[2023-06-30 07:58:33,297] [INFO] DFAST_QC pipeline started.
[2023-06-30 07:58:33,301] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 07:58:33,301] [INFO] DQC Reference Directory: /var/lib/cwl/stg79f1396d-51cc-49d2-910b-d5fc43923b94/dqc_reference
[2023-06-30 07:58:34,638] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 07:58:34,639] [INFO] Task started: Prodigal
[2023-06-30 07:58:34,639] [INFO] Running command: gunzip -c /var/lib/cwl/stgc1ba5b56-d6db-44ba-ae61-1f585578d768/GCA_900752755.1_ERS396297_56_genomic.fna.gz | prodigal -d GCA_900752755.1_ERS396297_56_genomic.fna/cds.fna -a GCA_900752755.1_ERS396297_56_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 07:58:49,351] [INFO] Task succeeded: Prodigal
[2023-06-30 07:58:49,352] [INFO] Task started: HMMsearch
[2023-06-30 07:58:49,352] [INFO] Running command: hmmsearch --tblout GCA_900752755.1_ERS396297_56_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg79f1396d-51cc-49d2-910b-d5fc43923b94/dqc_reference/reference_markers.hmm GCA_900752755.1_ERS396297_56_genomic.fna/protein.faa > /dev/null
[2023-06-30 07:58:49,612] [INFO] Task succeeded: HMMsearch
[2023-06-30 07:58:49,613] [INFO] Found 6/6 markers.
[2023-06-30 07:58:49,654] [INFO] Query marker FASTA was written to GCA_900752755.1_ERS396297_56_genomic.fna/markers.fasta
[2023-06-30 07:58:49,655] [INFO] Task started: Blastn
[2023-06-30 07:58:49,655] [INFO] Running command: blastn -query GCA_900752755.1_ERS396297_56_genomic.fna/markers.fasta -db /var/lib/cwl/stg79f1396d-51cc-49d2-910b-d5fc43923b94/dqc_reference/reference_markers.fasta -out GCA_900752755.1_ERS396297_56_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:58:50,278] [INFO] Task succeeded: Blastn
[2023-06-30 07:58:50,306] [INFO] Selected 18 target genomes.
[2023-06-30 07:58:50,307] [INFO] Target genome list was writen to GCA_900752755.1_ERS396297_56_genomic.fna/target_genomes.txt
[2023-06-30 07:58:50,309] [INFO] Task started: fastANI
[2023-06-30 07:58:50,309] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1ba5b56-d6db-44ba-ae61-1f585578d768/GCA_900752755.1_ERS396297_56_genomic.fna.gz --refList GCA_900752755.1_ERS396297_56_genomic.fna/target_genomes.txt --output GCA_900752755.1_ERS396297_56_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 07:59:03,184] [INFO] Task succeeded: fastANI
[2023-06-30 07:59:03,185] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg79f1396d-51cc-49d2-910b-d5fc43923b94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 07:59:03,185] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg79f1396d-51cc-49d2-910b-d5fc43923b94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 07:59:03,200] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2023-06-30 07:59:03,200] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-30 07:59:03,201] [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	99.0791	803	875	95	conclusive
Phocaeicola coprocola	strain=DSM 17136	GCA_000154845.1	310298	310298	suspected-type	True	78.374	192	875	95	below_threshold
Phocaeicola salanitronis	strain=DSM 18170	GCA_000190575.1	376805	376805	type	True	78.017	234	875	95	below_threshold
Phocaeicola intestinalis	strain=Sa1CVN1	GCA_014837065.1	2762212	2762212	type	True	77.8853	231	875	95	below_threshold
Phocaeicola barnesiae	strain=JCM 13652	GCA_000613645.1	376804	376804	type	True	77.746	205	875	95	below_threshold
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	77.7163	180	875	95	below_threshold
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	77.715	209	875	95	below_threshold
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	77.7085	183	875	95	below_threshold
Phocaeicola plebeius	strain=DSM 17135	GCA_000187895.1	310297	310297	suspected-type	True	77.5609	221	875	95	below_threshold
Phocaeicola dorei	strain=DSM 17855	GCA_025146415.1	357276	357276	type	True	77.1903	127	875	95	below_threshold
Bacteroides bouchesdurhonensis	strain=Marseille-P2653	GCA_900155865.1	1841855	1841855	type	True	77.059	60	875	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	76.4464	99	875	95	below_threshold
Bacteroides stercorirosoris	strain=DSM 26884	GCA_900142015.1	871324	871324	type	True	76.3808	84	875	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	76.3748	83	875	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 07:59:03,203] [INFO] DFAST Taxonomy check result was written to GCA_900752755.1_ERS396297_56_genomic.fna/tc_result.tsv
[2023-06-30 07:59:03,204] [INFO] ===== Taxonomy check completed =====
[2023-06-30 07:59:03,204] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 07:59:03,204] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg79f1396d-51cc-49d2-910b-d5fc43923b94/dqc_reference/checkm_data
[2023-06-30 07:59:03,205] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 07:59:03,237] [INFO] Task started: CheckM
[2023-06-30 07:59:03,238] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900752755.1_ERS396297_56_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900752755.1_ERS396297_56_genomic.fna/checkm_input GCA_900752755.1_ERS396297_56_genomic.fna/checkm_result
[2023-06-30 07:59:46,925] [INFO] Task succeeded: CheckM
[2023-06-30 07:59:46,926] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.80%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 07:59:46,950] [INFO] ===== Completeness check finished =====
[2023-06-30 07:59:46,950] [INFO] ===== Start GTDB Search =====
[2023-06-30 07:59:46,951] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900752755.1_ERS396297_56_genomic.fna/markers.fasta)
[2023-06-30 07:59:46,951] [INFO] Task started: Blastn
[2023-06-30 07:59:46,951] [INFO] Running command: blastn -query GCA_900752755.1_ERS396297_56_genomic.fna/markers.fasta -db /var/lib/cwl/stg79f1396d-51cc-49d2-910b-d5fc43923b94/dqc_reference/reference_markers_gtdb.fasta -out GCA_900752755.1_ERS396297_56_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:59:47,810] [INFO] Task succeeded: Blastn
[2023-06-30 07:59:47,832] [INFO] Selected 22 target genomes.
[2023-06-30 07:59:47,832] [INFO] Target genome list was writen to GCA_900752755.1_ERS396297_56_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 07:59:47,835] [INFO] Task started: fastANI
[2023-06-30 07:59:47,835] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1ba5b56-d6db-44ba-ae61-1f585578d768/GCA_900752755.1_ERS396297_56_genomic.fna.gz --refList GCA_900752755.1_ERS396297_56_genomic.fna/target_genomes_gtdb.txt --output GCA_900752755.1_ERS396297_56_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 08:00:00,469] [INFO] Task succeeded: fastANI
[2023-06-30 08:00:00,488] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 08:00:00,488] [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	99.0705	802	875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.97	98.76	0.92	0.88	6	conclusive
GCA_000432735.1	s__Phocaeicola sp000432735	79.2596	235	875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.41	98.37	0.86	0.85	3	-
GCF_000154845.1	s__Phocaeicola coprocola	78.374	192	875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.02	97.39	0.78	0.65	17	-
GCF_002161765.1	s__Phocaeicola merdavium	77.9074	217	875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.33	98.22	0.87	0.86	5	-
GCF_900128455.1	s__Phocaeicola mediterraneensis	77.8609	218	875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.66	98.61	0.84	0.80	3	-
GCF_000157915.1	s__Phocaeicola coprophilus	77.7204	181	875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.31	98.55	0.95	0.87	10	-
GCF_000374585.1	s__Phocaeicola barnesiae	77.7184	208	875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.58	98.10	0.88	0.84	8	-
GCA_902362595.1	s__Phocaeicola merdigallinarum	77.7018	241	875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.33	96.40	0.87	0.80	6	-
GCA_000436795.1	s__Phocaeicola sp000436795	77.6952	182	875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	99.87	99.87	0.96	0.96	3	-
GCF_900128495.1	s__Phocaeicola ilei	77.5939	164	875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.42	98.42	0.92	0.92	2	-
GCF_000187895.1	s__Phocaeicola plebeius	77.5375	222	875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	97.22	96.70	0.79	0.55	12	-
GCA_900553185.1	s__Phocaeicola sp900553185	77.5301	147	875	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	77.5285	161	875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.63	98.57	0.79	0.72	3	-
GCF_000382445.1	s__Phocaeicola massiliensis	77.2662	128	875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.84	98.03	0.86	0.62	25	-
GCF_900155865.1	s__Bacteroides bouchesdurhonensis	77.1003	59	875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.60	98.60	0.88	0.88	2	-
GCA_004558305.1	s__Phocaeicola plebeius_B	77.0374	93	875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142015.1	s__Bacteroides stercorirosoris	76.402	83	875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.49	98.12	0.84	0.77	7	-
GCF_014196225.1	s__Bacteroides pyogenes_A	76.1954	69	875	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.74	99.26	0.97	0.91	4	-
--------------------------------------------------------------------------------
[2023-06-30 08:00:00,490] [INFO] GTDB search result was written to GCA_900752755.1_ERS396297_56_genomic.fna/result_gtdb.tsv
[2023-06-30 08:00:00,491] [INFO] ===== GTDB Search completed =====
[2023-06-30 08:00:00,495] [INFO] DFAST_QC result json was written to GCA_900752755.1_ERS396297_56_genomic.fna/dqc_result.json
[2023-06-30 08:00:00,495] [INFO] DFAST_QC completed!
[2023-06-30 08:00:00,495] [INFO] Total running time: 0h1m27s