=Sa1YUN3	GCA_014837055.1	2762213	2762213	type	True	78.0257	196	1053	95	below_threshold
Phocaeicola intestinalis	strain=Sa1CVN1	GCA_014837065.1	2762212	2762212	type	True	77.7199	218	1053	95	below_threshold
Bacteroides zhangwenhongii	strain=HF-5287	GCA_009193325.2	2650157	2650157	type	True	77.3786	126	1053	95	below_threshold
Bacteroides thetaiotaomicron	strain=VPI 5482	GCA_022453665.1	818	818	type	True	77.3718	148	1053	95	below_threshold
Bacteroides faecalis	strain=KCTC 15687	GCA_003865075.1	2447885	2447885	type	True	77.0612	122	1053	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	77.0497	113	1053	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	76.7562	100	1053	95	below_threshold
Bacteroides eggerthii	strain=NCTC11155	GCA_900445565.1	28111	28111	type	True	76.7368	98	1053	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_000155815.1	28111	28111	type	True	76.7149	98	1053	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 22:10:47,432] [INFO] DFAST Taxonomy check result was written to GCA_944320545.1_BRZ_BF_bin132_genomic.fna/tc_result.tsv
[2023-06-28 22:10:47,433] [INFO] ===== Taxonomy check completed =====
[2023-06-28 22:10:47,433] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 22:10:47,433] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e52bf4e-fefb-4e5f-845c-e7c50513913f/dqc_reference/checkm_data
[2023-06-28 22:10:47,435] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 22:10:47,474] [INFO] Task started: CheckM
[2023-06-28 22:10:47,475] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944320545.1_BRZ_BF_bin132_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944320545.1_BRZ_BF_bin132_genomic.fna/checkm_input GCA_944320545.1_BRZ_BF_bin132_genomic.fna/checkm_result
[2023-06-28 22:11:32,523] [INFO] Task succeeded: CheckM
[2023-06-28 22:11:32,525] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.85%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 22:11:32,546] [INFO] ===== Completeness check finished =====
[2023-06-28 22:11:32,546] [INFO] ===== Start GTDB Search =====
[2023-06-28 22:11:32,547] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944320545.1_BRZ_BF_bin132_genomic.fna/markers.fasta)
[2023-06-28 22:11:32,547] [INFO] Task started: Blastn
[2023-06-28 22:11:32,547] [INFO] Running command: blastn -query GCA_944320545.1_BRZ_BF_bin132_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e52bf4e-fefb-4e5f-845c-e7c50513913f/dqc_reference/reference_markers_gtdb.fasta -out GCA_944320545.1_BRZ_BF_bin132_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:11:33,417] [INFO] Task succeeded: Blastn
[2023-06-28 22:11:33,422] [INFO] Selected 17 target genomes.
[2023-06-28 22:11:33,423] [INFO] Target genome list was writen to GCA_944320545.1_BRZ_BF_bin132_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 22:11:33,462] [INFO] Task started: fastANI
[2023-06-28 22:11:33,463] [INFO] Running command: fastANI --query /var/lib/cwl/stgd890e53b-d466-4dc6-aab8-1f75653c4a84/GCA_944320545.1_BRZ_BF_bin132_genomic.fna.gz --refList GCA_944320545.1_BRZ_BF_bin132_genomic.fna/target_genomes_gtdb.txt --output GCA_944320545.1_BRZ_BF_bin132_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 22:11:44,907] [INFO] Task succeeded: fastANI
[2023-06-28 22:11:44,926] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 22:11:44,926] [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_000154845.1	s__Phocaeicola coprocola	97.8777	871	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.02	97.39	0.78	0.65	17	conclusive
GCA_000432735.1	s__Phocaeicola sp000432735	83.2242	694	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.41	98.37	0.86	0.85	3	-
GCA_000436795.1	s__Phocaeicola sp000436795	82.8487	593	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.87	99.87	0.96	0.96	3	-
GCF_003437535.1	s__Phocaeicola plebeius_A	79.2574	298	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.72	95.85	0.84	0.73	27	-
GCF_000187895.1	s__Phocaeicola plebeius	79.1296	304	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.22	96.70	0.79	0.55	12	-
GCA_900542985.1	s__Phocaeicola sp900542985	79.128	298	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.63	98.57	0.79	0.72	3	-
GCA_902362595.1	s__Phocaeicola merdigallinarum	78.8594	272	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.33	96.40	0.87	0.80	6	-
GCF_000374585.1	s__Phocaeicola barnesiae	78.7633	262	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.58	98.10	0.88	0.84	8	-
GCF_900128495.1	s__Phocaeicola ilei	78.7098	318	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.42	98.42	0.92	0.92	2	-
GCA_900551445.1	s__Phocaeicola sp900551445	78.6816	216	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.87	97.79	0.75	0.72	3	-
GCF_000157915.1	s__Phocaeicola coprophilus	78.4585	272	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.31	98.55	0.95	0.87	10	-
GCA_900546645.1	s__Phocaeicola sp900546645	78.1114	217	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.94	98.88	0.79	0.75	3	-
GCF_016900695.1	s__Phocaeicola sp900540105	78.0895	198	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.97	98.76	0.92	0.88	6	-
GCA_900546095.1	s__Phocaeicola excrementipullorum	77.8946	138	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.76	98.76	0.83	0.83	2	-
GCF_000155815.1	s__Bacteroides eggerthii	76.7374	98	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.86	98.28	0.85	0.74	51	-
GCA_002293435.1	s__Bacteroides sp002293435	76.4935	78	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 22:11:44,928] [INFO] GTDB search result was written to GCA_944320545.1_BRZ_BF_bin132_genomic.fna/result_gtdb.tsv
[2023-06-28 22:11:44,929] [INFO] ===== GTDB Search completed =====
[2023-06-28 22:11:44,936] [INFO] DFAST_QC result json was written to GCA_944320545.1_BRZ_BF_bin132_genomic.fna/dqc_result.json
[2023-06-28 22:11:44,936] [INFO] DFAST_QC completed!
[2023-06-28 22:11:44,936] [INFO] Total running time: 0h1m27s