[2024-01-25 17:40:20,539] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:40:20,546] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:40:20,546] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d26de6d-82dd-4126-8b4b-270928e71d0e/dqc_reference
[2024-01-25 17:40:21,710] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:40:21,711] [INFO] Task started: Prodigal
[2024-01-25 17:40:21,711] [INFO] Running command: gunzip -c /var/lib/cwl/stg2dd6975a-b907-4359-b6cf-b5c44d97ef84/GCF_025822885.1_ASM2582288v1_genomic.fna.gz | prodigal -d GCF_025822885.1_ASM2582288v1_genomic.fna/cds.fna -a GCF_025822885.1_ASM2582288v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:40:35,720] [INFO] Task succeeded: Prodigal
[2024-01-25 17:40:35,720] [INFO] Task started: HMMsearch
[2024-01-25 17:40:35,720] [INFO] Running command: hmmsearch --tblout GCF_025822885.1_ASM2582288v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d26de6d-82dd-4126-8b4b-270928e71d0e/dqc_reference/reference_markers.hmm GCF_025822885.1_ASM2582288v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:40:36,033] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:40:36,034] [INFO] Found 6/6 markers.
[2024-01-25 17:40:36,090] [INFO] Query marker FASTA was written to GCF_025822885.1_ASM2582288v1_genomic.fna/markers.fasta
[2024-01-25 17:40:36,090] [INFO] Task started: Blastn
[2024-01-25 17:40:36,090] [INFO] Running command: blastn -query GCF_025822885.1_ASM2582288v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d26de6d-82dd-4126-8b4b-270928e71d0e/dqc_reference/reference_markers.fasta -out GCF_025822885.1_ASM2582288v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:37,121] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:37,124] [INFO] Selected 19 target genomes.
[2024-01-25 17:40:37,124] [INFO] Target genome list was writen to GCF_025822885.1_ASM2582288v1_genomic.fna/target_genomes.txt
[2024-01-25 17:40:37,139] [INFO] Task started: fastANI
[2024-01-25 17:40:37,139] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dd6975a-b907-4359-b6cf-b5c44d97ef84/GCF_025822885.1_ASM2582288v1_genomic.fna.gz --refList GCF_025822885.1_ASM2582288v1_genomic.fna/target_genomes.txt --output GCF_025822885.1_ASM2582288v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:40:57,118] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:57,118] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d26de6d-82dd-4126-8b4b-270928e71d0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:40:57,119] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d26de6d-82dd-4126-8b4b-270928e71d0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:40:57,130] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:40:57,130] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:40:57,130] [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
Mycobacterium kyorinense	strain=DSM 45166	GCA_002101735.1	487514	487514	type	True	82.8867	1052	1551	95	below_threshold
Mycobacterium kyorinense	strain=KUM060204T	GCA_000759695.1	487514	487514	type	True	82.8201	1038	1551	95	below_threshold
Mycobacterium celatum	strain=DSM 44243	GCA_002101595.1	28045	28045	type	True	82.7826	1051	1551	95	below_threshold
Mycobacterium branderi	strain=JCM 12687	GCA_010728725.1	43348	43348	type	True	82.7534	1083	1551	95	below_threshold
Mycobacterium branderi	strain=DSM 44624	GCA_002086575.1	43348	43348	type	True	82.7238	1060	1551	95	below_threshold
Mycobacterium celatum	strain=ATCC 51131	GCA_000974705.1	28045	28045	type	True	82.6771	799	1551	95	below_threshold
Mycobacterium fragae	strain=DSM 45731	GCA_002102185.1	1260918	1260918	type	True	81.5636	995	1551	95	below_threshold
Mycobacterium conspicuum	strain=DSM 44136	GCA_002102095.1	44010	44010	type	True	80.2619	846	1551	95	below_threshold
Mycobacterium conspicuum	strain=JCM 14738	GCA_010730195.1	44010	44010	type	True	80.2419	860	1551	95	below_threshold
Mycobacterium triplex	strain=DSM 44626	GCA_002102415.1	47839	47839	type	True	80.1251	821	1551	95	below_threshold
Mycobacterium triplex	strain=DSM 44626	GCA_000689255.1	47839	47839	type	True	80.0949	851	1551	95	below_threshold
Mycobacterium lacus	strain=DSM 44577	GCA_002102215.1	169765	169765	type	True	80.0685	769	1551	95	below_threshold
Mycobacterium marseillense	strain=JCM 17324	GCA_010731675.1	701042	701042	type	True	80.0651	859	1551	95	below_threshold
Mycobacterium marseillense	strain=DSM 45437	GCA_002086345.1	701042	701042	type	True	80.0148	834	1551	95	below_threshold
Mycobacterium shinjukuense	strain=JCM 14233	GCA_010730055.1	398694	398694	type	True	79.9566	704	1551	95	below_threshold
Mycobacterium shinjukuense	strain=CCUG 53584	GCA_002086755.1	398694	398694	type	True	79.9256	686	1551	95	below_threshold
Mycolicibacter terrae	strain=JCM 12143	GCA_010727125.1	1788	1788	type	True	79.2327	731	1551	95	below_threshold
Mycolicibacter terrae	strain=CIP 104321	GCA_002101955.1	1788	1788	type	True	79.177	728	1551	95	below_threshold
Mycolicibacter hiberniae	strain=ATCC 49874	GCA_002101655.1	29314	29314	type	True	78.8817	648	1551	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:40:57,131] [INFO] DFAST Taxonomy check result was written to GCF_025822885.1_ASM2582288v1_genomic.fna/tc_result.tsv
[2024-01-25 17:40:57,132] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:40:57,132] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:40:57,132] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d26de6d-82dd-4126-8b4b-270928e71d0e/dqc_reference/checkm_data
[2024-01-25 17:40:57,133] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:40:57,179] [INFO] Task started: CheckM
[2024-01-25 17:40:57,179] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025822885.1_ASM2582288v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025822885.1_ASM2582288v1_genomic.fna/checkm_input GCF_025822885.1_ASM2582288v1_genomic.fna/checkm_result
[2024-01-25 17:41:38,836] [INFO] Task succeeded: CheckM
[2024-01-25 17:41:38,837] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:41:38,858] [INFO] ===== Completeness check finished =====
[2024-01-25 17:41:38,859] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:41:38,859] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025822885.1_ASM2582288v1_genomic.fna/markers.fasta)
[2024-01-25 17:41:38,859] [INFO] Task started: Blastn
[2024-01-25 17:41:38,859] [INFO] Running command: blastn -query GCF_025822885.1_ASM2582288v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d26de6d-82dd-4126-8b4b-270928e71d0e/dqc_reference/reference_markers_gtdb.fasta -out GCF_025822885.1_ASM2582288v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:40,357] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:40,360] [INFO] Selected 14 target genomes.
[2024-01-25 17:41:40,360] [INFO] Target genome list was writen to GCF_025822885.1_ASM2582288v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:41:40,377] [INFO] Task started: fastANI
[2024-01-25 17:41:40,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dd6975a-b907-4359-b6cf-b5c44d97ef84/GCF_025822885.1_ASM2582288v1_genomic.fna.gz --refList GCF_025822885.1_ASM2582288v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025822885.1_ASM2582288v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:41:56,729] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:56,738] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:41:56,738] [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_002101905.1	s__Mycobacterium shimoidei	99.9825	1517	1551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.72	99.46	0.97	0.95	3	conclusive
GCF_002101735.1	s__Mycobacterium kyorinense	82.8927	1052	1551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.84	99.84	0.96	0.94	3	-
GCF_003402475.1	s__Mycobacterium sp003402475	82.8728	1073	1551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101595.1	s__Mycobacterium celatum	82.782	1050	1551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_010728725.1	s__Mycobacterium branderi	82.7607	1082	1551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002102185.1	s__Mycobacterium fragae	81.5675	994	1551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002102225.1	s__Mycobacterium interjectum_B	80.3119	895	1551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078675.2	s__Mycobacterium interjectum	80.3021	861	1551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019236925.1	s__Mycobacterium sp019236925	80.2651	784	1551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010730195.1	s__Mycobacterium conspicuum	80.2298	861	1551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_010731675.1	s__Mycobacterium marseillense	80.0695	858	1551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.64	95.51	0.95	0.90	6	-
GCF_010731535.1	s__Mycobacterium lacus	79.9815	796	1551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_010730055.1	s__Mycobacterium shinjukuense	79.9646	704	1551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002086455.1	s__Mycobacterium algericum	79.4139	701	1551	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.66	97.92	0.93	0.90	4	-
--------------------------------------------------------------------------------
[2024-01-25 17:41:56,740] [INFO] GTDB search result was written to GCF_025822885.1_ASM2582288v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:41:56,740] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:41:56,744] [INFO] DFAST_QC result json was written to GCF_025822885.1_ASM2582288v1_genomic.fna/dqc_result.json
[2024-01-25 17:41:56,745] [INFO] DFAST_QC completed!
[2024-01-25 17:41:56,745] [INFO] Total running time: 0h1m36s