[2023-06-13 16:35:20,185] [INFO] DFAST_QC pipeline started.
[2023-06-13 16:35:20,188] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 16:35:20,188] [INFO] DQC Reference Directory: /var/lib/cwl/stg95b792f9-60aa-4a6c-8bb7-b60b92c9c355/dqc_reference
[2023-06-13 16:35:21,337] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 16:35:21,338] [INFO] Task started: Prodigal
[2023-06-13 16:35:21,338] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf568cd4-3a44-4cd6-91f5-a80d1fb5843c/GCA_022482885.1_ASM2248288v1_genomic.fna.gz | prodigal -d GCA_022482885.1_ASM2248288v1_genomic.fna/cds.fna -a GCA_022482885.1_ASM2248288v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 16:35:29,555] [INFO] Task succeeded: Prodigal
[2023-06-13 16:35:29,556] [INFO] Task started: HMMsearch
[2023-06-13 16:35:29,556] [INFO] Running command: hmmsearch --tblout GCA_022482885.1_ASM2248288v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95b792f9-60aa-4a6c-8bb7-b60b92c9c355/dqc_reference/reference_markers.hmm GCA_022482885.1_ASM2248288v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 16:35:29,711] [INFO] Task succeeded: HMMsearch
[2023-06-13 16:35:29,713] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbf568cd4-3a44-4cd6-91f5-a80d1fb5843c/GCA_022482885.1_ASM2248288v1_genomic.fna.gz]
[2023-06-13 16:35:29,736] [INFO] Query marker FASTA was written to GCA_022482885.1_ASM2248288v1_genomic.fna/markers.fasta
[2023-06-13 16:35:29,737] [INFO] Task started: Blastn
[2023-06-13 16:35:29,737] [INFO] Running command: blastn -query GCA_022482885.1_ASM2248288v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95b792f9-60aa-4a6c-8bb7-b60b92c9c355/dqc_reference/reference_markers.fasta -out GCA_022482885.1_ASM2248288v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 16:35:30,240] [INFO] Task succeeded: Blastn
[2023-06-13 16:35:30,248] [INFO] Selected 17 target genomes.
[2023-06-13 16:35:30,249] [INFO] Target genome list was writen to GCA_022482885.1_ASM2248288v1_genomic.fna/target_genomes.txt
[2023-06-13 16:35:30,251] [INFO] Task started: fastANI
[2023-06-13 16:35:30,251] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf568cd4-3a44-4cd6-91f5-a80d1fb5843c/GCA_022482885.1_ASM2248288v1_genomic.fna.gz --refList GCA_022482885.1_ASM2248288v1_genomic.fna/target_genomes.txt --output GCA_022482885.1_ASM2248288v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 16:35:37,835] [INFO] Task succeeded: fastANI
[2023-06-13 16:35:37,835] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95b792f9-60aa-4a6c-8bb7-b60b92c9c355/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 16:35:37,836] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95b792f9-60aa-4a6c-8bb7-b60b92c9c355/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 16:35:37,850] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 16:35:37,850] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 16:35:37,850] [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
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	80.0123	260	859	95	below_threshold
Olsenella phocaeensis	strain=Marseille-P2936	GCA_900120385.1	1852385	1852385	type	True	79.8995	248	859	95	below_threshold
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	79.8512	271	859	95	below_threshold
Thermophilibacter immobilis	strain=LZLJ-2	GCA_015277515.1	2779519	2779519	type	True	79.6046	259	859	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	79.5122	227	859	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_000143845.1	133926	133926	suspected-type	True	79.1602	216	859	95	below_threshold
Parolsenella massiliensis	strain=Marseille-P3237	GCA_900143685.1	1871022	1871022	type	True	79.1491	206	859	95	below_threshold
Parolsenella catena	strain=JCM 31932	GCA_003966955.1	2003188	2003188	type	True	79.1451	192	859	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_001437585.1	133926	133926	suspected-type	True	79.1369	215	859	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	77.8337	84	859	95	below_threshold
Enorma shizhengliae	strain=HF-1365	GCA_009676995.1	2606615	2606615	type	True	77.7298	102	859	95	below_threshold
Collinsella vaginalis	strain=Marseille-P2666	GCA_900176655.1	1870987	1870987	type	True	77.5278	100	859	95	below_threshold
Gordonibacter urolithinfaciens	strain=DSM 27213T	GCA_900199375.1	1335613	1335613	type	True	77.0807	76	859	95	below_threshold
Gordonibacter urolithinfaciens	strain=DSM 27213	GCA_003788975.1	1335613	1335613	type	True	76.7898	75	859	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 16:35:37,853] [INFO] DFAST Taxonomy check result was written to GCA_022482885.1_ASM2248288v1_genomic.fna/tc_result.tsv
[2023-06-13 16:35:37,854] [INFO] ===== Taxonomy check completed =====
[2023-06-13 16:35:37,854] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 16:35:37,854] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95b792f9-60aa-4a6c-8bb7-b60b92c9c355/dqc_reference/checkm_data
[2023-06-13 16:35:37,856] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 16:35:37,883] [INFO] Task started: CheckM
[2023-06-13 16:35:37,883] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022482885.1_ASM2248288v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022482885.1_ASM2248288v1_genomic.fna/checkm_input GCA_022482885.1_ASM2248288v1_genomic.fna/checkm_result
[2023-06-13 16:36:06,012] [INFO] Task succeeded: CheckM
[2023-06-13 16:36:06,013] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 16:36:06,030] [INFO] ===== Completeness check finished =====
[2023-06-13 16:36:06,030] [INFO] ===== Start GTDB Search =====
[2023-06-13 16:36:06,031] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022482885.1_ASM2248288v1_genomic.fna/markers.fasta)
[2023-06-13 16:36:06,031] [INFO] Task started: Blastn
[2023-06-13 16:36:06,031] [INFO] Running command: blastn -query GCA_022482885.1_ASM2248288v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95b792f9-60aa-4a6c-8bb7-b60b92c9c355/dqc_reference/reference_markers_gtdb.fasta -out GCA_022482885.1_ASM2248288v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 16:36:06,581] [INFO] Task succeeded: Blastn
[2023-06-13 16:36:06,589] [INFO] Selected 10 target genomes.
[2023-06-13 16:36:06,589] [INFO] Target genome list was writen to GCA_022482885.1_ASM2248288v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 16:36:06,617] [INFO] Task started: fastANI
[2023-06-13 16:36:06,617] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf568cd4-3a44-4cd6-91f5-a80d1fb5843c/GCA_022482885.1_ASM2248288v1_genomic.fna.gz --refList GCA_022482885.1_ASM2248288v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022482885.1_ASM2248288v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 16:36:11,737] [INFO] Task succeeded: fastANI
[2023-06-13 16:36:11,747] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 16:36:11,748] [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_900548775.1	s__Tractidigestivibacter sp900548775	87.2119	502	859	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	98.69	98.21	0.83	0.74	10	-
GCA_902834555.1	s__Tractidigestivibacter sp902834555	87.046	585	859	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900119625.1	s__Tractidigestivibacter sp900119625	86.9783	563	859	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	96.91	96.91	0.78	0.78	2	-
GCF_001494635.1	s__Tractidigestivibacter scatoligenes	86.9289	576	859	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000752675.2	s__Tractidigestivibacter sp000752675	86.8226	576	859	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	98.74	96.78	0.93	0.90	14	-
GCA_900768455.1	s__Tractidigestivibacter sp900768455	86.8077	477	859	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	97.35	97.35	0.93	0.93	2	-
GCA_902773995.1	s__Tractidigestivibacter sp902773995	86.7289	523	859	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	98.13	97.55	0.87	0.83	4	-
GCA_900770865.1	s__Tractidigestivibacter sp900770865	86.4409	373	859	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214175.1	s__Tractidigestivibacter sp905214175	85.9877	350	859	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004557505.1	s__Tractidigestivibacter sp004557505	85.3426	509	859	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 16:36:11,750] [INFO] GTDB search result was written to GCA_022482885.1_ASM2248288v1_genomic.fna/result_gtdb.tsv
[2023-06-13 16:36:11,751] [INFO] ===== GTDB Search completed =====
[2023-06-13 16:36:11,755] [INFO] DFAST_QC result json was written to GCA_022482885.1_ASM2248288v1_genomic.fna/dqc_result.json
[2023-06-13 16:36:11,755] [INFO] DFAST_QC completed!
[2023-06-13 16:36:11,755] [INFO] Total running time: 0h0m52s