[2023-06-28 19:29:52,720] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:29:52,723] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:29:52,723] [INFO] DQC Reference Directory: /var/lib/cwl/stg69845a80-088c-4136-9716-c8489e83b0e7/dqc_reference
[2023-06-28 19:29:54,062] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:29:54,063] [INFO] Task started: Prodigal
[2023-06-28 19:29:54,063] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6d88ad5-d772-4148-ae09-e7104c2d6e27/GCA_020200255.1_ASM2020025v1_genomic.fna.gz | prodigal -d GCA_020200255.1_ASM2020025v1_genomic.fna/cds.fna -a GCA_020200255.1_ASM2020025v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:30:09,889] [INFO] Task succeeded: Prodigal
[2023-06-28 19:30:09,889] [INFO] Task started: HMMsearch
[2023-06-28 19:30:09,889] [INFO] Running command: hmmsearch --tblout GCA_020200255.1_ASM2020025v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69845a80-088c-4136-9716-c8489e83b0e7/dqc_reference/reference_markers.hmm GCA_020200255.1_ASM2020025v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:30:10,165] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:30:10,166] [INFO] Found 6/6 markers.
[2023-06-28 19:30:10,204] [INFO] Query marker FASTA was written to GCA_020200255.1_ASM2020025v1_genomic.fna/markers.fasta
[2023-06-28 19:30:10,204] [INFO] Task started: Blastn
[2023-06-28 19:30:10,205] [INFO] Running command: blastn -query GCA_020200255.1_ASM2020025v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69845a80-088c-4136-9716-c8489e83b0e7/dqc_reference/reference_markers.fasta -out GCA_020200255.1_ASM2020025v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:30:10,908] [INFO] Task succeeded: Blastn
[2023-06-28 19:30:10,913] [INFO] Selected 30 target genomes.
[2023-06-28 19:30:10,914] [INFO] Target genome list was writen to GCA_020200255.1_ASM2020025v1_genomic.fna/target_genomes.txt
[2023-06-28 19:30:10,924] [INFO] Task started: fastANI
[2023-06-28 19:30:10,924] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6d88ad5-d772-4148-ae09-e7104c2d6e27/GCA_020200255.1_ASM2020025v1_genomic.fna.gz --refList GCA_020200255.1_ASM2020025v1_genomic.fna/target_genomes.txt --output GCA_020200255.1_ASM2020025v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:30:30,831] [INFO] Task succeeded: fastANI
[2023-06-28 19:30:30,832] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69845a80-088c-4136-9716-c8489e83b0e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:30:30,832] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69845a80-088c-4136-9716-c8489e83b0e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:30:30,841] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 19:30:30,842] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 19:30:30,842] [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
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	74.8001	107	1132	95	below_threshold
Roseiarcus fermentans	strain=DSM 24875	GCA_003315135.1	1473586	1473586	type	True	74.782	110	1132	95	below_threshold
Halorubrum persicum	strain=C49	GCA_002727125.1	1383844	1383844	type	True	74.7458	64	1132	95	below_threshold
Halorubrum depositum	strain=Y78	GCA_007671725.1	2583992	2583992	type	True	74.7197	54	1132	95	below_threshold
Ornithinimicrobium humiphilum	strain=DSM 12362	GCA_006716885.1	125288	125288	type	True	74.7009	52	1132	95	below_threshold
Millisia brevis	strain=NBRC 105863	GCA_001552615.1	264148	264148	type	True	74.6925	65	1132	95	below_threshold
Nocardia noduli	strain=ncl1	GCA_019038455.1	2815722	2815722	type	True	74.6016	75	1132	95	below_threshold
Halorubrum arcis	strain=JCM 13916	GCA_000337015.1	368454	368454	type	True	74.5808	55	1132	95	below_threshold
Halorubrum coriense	strain=DSM 10284	GCA_000337035.1	64713	64713	type	True	74.5731	73	1132	95	below_threshold
Nocardia aurea	strain=SYSU K10002	GCA_003123685.1	2144174	2144174	type	True	74.5514	64	1132	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 19:30:30,844] [INFO] DFAST Taxonomy check result was written to GCA_020200255.1_ASM2020025v1_genomic.fna/tc_result.tsv
[2023-06-28 19:30:30,845] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:30:30,845] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:30:30,845] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69845a80-088c-4136-9716-c8489e83b0e7/dqc_reference/checkm_data
[2023-06-28 19:30:30,846] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:30:30,884] [INFO] Task started: CheckM
[2023-06-28 19:30:30,884] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020200255.1_ASM2020025v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020200255.1_ASM2020025v1_genomic.fna/checkm_input GCA_020200255.1_ASM2020025v1_genomic.fna/checkm_result
[2023-06-28 19:31:15,724] [INFO] Task succeeded: CheckM
[2023-06-28 19:31:15,725] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 19:31:15,747] [INFO] ===== Completeness check finished =====
[2023-06-28 19:31:15,747] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:31:15,748] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020200255.1_ASM2020025v1_genomic.fna/markers.fasta)
[2023-06-28 19:31:15,748] [INFO] Task started: Blastn
[2023-06-28 19:31:15,748] [INFO] Running command: blastn -query GCA_020200255.1_ASM2020025v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg69845a80-088c-4136-9716-c8489e83b0e7/dqc_reference/reference_markers_gtdb.fasta -out GCA_020200255.1_ASM2020025v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:31:16,756] [INFO] Task succeeded: Blastn
[2023-06-28 19:31:16,760] [INFO] Selected 26 target genomes.
[2023-06-28 19:31:16,761] [INFO] Target genome list was writen to GCA_020200255.1_ASM2020025v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:31:16,780] [INFO] Task started: fastANI
[2023-06-28 19:31:16,780] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6d88ad5-d772-4148-ae09-e7104c2d6e27/GCA_020200255.1_ASM2020025v1_genomic.fna.gz --refList GCA_020200255.1_ASM2020025v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020200255.1_ASM2020025v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:31:35,344] [INFO] Task succeeded: fastANI
[2023-06-28 19:31:35,363] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 19:31:35,363] [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_003222385.1	s__Gp7-AA6 sp003222385	77.3328	309	1132	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5066;f__Gp7-AA6;g__Gp7-AA6	95.0	99.28	99.28	0.94	0.94	2	-
GCA_016716705.1	s__UBA5066 sp016716705	76.1134	130	1132	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5066;f__UBA5066;g__UBA5066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716715.1	s__Fen-183 sp016716715	76.0457	190	1132	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5066;f__UBA5066;g__Fen-183	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719485.1	s__UBA5066 sp016719485	75.9186	141	1132	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5066;f__UBA5066;g__UBA5066	95.0	97.48	97.48	0.88	0.88	2	-
GCA_008363385.1	s__RHKY01 sp008363385	75.8045	172	1132	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5066;f__UBA5066;g__RHKY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017999215.1	s__UBA5066 sp017999215	75.7908	137	1132	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5066;f__UBA5066;g__UBA5066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903845115.1	s__CAIMWE01 sp903845115	75.7546	140	1132	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5066;f__UBA5066;g__CAIMWE01	95.0	99.85	99.67	0.96	0.93	7	-
GCA_003152095.1	s__Fen-183 sp003152095	75.6871	119	1132	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5066;f__UBA5066;g__Fen-183	95.0	99.53	99.53	0.90	0.90	2	-
GCA_002414905.1	s__UBA5066 sp002414905	75.3181	98	1132	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5066;f__UBA5066;g__UBA5066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017860005.1	s__JACTMI01 sp017860005	75.3113	124	1132	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003170135.1	s__Fen-181 sp003170135	75.2463	95	1132	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Fen-181;g__Fen-181	95.0	99.94	99.94	0.97	0.97	2	-
GCF_004135735.1	s__Sorangium cellulosum_F	74.9221	202	1132	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713665.1	s__JADJOR01 sp016713665	74.8969	126	1132	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__JADJOR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552615.1	s__Millisia brevis	74.7019	63	1132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Millisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003123685.1	s__Nocardia aurea	74.5485	65	1132	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	95.19	95.19	0.76	0.76	2	-
--------------------------------------------------------------------------------
[2023-06-28 19:31:35,366] [INFO] GTDB search result was written to GCA_020200255.1_ASM2020025v1_genomic.fna/result_gtdb.tsv
[2023-06-28 19:31:35,366] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:31:35,370] [INFO] DFAST_QC result json was written to GCA_020200255.1_ASM2020025v1_genomic.fna/dqc_result.json
[2023-06-28 19:31:35,370] [INFO] DFAST_QC completed!
[2023-06-28 19:31:35,370] [INFO] Total running time: 0h1m43s