[2024-01-25 17:46:20,394] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:46:20,395] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:46:20,395] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d7070c9-4ad8-4328-bafb-35cb1bb2b9af/dqc_reference
[2024-01-25 17:46:21,604] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:46:21,605] [INFO] Task started: Prodigal
[2024-01-25 17:46:21,605] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ca0c61e-3f60-4c8f-a3da-65a6ee340af6/GCF_022834715.1_ASM2283471v1_genomic.fna.gz | prodigal -d GCF_022834715.1_ASM2283471v1_genomic.fna/cds.fna -a GCF_022834715.1_ASM2283471v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:46:27,722] [INFO] Task succeeded: Prodigal
[2024-01-25 17:46:27,722] [INFO] Task started: HMMsearch
[2024-01-25 17:46:27,722] [INFO] Running command: hmmsearch --tblout GCF_022834715.1_ASM2283471v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d7070c9-4ad8-4328-bafb-35cb1bb2b9af/dqc_reference/reference_markers.hmm GCF_022834715.1_ASM2283471v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:46:27,904] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:46:27,905] [INFO] Found 6/6 markers.
[2024-01-25 17:46:27,927] [INFO] Query marker FASTA was written to GCF_022834715.1_ASM2283471v1_genomic.fna/markers.fasta
[2024-01-25 17:46:27,927] [INFO] Task started: Blastn
[2024-01-25 17:46:27,927] [INFO] Running command: blastn -query GCF_022834715.1_ASM2283471v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d7070c9-4ad8-4328-bafb-35cb1bb2b9af/dqc_reference/reference_markers.fasta -out GCF_022834715.1_ASM2283471v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:28,625] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:28,628] [INFO] Selected 12 target genomes.
[2024-01-25 17:46:28,628] [INFO] Target genome list was writen to GCF_022834715.1_ASM2283471v1_genomic.fna/target_genomes.txt
[2024-01-25 17:46:28,632] [INFO] Task started: fastANI
[2024-01-25 17:46:28,632] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ca0c61e-3f60-4c8f-a3da-65a6ee340af6/GCF_022834715.1_ASM2283471v1_genomic.fna.gz --refList GCF_022834715.1_ASM2283471v1_genomic.fna/target_genomes.txt --output GCF_022834715.1_ASM2283471v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:46:34,072] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:34,072] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d7070c9-4ad8-4328-bafb-35cb1bb2b9af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:46:34,072] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d7070c9-4ad8-4328-bafb-35cb1bb2b9af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:46:34,081] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:46:34,082] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:46:34,082] [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	80.0805	231	742	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	79.9539	252	742	95	below_threshold
Parolsenella massiliensis	strain=Marseille-P3237	GCA_900143685.1	1871022	1871022	type	True	79.7119	238	742	95	below_threshold
Parolsenella catena	strain=JCM 31932	GCA_003966955.1	2003188	2003188	type	True	79.7008	226	742	95	below_threshold
Olsenella phocaeensis	strain=Marseille-P2936	GCA_900120385.1	1852385	1852385	type	True	79.6174	208	742	95	below_threshold
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	79.5871	277	742	95	below_threshold
Thermophilibacter immobilis	strain=LZLJ-2	GCA_015277515.1	2779519	2779519	type	True	79.5252	215	742	95	below_threshold
Olsenella urininfantis	strain=Marseille-P3197	GCA_900155635.1	1871033	1871033	type	True	79.0887	190	742	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	78.9127	208	742	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	78.8906	178	742	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	78.7365	196	742	95	below_threshold
Eggerthella guodeyinii	strain=HF-1101	GCA_009834925.2	2690837	2690837	type	True	77.6064	140	742	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:46:34,083] [INFO] DFAST Taxonomy check result was written to GCF_022834715.1_ASM2283471v1_genomic.fna/tc_result.tsv
[2024-01-25 17:46:34,084] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:46:34,084] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:46:34,084] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d7070c9-4ad8-4328-bafb-35cb1bb2b9af/dqc_reference/checkm_data
[2024-01-25 17:46:34,085] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:46:34,109] [INFO] Task started: CheckM
[2024-01-25 17:46:34,110] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022834715.1_ASM2283471v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022834715.1_ASM2283471v1_genomic.fna/checkm_input GCF_022834715.1_ASM2283471v1_genomic.fna/checkm_result
[2024-01-25 17:46:57,061] [INFO] Task succeeded: CheckM
[2024-01-25 17:46:57,062] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:46:57,078] [INFO] ===== Completeness check finished =====
[2024-01-25 17:46:57,078] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:46:57,078] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022834715.1_ASM2283471v1_genomic.fna/markers.fasta)
[2024-01-25 17:46:57,078] [INFO] Task started: Blastn
[2024-01-25 17:46:57,078] [INFO] Running command: blastn -query GCF_022834715.1_ASM2283471v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d7070c9-4ad8-4328-bafb-35cb1bb2b9af/dqc_reference/reference_markers_gtdb.fasta -out GCF_022834715.1_ASM2283471v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:58,353] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:58,355] [INFO] Selected 17 target genomes.
[2024-01-25 17:46:58,356] [INFO] Target genome list was writen to GCF_022834715.1_ASM2283471v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:46:58,377] [INFO] Task started: fastANI
[2024-01-25 17:46:58,377] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ca0c61e-3f60-4c8f-a3da-65a6ee340af6/GCF_022834715.1_ASM2283471v1_genomic.fna.gz --refList GCF_022834715.1_ASM2283471v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022834715.1_ASM2283471v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:47:05,984] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:05,995] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:47:05,995] [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_004793665.1	s__NM07-P-09 sp004793665	99.4356	718	742	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__NM07-P-09	95.0	99.12	98.60	0.95	0.93	6	conclusive
GCF_012584445.1	s__NM07-P-09 sp012584445	80.8237	323	742	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__NM07-P-09	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004793925.1	s__NM07-P-09 sp004793925	80.6689	301	742	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__NM07-P-09	95.0	99.80	99.80	0.98	0.98	2	-
GCF_002159735.1	s__Thermophilibacter sp002159735	80.2186	233	742	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014982725.1	s__Thermophilibacter sp014982725	80.2137	246	742	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	80.1875	241	742	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215465.1	s__Paratractidigestivibacter sp905215465	79.978	226	742	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Paratractidigestivibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143685.1	s__Parolsenella massiliensis	79.6374	238	742	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	96.67	96.67	0.91	0.91	2	-
GCF_016900775.1	s__Thermophilibacter uli_A	79.6046	272	742	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901212675.1	s__Parolsenella uli_B	79.5611	262	742	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	96.31	96.31	0.90	0.90	2	-
GCA_019116265.1	s__Thermophilibacter stercoravium	79.546	197	742	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902791035.1	s__CADAUA01 sp900315375	79.5017	235	742	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__CADAUA01	95.0	99.88	99.88	0.96	0.96	2	-
GCA_900543875.1	s__Parolsenella sp900543875	79.4845	207	742	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	98.15	98.15	0.88	0.88	2	-
GCA_902795065.1	s__RUG721 sp900321745	79.3539	188	742	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__RUG721	95.0	99.01	98.55	0.89	0.82	11	-
GCA_900549525.1	s__Parolsenella sp900549525	79.0766	184	742	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	99.58	99.58	0.87	0.87	2	-
GCA_902779675.1	s__UBA1367 sp902779675	78.9968	204	742	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	97.95	97.30	0.86	0.82	4	-
GCF_900605015.1	s__Tractidigestivibacter sp900605015	78.4819	182	742	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Tractidigestivibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:47:05,997] [INFO] GTDB search result was written to GCF_022834715.1_ASM2283471v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:47:05,997] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:47:06,005] [INFO] DFAST_QC result json was written to GCF_022834715.1_ASM2283471v1_genomic.fna/dqc_result.json
[2024-01-25 17:47:06,005] [INFO] DFAST_QC completed!
[2024-01-25 17:47:06,005] [INFO] Total running time: 0h0m46s