[2023-06-13 13:25:14,303] [INFO] DFAST_QC pipeline started.
[2023-06-13 13:25:14,305] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 13:25:14,305] [INFO] DQC Reference Directory: /var/lib/cwl/stg53251aa4-3996-4676-938d-6cf27fccfefb/dqc_reference
[2023-06-13 13:25:15,491] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 13:25:15,492] [INFO] Task started: Prodigal
[2023-06-13 13:25:15,492] [INFO] Running command: gunzip -c /var/lib/cwl/stg0075e342-a6bb-4759-899c-ae71bfbc7ff0/GCA_022645985.1_ASM2264598v1_genomic.fna.gz | prodigal -d GCA_022645985.1_ASM2264598v1_genomic.fna/cds.fna -a GCA_022645985.1_ASM2264598v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 13:25:22,058] [INFO] Task succeeded: Prodigal
[2023-06-13 13:25:22,058] [INFO] Task started: HMMsearch
[2023-06-13 13:25:22,059] [INFO] Running command: hmmsearch --tblout GCA_022645985.1_ASM2264598v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53251aa4-3996-4676-938d-6cf27fccfefb/dqc_reference/reference_markers.hmm GCA_022645985.1_ASM2264598v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 13:25:22,298] [INFO] Task succeeded: HMMsearch
[2023-06-13 13:25:22,300] [INFO] Found 6/6 markers.
[2023-06-13 13:25:22,323] [INFO] Query marker FASTA was written to GCA_022645985.1_ASM2264598v1_genomic.fna/markers.fasta
[2023-06-13 13:25:22,323] [INFO] Task started: Blastn
[2023-06-13 13:25:22,323] [INFO] Running command: blastn -query GCA_022645985.1_ASM2264598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53251aa4-3996-4676-938d-6cf27fccfefb/dqc_reference/reference_markers.fasta -out GCA_022645985.1_ASM2264598v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:25:23,004] [INFO] Task succeeded: Blastn
[2023-06-13 13:25:23,009] [INFO] Selected 15 target genomes.
[2023-06-13 13:25:23,009] [INFO] Target genome list was writen to GCA_022645985.1_ASM2264598v1_genomic.fna/target_genomes.txt
[2023-06-13 13:25:23,011] [INFO] Task started: fastANI
[2023-06-13 13:25:23,011] [INFO] Running command: fastANI --query /var/lib/cwl/stg0075e342-a6bb-4759-899c-ae71bfbc7ff0/GCA_022645985.1_ASM2264598v1_genomic.fna.gz --refList GCA_022645985.1_ASM2264598v1_genomic.fna/target_genomes.txt --output GCA_022645985.1_ASM2264598v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 13:25:29,046] [INFO] Task succeeded: fastANI
[2023-06-13 13:25:29,046] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53251aa4-3996-4676-938d-6cf27fccfefb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 13:25:29,046] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53251aa4-3996-4676-938d-6cf27fccfefb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 13:25:29,064] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 13:25:29,064] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 13:25:29,065] [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	79.1823	175	700	95	below_threshold
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	78.4531	182	700	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	78.3138	181	700	95	below_threshold
Parolsenella massiliensis	strain=Marseille-P3237	GCA_900143685.1	1871022	1871022	type	True	78.2223	135	700	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_000143845.1	133926	133926	suspected-type	True	78.1566	159	700	95	below_threshold
Parolsenella catena	strain=JCM 31932	GCA_003966955.1	2003188	2003188	type	True	78.0607	143	700	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_001437585.1	133926	133926	suspected-type	True	78.0346	163	700	95	below_threshold
Olsenella urininfantis	strain=Marseille-P3197	GCA_900155635.1	1871033	1871033	type	True	77.9922	145	700	95	below_threshold
Olsenella phocaeensis	strain=Marseille-P2936	GCA_900120385.1	1852385	1852385	type	True	77.897	166	700	95	below_threshold
Olsenella massiliensis	strain=SIT9	GCA_001457795.1	1622075	1622075	type	True	77.8294	140	700	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	77.2679	111	700	95	below_threshold
Slackia exigua	strain=NCTC12994	GCA_900450505.1	84109	84109	type	True	76.4329	50	700	95	below_threshold
Slackia exigua	strain=ATCC 700122	GCA_000162875.1	84109	84109	type	True	76.3592	52	700	95	below_threshold
Eggerthella guodeyinii	strain=HF-1101	GCA_009834925.2	2690837	2690837	type	True	76.2441	60	700	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 13:25:29,067] [INFO] DFAST Taxonomy check result was written to GCA_022645985.1_ASM2264598v1_genomic.fna/tc_result.tsv
[2023-06-13 13:25:29,068] [INFO] ===== Taxonomy check completed =====
[2023-06-13 13:25:29,068] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 13:25:29,069] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53251aa4-3996-4676-938d-6cf27fccfefb/dqc_reference/checkm_data
[2023-06-13 13:25:29,070] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 13:25:29,096] [INFO] Task started: CheckM
[2023-06-13 13:25:29,096] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022645985.1_ASM2264598v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022645985.1_ASM2264598v1_genomic.fna/checkm_input GCA_022645985.1_ASM2264598v1_genomic.fna/checkm_result
[2023-06-13 13:25:54,316] [INFO] Task succeeded: CheckM
[2023-06-13 13:25:54,318] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 13:25:54,343] [INFO] ===== Completeness check finished =====
[2023-06-13 13:25:54,344] [INFO] ===== Start GTDB Search =====
[2023-06-13 13:25:54,344] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022645985.1_ASM2264598v1_genomic.fna/markers.fasta)
[2023-06-13 13:25:54,345] [INFO] Task started: Blastn
[2023-06-13 13:25:54,345] [INFO] Running command: blastn -query GCA_022645985.1_ASM2264598v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53251aa4-3996-4676-938d-6cf27fccfefb/dqc_reference/reference_markers_gtdb.fasta -out GCA_022645985.1_ASM2264598v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:25:55,413] [INFO] Task succeeded: Blastn
[2023-06-13 13:25:55,419] [INFO] Selected 18 target genomes.
[2023-06-13 13:25:55,420] [INFO] Target genome list was writen to GCA_022645985.1_ASM2264598v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 13:25:55,429] [INFO] Task started: fastANI
[2023-06-13 13:25:55,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg0075e342-a6bb-4759-899c-ae71bfbc7ff0/GCA_022645985.1_ASM2264598v1_genomic.fna.gz --refList GCA_022645985.1_ASM2264598v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022645985.1_ASM2264598v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 13:26:02,684] [INFO] Task succeeded: fastANI
[2023-06-13 13:26:02,699] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 13:26:02,699] [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	97.1746	606	700	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	83.1925	421	700	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA7748	95.0	98.35	97.65	0.88	0.82	5	-
GCA_902780325.1	s__Parafannyhessea sp902787335	79.0675	155	700	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	97.70	97.32	0.78	0.75	9	-
GCA_003862195.1	s__Parafannyhessea sp003862195	78.9722	212	700	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parafannyhessea	95.0	97.29	97.22	0.87	0.87	4	-
GCA_900314575.1	s__UBA7741 sp900314575	78.8398	195	700	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA7741	95.0	99.08	98.17	0.92	0.85	3	-
GCF_014982725.1	s__Thermophilibacter sp014982725	78.7565	162	700	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016899935.1	s__Thermophilibacter uli_B	78.4719	163	700	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002331575.1	s__Olsenella_D sp002331575	78.4422	184	700	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_902772435.1	s__UBA1367 sp902772435	78.2849	141	700	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000752675.2	s__Tractidigestivibacter sp000752675	78.2753	187	700	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	98.74	96.78	0.93	0.90	14	-
GCA_900770865.1	s__Tractidigestivibacter sp900770865	78.2623	139	700	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902795065.1	s__RUG721 sp900321745	78.1594	146	700	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__RUG721	95.0	99.01	98.55	0.89	0.82	11	-
GCF_000143845.1	s__Olsenella uli	78.1566	159	700	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Olsenella	95.0	99.32	99.02	0.94	0.91	5	-
GCA_900314495.1	s__UBA7741 sp900314495	78.097	164	700	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA7741	95.0	98.85	98.57	0.91	0.87	9	-
GCF_003966955.1	s__Parolsenella catena	78.0607	143	700	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	98.03	97.75	0.95	0.92	5	-
GCA_019116525.1	s__Thermophilibacter pullistercoris	77.823	136	700	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549525.1	s__Parolsenella sp900549525	77.5799	112	700	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	99.58	99.58	0.87	0.87	2	-
GCA_900314645.1	s__UBA1367 sp900314645	77.4119	125	700	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	98.42	97.54	0.93	0.89	4	-
--------------------------------------------------------------------------------
[2023-06-13 13:26:02,702] [INFO] GTDB search result was written to GCA_022645985.1_ASM2264598v1_genomic.fna/result_gtdb.tsv
[2023-06-13 13:26:02,702] [INFO] ===== GTDB Search completed =====
[2023-06-13 13:26:02,706] [INFO] DFAST_QC result json was written to GCA_022645985.1_ASM2264598v1_genomic.fna/dqc_result.json
[2023-06-13 13:26:02,706] [INFO] DFAST_QC completed!
[2023-06-13 13:26:02,707] [INFO] Total running time: 0h0m48s