[2024-01-24 14:30:59,538] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:59,540] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:59,540] [INFO] DQC Reference Directory: /var/lib/cwl/stga992d9a5-5673-49f5-9bd4-cc95e585b4bb/dqc_reference
[2024-01-24 14:31:00,875] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:00,876] [INFO] Task started: Prodigal
[2024-01-24 14:31:00,876] [INFO] Running command: gunzip -c /var/lib/cwl/stg97dc5c63-1e2d-401a-9519-696df3ef4889/GCF_014191505.1_ASM1419150v1_genomic.fna.gz | prodigal -d GCF_014191505.1_ASM1419150v1_genomic.fna/cds.fna -a GCF_014191505.1_ASM1419150v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:17,013] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:17,014] [INFO] Task started: HMMsearch
[2024-01-24 14:31:17,014] [INFO] Running command: hmmsearch --tblout GCF_014191505.1_ASM1419150v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga992d9a5-5673-49f5-9bd4-cc95e585b4bb/dqc_reference/reference_markers.hmm GCF_014191505.1_ASM1419150v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:17,440] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:17,441] [INFO] Found 6/6 markers.
[2024-01-24 14:31:17,488] [INFO] Query marker FASTA was written to GCF_014191505.1_ASM1419150v1_genomic.fna/markers.fasta
[2024-01-24 14:31:17,488] [INFO] Task started: Blastn
[2024-01-24 14:31:17,488] [INFO] Running command: blastn -query GCF_014191505.1_ASM1419150v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga992d9a5-5673-49f5-9bd4-cc95e585b4bb/dqc_reference/reference_markers.fasta -out GCF_014191505.1_ASM1419150v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:18,306] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:18,310] [INFO] Selected 21 target genomes.
[2024-01-24 14:31:18,311] [INFO] Target genome list was writen to GCF_014191505.1_ASM1419150v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:18,321] [INFO] Task started: fastANI
[2024-01-24 14:31:18,321] [INFO] Running command: fastANI --query /var/lib/cwl/stg97dc5c63-1e2d-401a-9519-696df3ef4889/GCF_014191505.1_ASM1419150v1_genomic.fna.gz --refList GCF_014191505.1_ASM1419150v1_genomic.fna/target_genomes.txt --output GCF_014191505.1_ASM1419150v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:39,538] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:39,539] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga992d9a5-5673-49f5-9bd4-cc95e585b4bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:39,539] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga992d9a5-5673-49f5-9bd4-cc95e585b4bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:39,555] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:39,555] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:39,556] [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
Hoyosella altamirensis	strain=DSM 45258	GCA_014191505.1	616997	616997	type	True	100.0	1579	1583	95	conclusive
Hoyosella subflava	strain=DQS3-9A1	GCA_000214175.1	639313	639313	type	True	92.5532	1376	1583	95	below_threshold
Hoyosella suaedae	strain=LNNU 331112	GCA_008312885.1	2605429	2605429	type	True	77.8837	271	1583	95	below_threshold
Hoyosella lacisalsi	strain=G463	GCA_014841105.1	2742202	2742202	type	True	77.7669	256	1583	95	below_threshold
Rhodococcus ruber	strain=DSM 43338	GCA_001646835.1	1830	1830	type	True	77.3875	190	1583	95	below_threshold
Rhodococcus ruber	strain=NBRC 15591	GCA_001894945.1	1830	1830	type	True	77.3458	192	1583	95	below_threshold
Prescottella equi	strain=NCTC1621	GCA_900455845.1	43767	43767	type	True	77.2014	191	1583	95	below_threshold
Rhodococcus pseudokoreensis	strain=R79	GCA_017068395.1	2811421	2811421	type	True	77.1193	231	1583	95	below_threshold
Prescottella equi	strain=NBRC 101255	GCA_001552575.1	43767	43767	type	True	76.9183	185	1583	95	below_threshold
Prescottella equi	strain=DSM 20307	GCA_002094305.1	43767	43767	type	True	76.9077	185	1583	95	below_threshold
Gordonia rubripertincta	strain=NBRC 101908	GCA_000327325.1	36822	36822	type	True	76.886	129	1583	95	below_threshold
Nocardia araoensis	strain=NBRC 100135	GCA_000308435.1	228600	228600	type	True	76.8646	164	1583	95	below_threshold
Mycolicibacterium chitae	strain=JCM 12403	GCA_010727725.1	1792	1792	type	True	76.8063	135	1583	95	below_threshold
[Mycobacterium] fortunisiensis	strain=TNTM28	GCA_019050325.1	2600579	2600579	type	True	76.7779	116	1583	95	below_threshold
Rhodococcus opacus	strain=ATCC 51881	GCA_012396235.1	37919	37919	type	True	76.7539	201	1583	95	below_threshold
Rhodococcus opacus	strain=DSM 43205	GCA_001646735.1	37919	37919	type	True	76.7358	204	1583	95	below_threshold
Mycobacterium aquaticum	strain=RW6	GCA_002086485.1	1927124	1927124	type	True	76.4681	123	1583	95	below_threshold
Phytoactinopolyspora alkaliphila	strain=CGMCC 4.7225	GCA_010550695.1	1783498	1783498	type	True	76.1563	50	1583	95	below_threshold
Mycolicibacterium stellerae	strain=CECT 8783	GCA_003719305.1	2358193	2358193	type	True	76.1412	121	1583	95	below_threshold
Amycolatopsis nivea	strain=CFH S0261	GCA_004522235.1	1644109	1644109	type	True	76.1237	139	1583	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:39,557] [INFO] DFAST Taxonomy check result was written to GCF_014191505.1_ASM1419150v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:39,558] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:39,558] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:39,558] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga992d9a5-5673-49f5-9bd4-cc95e585b4bb/dqc_reference/checkm_data
[2024-01-24 14:31:39,560] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:39,609] [INFO] Task started: CheckM
[2024-01-24 14:31:39,609] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014191505.1_ASM1419150v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014191505.1_ASM1419150v1_genomic.fna/checkm_input GCF_014191505.1_ASM1419150v1_genomic.fna/checkm_result
[2024-01-24 14:32:27,245] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:27,246] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:27,266] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:27,266] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:27,266] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014191505.1_ASM1419150v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:27,267] [INFO] Task started: Blastn
[2024-01-24 14:32:27,267] [INFO] Running command: blastn -query GCF_014191505.1_ASM1419150v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga992d9a5-5673-49f5-9bd4-cc95e585b4bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_014191505.1_ASM1419150v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:28,299] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:28,304] [INFO] Selected 21 target genomes.
[2024-01-24 14:32:28,304] [INFO] Target genome list was writen to GCF_014191505.1_ASM1419150v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:28,326] [INFO] Task started: fastANI
[2024-01-24 14:32:28,326] [INFO] Running command: fastANI --query /var/lib/cwl/stg97dc5c63-1e2d-401a-9519-696df3ef4889/GCF_014191505.1_ASM1419150v1_genomic.fna.gz --refList GCF_014191505.1_ASM1419150v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014191505.1_ASM1419150v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:49,553] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:49,580] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:49,583] [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_014191505.1	s__Hoyosella altamirensis	100.0	1578	1583	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Hoyosella	95.0	99.98	99.98	0.97	0.97	2	conclusive
GCF_000214175.1	s__Hoyosella subflava	92.5532	1376	1583	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Hoyosella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008312885.1	s__Hoyosella sp008312885	77.902	270	1583	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Hoyosella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014841105.1	s__Hoyosella sp014841105	77.7669	256	1583	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Hoyosella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001894945.1	s__Rhodococcus ruber	77.3604	191	1583	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.84	95.07	0.94	0.85	19	-
GCF_000686025.1	s__Rhodococcus_C sp000686025	77.3144	130	1583	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus_C	95.0	97.13	95.65	0.89	0.88	5	-
GCF_900455735.1	s__Rhodococcus wratislaviensis	77.1611	202	1583	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.31	98.94	0.95	0.93	4	-
GCF_017068395.1	s__Rhodococcus sp002165735	77.0612	229	1583	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	96.37	95.32	0.78	0.69	5	-
GCF_001646645.1	s__Rhodococcus hoagii	76.9873	175	1583	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	99.01	98.63	0.96	0.88	61	-
GCF_012726195.1	s__Rhodococcus sp012726195	76.9055	145	1583	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003051005.1	s__Rhodococcus sp003051005	76.8146	176	1583	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612985.1	s__Nocardia gamkensis	76.7845	153	1583	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.7192	100.00	100.00	1.00	0.99	3	-
GCF_019050325.1	s__Mycobacterium fortunisiensis	76.7779	116	1583	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012396235.1	s__Rhodococcus opacus	76.7539	201	1583	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	98.04	95.98	0.86	0.77	23	-
GCF_001953975.1	s__Mycobacterium sp001953975	76.6581	111	1583	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.19	98.19	0.92	0.92	2	-
GCA_011620645.1	s__Mycobacterium sp011620645	76.5515	88	1583	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001668615.1	s__Mycobacterium sp001668615	76.4518	112	1583	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086485.1	s__Mycobacterium aquaticum	76.4513	124	1583	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019038435.1	s__Nocardia sp019038435	76.4256	144	1583	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:49,585] [INFO] GTDB search result was written to GCF_014191505.1_ASM1419150v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:49,585] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:49,592] [INFO] DFAST_QC result json was written to GCF_014191505.1_ASM1419150v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:49,592] [INFO] DFAST_QC completed!
[2024-01-24 14:32:49,592] [INFO] Total running time: 0h1m50s