[2024-01-24 12:44:08,614] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:08,616] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:08,616] [INFO] DQC Reference Directory: /var/lib/cwl/stg90ab584c-ad5d-44b2-9100-ce54c491ae12/dqc_reference
[2024-01-24 12:44:09,897] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:09,898] [INFO] Task started: Prodigal
[2024-01-24 12:44:09,898] [INFO] Running command: gunzip -c /var/lib/cwl/stg8450fea1-5fb1-4077-a24f-c8b1b28e579f/GCF_014837055.1_ASM1483705v1_genomic.fna.gz | prodigal -d GCF_014837055.1_ASM1483705v1_genomic.fna/cds.fna -a GCF_014837055.1_ASM1483705v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:28,313] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:28,314] [INFO] Task started: HMMsearch
[2024-01-24 12:44:28,314] [INFO] Running command: hmmsearch --tblout GCF_014837055.1_ASM1483705v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90ab584c-ad5d-44b2-9100-ce54c491ae12/dqc_reference/reference_markers.hmm GCF_014837055.1_ASM1483705v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:28,649] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:28,651] [INFO] Found 6/6 markers.
[2024-01-24 12:44:28,685] [INFO] Query marker FASTA was written to GCF_014837055.1_ASM1483705v1_genomic.fna/markers.fasta
[2024-01-24 12:44:28,685] [INFO] Task started: Blastn
[2024-01-24 12:44:28,685] [INFO] Running command: blastn -query GCF_014837055.1_ASM1483705v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90ab584c-ad5d-44b2-9100-ce54c491ae12/dqc_reference/reference_markers.fasta -out GCF_014837055.1_ASM1483705v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:29,311] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:29,316] [INFO] Selected 19 target genomes.
[2024-01-24 12:44:29,317] [INFO] Target genome list was writen to GCF_014837055.1_ASM1483705v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:29,329] [INFO] Task started: fastANI
[2024-01-24 12:44:29,329] [INFO] Running command: fastANI --query /var/lib/cwl/stg8450fea1-5fb1-4077-a24f-c8b1b28e579f/GCF_014837055.1_ASM1483705v1_genomic.fna.gz --refList GCF_014837055.1_ASM1483705v1_genomic.fna/target_genomes.txt --output GCF_014837055.1_ASM1483705v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:43,509] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:43,510] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90ab584c-ad5d-44b2-9100-ce54c491ae12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:43,510] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90ab584c-ad5d-44b2-9100-ce54c491ae12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:43,522] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:44:43,522] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:43,522] [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 faecium	strain=Sa1YUN3	GCA_014837055.1	2762213	2762213	type	True	100.0	1132	1132	95	conclusive
Bacteroides bouchesdurhonensis	strain=Marseille-P2653	GCA_900155865.1	1841855	1841855	type	True	80.7576	113	1132	95	below_threshold
Phocaeicola faecicola	strain=AGMB03916	GCA_013618865.1	2739389	2739389	type	True	79.7039	261	1132	95	below_threshold
Phocaeicola dorei	strain=DSM 17855	GCA_025146415.1	357276	357276	type	True	79.3195	185	1132	95	below_threshold
Phocaeicola barnesiae	strain=JCM 13652	GCA_000613645.1	376804	376804	type	True	79.314	279	1132	95	below_threshold
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	79.2818	281	1132	95	below_threshold
Phocaeicola intestinalis	strain=Sa1CVN1	GCA_014837065.1	2762212	2762212	type	True	79.1605	266	1132	95	below_threshold
Phocaeicola salanitronis	strain=DSM 18170	GCA_000190575.1	376805	376805	type	True	79.1249	299	1132	95	below_threshold
Phocaeicola coprocola	strain=DSM 17136	GCA_000154845.1	310298	310298	suspected-type	True	78.7225	249	1132	95	below_threshold
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	78.3701	278	1132	95	below_threshold
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	78.1703	227	1132	95	below_threshold
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	78.1495	230	1132	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	78.0553	128	1132	95	below_threshold
Bacteroides stercorirosoris	strain=DSM 26884	GCA_900142015.1	871324	871324	type	True	77.5764	115	1132	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	77.4998	111	1132	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:43,524] [INFO] DFAST Taxonomy check result was written to GCF_014837055.1_ASM1483705v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:43,524] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:43,525] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:43,525] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90ab584c-ad5d-44b2-9100-ce54c491ae12/dqc_reference/checkm_data
[2024-01-24 12:44:43,526] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:43,567] [INFO] Task started: CheckM
[2024-01-24 12:44:43,567] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014837055.1_ASM1483705v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014837055.1_ASM1483705v1_genomic.fna/checkm_input GCF_014837055.1_ASM1483705v1_genomic.fna/checkm_result
[2024-01-24 12:45:36,662] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:36,664] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:36,685] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:36,685] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:36,686] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014837055.1_ASM1483705v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:36,686] [INFO] Task started: Blastn
[2024-01-24 12:45:36,687] [INFO] Running command: blastn -query GCF_014837055.1_ASM1483705v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90ab584c-ad5d-44b2-9100-ce54c491ae12/dqc_reference/reference_markers_gtdb.fasta -out GCF_014837055.1_ASM1483705v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:37,525] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:37,529] [INFO] Selected 24 target genomes.
[2024-01-24 12:45:37,530] [INFO] Target genome list was writen to GCF_014837055.1_ASM1483705v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:37,573] [INFO] Task started: fastANI
[2024-01-24 12:45:37,574] [INFO] Running command: fastANI --query /var/lib/cwl/stg8450fea1-5fb1-4077-a24f-c8b1b28e579f/GCF_014837055.1_ASM1483705v1_genomic.fna.gz --refList GCF_014837055.1_ASM1483705v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014837055.1_ASM1483705v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:52,082] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:52,102] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:52,102] [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_016900695.1	s__Phocaeicola sp900540105	98.98	946	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.97	98.76	0.92	0.88	6	conclusive
GCF_900155865.1	s__Bacteroides bouchesdurhonensis	80.789	113	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.60	98.60	0.88	0.88	2	-
GCA_902362595.1	s__Phocaeicola merdigallinarum	79.8591	326	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.33	96.40	0.87	0.80	6	-
GCF_013618865.1	s__Phocaeicola sp900541515	79.6845	262	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.28	99.22	0.94	0.91	4	-
GCF_000374585.1	s__Phocaeicola barnesiae	79.2837	282	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.58	98.10	0.88	0.84	8	-
GCF_002161765.1	s__Phocaeicola merdavium	79.2675	279	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.33	98.22	0.87	0.86	5	-
GCF_000190575.1	s__Phocaeicola salanitronis	79.1111	302	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.68	97.68	0.88	0.88	2	-
GCF_900128495.1	s__Phocaeicola ilei	79.0932	228	1132	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	78.9881	283	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.72	95.85	0.84	0.73	27	-
GCF_900128455.1	s__Phocaeicola mediterraneensis	78.8964	303	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.66	98.61	0.84	0.80	3	-
GCF_000154845.1	s__Phocaeicola coprocola	78.7184	252	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.02	97.39	0.78	0.65	17	-
GCF_000187895.1	s__Phocaeicola plebeius	78.3543	279	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.22	96.70	0.79	0.55	12	-
GCA_900552075.1	s__Phocaeicola sp900552075	78.2475	191	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000157915.1	s__Phocaeicola coprophilus	78.1703	227	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.31	98.55	0.95	0.87	10	-
GCA_000432735.1	s__Phocaeicola sp000432735	77.9705	253	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.41	98.37	0.86	0.85	3	-
GCA_900542985.1	s__Phocaeicola sp900542985	77.7839	197	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.63	98.57	0.79	0.72	3	-
GCA_000434735.1	s__Phocaeicola sp000434735	77.6494	171	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.56	97.52	0.82	0.81	3	-
GCF_900142015.1	s__Bacteroides stercorirosoris	77.6061	113	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.49	98.12	0.84	0.77	7	-
GCA_000436795.1	s__Phocaeicola sp000436795	77.3952	191	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.87	99.87	0.96	0.96	3	-
GCA_004558305.1	s__Phocaeicola plebeius_B	76.986	119	1132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:52,104] [INFO] GTDB search result was written to GCF_014837055.1_ASM1483705v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:52,104] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:52,108] [INFO] DFAST_QC result json was written to GCF_014837055.1_ASM1483705v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:52,109] [INFO] DFAST_QC completed!
[2024-01-24 12:45:52,109] [INFO] Total running time: 0h1m43s