[2023-06-13 11:30:16,060] [INFO] DFAST_QC pipeline started.
[2023-06-13 11:30:16,064] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 11:30:16,064] [INFO] DQC Reference Directory: /var/lib/cwl/stg5853a10d-ea3c-4154-8595-84e4ef63171e/dqc_reference
[2023-06-13 11:30:17,552] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 11:30:17,553] [INFO] Task started: Prodigal
[2023-06-13 11:30:17,553] [INFO] Running command: gunzip -c /var/lib/cwl/stg677d2a3d-2156-4e55-b4a5-87f9b9c43952/GCA_022482585.1_ASM2248258v1_genomic.fna.gz | prodigal -d GCA_022482585.1_ASM2248258v1_genomic.fna/cds.fna -a GCA_022482585.1_ASM2248258v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 11:30:25,056] [INFO] Task succeeded: Prodigal
[2023-06-13 11:30:25,057] [INFO] Task started: HMMsearch
[2023-06-13 11:30:25,057] [INFO] Running command: hmmsearch --tblout GCA_022482585.1_ASM2248258v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5853a10d-ea3c-4154-8595-84e4ef63171e/dqc_reference/reference_markers.hmm GCA_022482585.1_ASM2248258v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 11:30:25,273] [INFO] Task succeeded: HMMsearch
[2023-06-13 11:30:25,274] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg677d2a3d-2156-4e55-b4a5-87f9b9c43952/GCA_022482585.1_ASM2248258v1_genomic.fna.gz]
[2023-06-13 11:30:25,308] [INFO] Query marker FASTA was written to GCA_022482585.1_ASM2248258v1_genomic.fna/markers.fasta
[2023-06-13 11:30:25,308] [INFO] Task started: Blastn
[2023-06-13 11:30:25,309] [INFO] Running command: blastn -query GCA_022482585.1_ASM2248258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5853a10d-ea3c-4154-8595-84e4ef63171e/dqc_reference/reference_markers.fasta -out GCA_022482585.1_ASM2248258v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:30:25,931] [INFO] Task succeeded: Blastn
[2023-06-13 11:30:25,935] [INFO] Selected 23 target genomes.
[2023-06-13 11:30:25,935] [INFO] Target genome list was writen to GCA_022482585.1_ASM2248258v1_genomic.fna/target_genomes.txt
[2023-06-13 11:30:25,940] [INFO] Task started: fastANI
[2023-06-13 11:30:25,941] [INFO] Running command: fastANI --query /var/lib/cwl/stg677d2a3d-2156-4e55-b4a5-87f9b9c43952/GCA_022482585.1_ASM2248258v1_genomic.fna.gz --refList GCA_022482585.1_ASM2248258v1_genomic.fna/target_genomes.txt --output GCA_022482585.1_ASM2248258v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 11:30:39,184] [INFO] Task succeeded: fastANI
[2023-06-13 11:30:39,185] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5853a10d-ea3c-4154-8595-84e4ef63171e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 11:30:39,185] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5853a10d-ea3c-4154-8595-84e4ef63171e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 11:30:39,200] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 11:30:39,200] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 11:30:39,200] [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
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	78.7439	192	796	95	below_threshold
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	78.6762	184	796	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_000143845.1	133926	133926	suspected-type	True	78.4753	157	796	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	78.4646	183	796	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_001437585.1	133926	133926	suspected-type	True	78.4023	153	796	95	below_threshold
Parolsenella catena	strain=JCM 31932	GCA_003966955.1	2003188	2003188	type	True	78.361	140	796	95	below_threshold
Olsenella massiliensis	strain=SIT9	GCA_001457795.1	1622075	1622075	type	True	78.2902	137	796	95	below_threshold
Olsenella phocaeensis	strain=Marseille-P2936	GCA_900120385.1	1852385	1852385	type	True	78.175	165	796	95	below_threshold
Thermophilibacter immobilis	strain=LZLJ-2	GCA_015277515.1	2779519	2779519	type	True	78.0003	161	796	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	77.8883	81	796	95	below_threshold
Eggerthella guodeyinii	strain=HF-1101	GCA_009834925.2	2690837	2690837	type	True	77.1511	71	796	95	below_threshold
Gordonibacter pamelaeae	strain=7-10-1-bT	GCA_000210055.1	471189	471189	type	True	76.8647	57	796	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 11:30:39,203] [INFO] DFAST Taxonomy check result was written to GCA_022482585.1_ASM2248258v1_genomic.fna/tc_result.tsv
[2023-06-13 11:30:39,203] [INFO] ===== Taxonomy check completed =====
[2023-06-13 11:30:39,204] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 11:30:39,204] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5853a10d-ea3c-4154-8595-84e4ef63171e/dqc_reference/checkm_data
[2023-06-13 11:30:39,205] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 11:30:39,235] [INFO] Task started: CheckM
[2023-06-13 11:30:39,235] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022482585.1_ASM2248258v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022482585.1_ASM2248258v1_genomic.fna/checkm_input GCA_022482585.1_ASM2248258v1_genomic.fna/checkm_result
[2023-06-13 11:31:06,629] [INFO] Task succeeded: CheckM
[2023-06-13 11:31:06,630] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 11:31:06,652] [INFO] ===== Completeness check finished =====
[2023-06-13 11:31:06,652] [INFO] ===== Start GTDB Search =====
[2023-06-13 11:31:06,653] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022482585.1_ASM2248258v1_genomic.fna/markers.fasta)
[2023-06-13 11:31:06,653] [INFO] Task started: Blastn
[2023-06-13 11:31:06,653] [INFO] Running command: blastn -query GCA_022482585.1_ASM2248258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5853a10d-ea3c-4154-8595-84e4ef63171e/dqc_reference/reference_markers_gtdb.fasta -out GCA_022482585.1_ASM2248258v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 11:31:07,653] [INFO] Task succeeded: Blastn
[2023-06-13 11:31:07,658] [INFO] Selected 22 target genomes.
[2023-06-13 11:31:07,659] [INFO] Target genome list was writen to GCA_022482585.1_ASM2248258v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 11:31:07,670] [INFO] Task started: fastANI
[2023-06-13 11:31:07,670] [INFO] Running command: fastANI --query /var/lib/cwl/stg677d2a3d-2156-4e55-b4a5-87f9b9c43952/GCA_022482585.1_ASM2248258v1_genomic.fna.gz --refList GCA_022482585.1_ASM2248258v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022482585.1_ASM2248258v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 11:31:18,461] [INFO] Task succeeded: fastANI
[2023-06-13 11:31:18,483] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 11:31:18,483] [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_900314535.1	s__UBA7748 sp900314535	96.0712	581	796	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA7748	95.0	97.59	96.11	0.86	0.80	25	conclusive
GCA_900313905.1	s__UBA7748 sp900313905	82.8311	441	796	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA7748	95.0	98.35	97.65	0.88	0.82	5	-
GCA_000752675.2	s__Tractidigestivibacter sp000752675	79.3203	197	796	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	98.74	96.78	0.93	0.90	14	-
GCF_018128285.1	s__UBA7748 sp003862175	79.2359	219	796	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA7748	95.0	97.46	97.46	0.77	0.77	2	-
GCF_900119625.1	s__Tractidigestivibacter sp900119625	79.0853	203	796	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	96.91	96.91	0.78	0.78	2	-
GCA_900314575.1	s__UBA7741 sp900314575	79.0055	193	796	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA7741	95.0	99.08	98.17	0.92	0.85	3	-
GCF_012844235.1	s__Parafannyhessea sp900538935	78.9996	203	796	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	96.97	96.59	0.88	0.86	4	-
GCA_902834555.1	s__Tractidigestivibacter sp902834555	78.9731	193	796	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_900770865.1	s__Tractidigestivibacter sp900770865	78.8005	147	796	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002331575.1	s__Olsenella_D sp002331575	78.779	179	796	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902780325.1	s__Parafannyhessea sp902787335	78.676	160	796	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	97.70	97.32	0.78	0.75	9	-
GCF_001494635.1	s__Tractidigestivibacter scatoligenes	78.6266	202	796	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902773995.1	s__Tractidigestivibacter sp902773995	78.626	190	796	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	98.13	97.55	0.87	0.83	4	-
GCF_016899935.1	s__Thermophilibacter uli_B	78.5576	172	796	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119385.1	s__Thermophilibacter mediterraneus	78.465	183	796	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111255.1	s__Parafannyhessea umbonata_A	78.1138	163	796	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	99.32	99.30	0.95	0.94	4	-
GCA_019116525.1	s__Thermophilibacter pullistercoris	78.077	131	796	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544655.1	s__Parolsenella sp900544655	77.9568	91	796	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	99.93	99.93	0.89	0.89	2	-
GCA_015062715.1	s__SIG37 sp015062715	77.9431	114	796	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__SIG37	95.0	96.94	96.94	0.73	0.73	2	-
GCA_900314645.1	s__UBA1367 sp900314645	77.3798	126	796	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	98.42	97.54	0.93	0.89	4	-
GCA_017941705.1	s__UBA1367 sp017941705	77.2684	109	796	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902795635.1	s__CADBMC01 sp902795635	76.647	114	796	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__CADBMC01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 11:31:18,485] [INFO] GTDB search result was written to GCA_022482585.1_ASM2248258v1_genomic.fna/result_gtdb.tsv
[2023-06-13 11:31:18,486] [INFO] ===== GTDB Search completed =====
[2023-06-13 11:31:18,491] [INFO] DFAST_QC result json was written to GCA_022482585.1_ASM2248258v1_genomic.fna/dqc_result.json
[2023-06-13 11:31:18,491] [INFO] DFAST_QC completed!
[2023-06-13 11:31:18,491] [INFO] Total running time: 0h1m2s