[2023-06-14 00:12:47,780] [INFO] DFAST_QC pipeline started.
[2023-06-14 00:12:47,785] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 00:12:47,786] [INFO] DQC Reference Directory: /var/lib/cwl/stg99c85536-e3ba-40d3-94df-0c116019cd6d/dqc_reference
[2023-06-14 00:12:49,568] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 00:12:49,569] [INFO] Task started: Prodigal
[2023-06-14 00:12:49,569] [INFO] Running command: gunzip -c /var/lib/cwl/stg64968489-a5e0-4265-b5d9-2a241c870459/GCA_022725735.1_ASM2272573v1_genomic.fna.gz | prodigal -d GCA_022725735.1_ASM2272573v1_genomic.fna/cds.fna -a GCA_022725735.1_ASM2272573v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 00:12:56,813] [INFO] Task succeeded: Prodigal
[2023-06-14 00:12:56,813] [INFO] Task started: HMMsearch
[2023-06-14 00:12:56,813] [INFO] Running command: hmmsearch --tblout GCA_022725735.1_ASM2272573v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99c85536-e3ba-40d3-94df-0c116019cd6d/dqc_reference/reference_markers.hmm GCA_022725735.1_ASM2272573v1_genomic.fna/protein.faa > /dev/null
[2023-06-14 00:12:57,040] [INFO] Task succeeded: HMMsearch
[2023-06-14 00:12:57,041] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg64968489-a5e0-4265-b5d9-2a241c870459/GCA_022725735.1_ASM2272573v1_genomic.fna.gz]
[2023-06-14 00:12:57,065] [INFO] Query marker FASTA was written to GCA_022725735.1_ASM2272573v1_genomic.fna/markers.fasta
[2023-06-14 00:12:57,065] [INFO] Task started: Blastn
[2023-06-14 00:12:57,065] [INFO] Running command: blastn -query GCA_022725735.1_ASM2272573v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99c85536-e3ba-40d3-94df-0c116019cd6d/dqc_reference/reference_markers.fasta -out GCA_022725735.1_ASM2272573v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 00:12:57,858] [INFO] Task succeeded: Blastn
[2023-06-14 00:12:57,861] [INFO] Selected 15 target genomes.
[2023-06-14 00:12:57,861] [INFO] Target genome list was writen to GCA_022725735.1_ASM2272573v1_genomic.fna/target_genomes.txt
[2023-06-14 00:12:57,862] [INFO] Task started: fastANI
[2023-06-14 00:12:57,862] [INFO] Running command: fastANI --query /var/lib/cwl/stg64968489-a5e0-4265-b5d9-2a241c870459/GCA_022725735.1_ASM2272573v1_genomic.fna.gz --refList GCA_022725735.1_ASM2272573v1_genomic.fna/target_genomes.txt --output GCA_022725735.1_ASM2272573v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 00:13:04,459] [INFO] Task succeeded: fastANI
[2023-06-14 00:13:04,460] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99c85536-e3ba-40d3-94df-0c116019cd6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 00:13:04,460] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99c85536-e3ba-40d3-94df-0c116019cd6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 00:13:04,468] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-14 00:13:04,468] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-14 00:13:04,468] [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
Parolsenella catena	strain=JCM 31932	GCA_003966955.1	2003188	2003188	type	True	82.8621	352	790	95	below_threshold
Parolsenella massiliensis	strain=Marseille-P3237	GCA_900143685.1	1871022	1871022	type	True	82.6866	362	790	95	below_threshold
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	80.236	288	790	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	79.9082	280	790	95	below_threshold
Thermophilibacter immobilis	strain=LZLJ-2	GCA_015277515.1	2779519	2779519	type	True	79.7456	246	790	95	below_threshold
Olsenella phocaeensis	strain=Marseille-P2936	GCA_900120385.1	1852385	1852385	type	True	79.4647	202	790	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	79.3416	222	790	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	79.1899	223	790	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	79.0181	208	790	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_001437585.1	133926	133926	suspected-type	True	78.7405	172	790	95	below_threshold
Olsenella uli	strain=DSM 7084	GCA_000143845.1	133926	133926	suspected-type	True	78.7094	177	790	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-14 00:13:04,470] [INFO] DFAST Taxonomy check result was written to GCA_022725735.1_ASM2272573v1_genomic.fna/tc_result.tsv
[2023-06-14 00:13:04,470] [INFO] ===== Taxonomy check completed =====
[2023-06-14 00:13:04,470] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 00:13:04,471] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99c85536-e3ba-40d3-94df-0c116019cd6d/dqc_reference/checkm_data
[2023-06-14 00:13:04,471] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 00:13:04,503] [INFO] Task started: CheckM
[2023-06-14 00:13:04,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022725735.1_ASM2272573v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022725735.1_ASM2272573v1_genomic.fna/checkm_input GCA_022725735.1_ASM2272573v1_genomic.fna/checkm_result
[2023-06-14 00:13:29,265] [INFO] Task succeeded: CheckM
[2023-06-14 00:13:29,266] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 00:13:29,282] [INFO] ===== Completeness check finished =====
[2023-06-14 00:13:29,283] [INFO] ===== Start GTDB Search =====
[2023-06-14 00:13:29,283] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022725735.1_ASM2272573v1_genomic.fna/markers.fasta)
[2023-06-14 00:13:29,283] [INFO] Task started: Blastn
[2023-06-14 00:13:29,283] [INFO] Running command: blastn -query GCA_022725735.1_ASM2272573v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99c85536-e3ba-40d3-94df-0c116019cd6d/dqc_reference/reference_markers_gtdb.fasta -out GCA_022725735.1_ASM2272573v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 00:13:30,748] [INFO] Task succeeded: Blastn
[2023-06-14 00:13:30,751] [INFO] Selected 13 target genomes.
[2023-06-14 00:13:30,751] [INFO] Target genome list was writen to GCA_022725735.1_ASM2272573v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 00:13:30,752] [INFO] Task started: fastANI
[2023-06-14 00:13:30,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg64968489-a5e0-4265-b5d9-2a241c870459/GCA_022725735.1_ASM2272573v1_genomic.fna.gz --refList GCA_022725735.1_ASM2272573v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022725735.1_ASM2272573v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 00:13:36,086] [INFO] Task succeeded: fastANI
[2023-06-14 00:13:36,107] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-14 00:13:36,107] [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_901212675.1	s__Parolsenella uli_B	96.3966	594	790	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	96.31	96.31	0.90	0.90	2	conclusive
GCF_901212655.1	s__Parolsenella uli_A	85.0202	422	790	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549525.1	s__Parolsenella sp900549525	84.0761	345	790	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	99.58	99.58	0.87	0.87	2	-
GCF_003966955.1	s__Parolsenella catena	82.8786	351	790	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	98.03	97.75	0.95	0.92	5	-
GCA_900543875.1	s__Parolsenella sp900543875	82.7016	313	790	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	98.15	98.15	0.88	0.88	2	-
GCF_900143685.1	s__Parolsenella massiliensis	82.6866	362	790	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	96.67	96.67	0.91	0.91	2	-
GCA_900544655.1	s__Parolsenella sp900544655	81.6854	197	790	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	99.93	99.93	0.89	0.89	2	-
GCA_900552935.1	s__Parolsenella sp900552935	81.084	225	790	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Parolsenella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116265.1	s__Thermophilibacter stercoravium	80.4334	216	790	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159625.1	s__Thermophilibacter avicola	80.2873	262	790	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	97.98	97.98	0.90	0.90	2	-
GCF_016899935.1	s__Thermophilibacter uli_B	80.1625	270	790	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540955.1	s__Paratractidigestivibacter sp900540955	79.6485	215	790	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Paratractidigestivibacter	95.0	96.08	96.08	0.89	0.89	2	-
GCA_900752345.1	s__Collinsella sp900752345	78.5035	124	790	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-14 00:13:36,109] [INFO] GTDB search result was written to GCA_022725735.1_ASM2272573v1_genomic.fna/result_gtdb.tsv
[2023-06-14 00:13:36,109] [INFO] ===== GTDB Search completed =====
[2023-06-14 00:13:36,112] [INFO] DFAST_QC result json was written to GCA_022725735.1_ASM2272573v1_genomic.fna/dqc_result.json
[2023-06-14 00:13:36,113] [INFO] DFAST_QC completed!
[2023-06-14 00:13:36,113] [INFO] Total running time: 0h0m48s