[2024-01-24 12:45:10,350] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:10,352] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:10,352] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d0f07d6-8528-4339-9918-25dbb7e7ef33/dqc_reference
[2024-01-24 12:45:13,081] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:13,082] [INFO] Task started: Prodigal
[2024-01-24 12:45:13,082] [INFO] Running command: gunzip -c /var/lib/cwl/stgbeb4b6d0-76bc-4e62-a922-0f4437de864f/GCF_010731835.1_ASM1073183v1_genomic.fna.gz | prodigal -d GCF_010731835.1_ASM1073183v1_genomic.fna/cds.fna -a GCF_010731835.1_ASM1073183v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:26,173] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:26,173] [INFO] Task started: HMMsearch
[2024-01-24 12:45:26,173] [INFO] Running command: hmmsearch --tblout GCF_010731835.1_ASM1073183v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d0f07d6-8528-4339-9918-25dbb7e7ef33/dqc_reference/reference_markers.hmm GCF_010731835.1_ASM1073183v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:26,463] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:26,464] [INFO] Found 6/6 markers.
[2024-01-24 12:45:26,510] [INFO] Query marker FASTA was written to GCF_010731835.1_ASM1073183v1_genomic.fna/markers.fasta
[2024-01-24 12:45:26,510] [INFO] Task started: Blastn
[2024-01-24 12:45:26,510] [INFO] Running command: blastn -query GCF_010731835.1_ASM1073183v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d0f07d6-8528-4339-9918-25dbb7e7ef33/dqc_reference/reference_markers.fasta -out GCF_010731835.1_ASM1073183v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:27,690] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:27,693] [INFO] Selected 23 target genomes.
[2024-01-24 12:45:27,694] [INFO] Target genome list was writen to GCF_010731835.1_ASM1073183v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:27,704] [INFO] Task started: fastANI
[2024-01-24 12:45:27,704] [INFO] Running command: fastANI --query /var/lib/cwl/stgbeb4b6d0-76bc-4e62-a922-0f4437de864f/GCF_010731835.1_ASM1073183v1_genomic.fna.gz --refList GCF_010731835.1_ASM1073183v1_genomic.fna/target_genomes.txt --output GCF_010731835.1_ASM1073183v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:49,437] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:49,437] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d0f07d6-8528-4339-9918-25dbb7e7ef33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:49,438] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d0f07d6-8528-4339-9918-25dbb7e7ef33/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:49,455] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:45:49,455] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:45:49,455] [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
Mycolicibacter kumamotonensis	strain=DSM 45093	GCA_002086285.1	354243	354243	type	True	80.7794	779	1385	95	below_threshold
Mycolicibacter senuensis	strain=DSM 44999	GCA_002101885.1	386913	386913	type	True	80.6279	756	1385	95	below_threshold
Mycolicibacter senuensis	strain=JCM 16017	GCA_010723225.1	386913	386913	type	True	80.5919	770	1385	95	below_threshold
Mycolicibacter longobardus	strain=DSM 45394	GCA_002102265.1	1108812	1108812	type	True	80.5513	745	1385	95	below_threshold
Mycolicibacter terrae	strain=JCM 12143	GCA_010727125.1	1788	1788	type	True	80.4916	738	1385	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	80.4492	678	1385	95	below_threshold
Mycolicibacter terrae	strain=CIP 104321	GCA_002101955.1	1788	1788	type	True	80.446	737	1385	95	below_threshold
Mycolicibacterium fallax	strain=DSM 44179	GCA_002101995.1	1793	1793	type	True	80.4014	675	1385	95	below_threshold
Mycolicibacter kumamotonensis	strain=CST 7247	GCA_010093495.1	354243	354243	type	True	80.4011	743	1385	95	below_threshold
Mycolicibacterium thermoresistibile	strain=NCTC10409	GCA_900187065.1	1797	1797	type	True	80.0084	681	1385	95	below_threshold
Mycolicibacterium thermoresistibile	strain=ATCC 19527	GCA_000234585.2	1797	1797	type	True	79.9352	681	1385	95	below_threshold
Mycolicibacter nonchromogenicus	strain=DSM 44164	GCA_002101775.1	1782	1782	type	True	79.9333	682	1385	95	below_threshold
Mycolicibacter hiberniae	strain=ATCC 49874	GCA_002101655.1	29314	29314	type	True	79.9137	667	1385	95	below_threshold
Mycolicibacterium thermoresistibile	strain=JCM6362	GCA_001570505.1	1797	1797	type	True	79.8708	680	1385	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=DSM 43826	GCA_001044235.1	37916	37916	type	True	79.8633	680	1385	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	79.8498	674	1385	95	below_threshold
Mycolicibacterium brumae	strain=ATCC 51384	GCA_025215495.1	85968	85968	type	True	79.7956	600	1385	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_005670675.1	258533	258533	type	True	79.7573	659	1385	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_000613185.1	258533	258533	type	True	79.7346	664	1385	95	below_threshold
Mycolicibacterium psychrotolerans	strain=JCM 13323	GCA_010729305.1	216929	216929	type	True	79.4089	624	1385	95	below_threshold
Mycobacterium kubicae	strain=JCM 13573	GCA_015689175.1	120959	120959	type	True	79.3898	597	1385	95	below_threshold
Mycobacterium kubicae	strain=CIP 106428	GCA_002101745.1	120959	120959	type	True	79.3524	595	1385	95	below_threshold
Mycobacterium kubicae	strain=JCM 13573	GCA_010723135.1	120959	120959	type	True	79.3423	602	1385	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:49,457] [INFO] DFAST Taxonomy check result was written to GCF_010731835.1_ASM1073183v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:49,459] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:49,459] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:49,460] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d0f07d6-8528-4339-9918-25dbb7e7ef33/dqc_reference/checkm_data
[2024-01-24 12:45:49,462] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:49,505] [INFO] Task started: CheckM
[2024-01-24 12:45:49,505] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010731835.1_ASM1073183v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010731835.1_ASM1073183v1_genomic.fna/checkm_input GCF_010731835.1_ASM1073183v1_genomic.fna/checkm_result
[2024-01-24 12:46:37,525] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:37,527] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:37,549] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:37,549] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:37,550] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010731835.1_ASM1073183v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:37,550] [INFO] Task started: Blastn
[2024-01-24 12:46:37,550] [INFO] Running command: blastn -query GCF_010731835.1_ASM1073183v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d0f07d6-8528-4339-9918-25dbb7e7ef33/dqc_reference/reference_markers_gtdb.fasta -out GCF_010731835.1_ASM1073183v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:39,156] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:39,161] [INFO] Selected 20 target genomes.
[2024-01-24 12:46:39,161] [INFO] Target genome list was writen to GCF_010731835.1_ASM1073183v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:39,199] [INFO] Task started: fastANI
[2024-01-24 12:46:39,200] [INFO] Running command: fastANI --query /var/lib/cwl/stgbeb4b6d0-76bc-4e62-a922-0f4437de864f/GCF_010731835.1_ASM1073183v1_genomic.fna.gz --refList GCF_010731835.1_ASM1073183v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010731835.1_ASM1073183v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:58,808] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:58,824] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:58,824] [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_002104795.1	s__Mycobacterium koreense	99.9446	1287	1385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.42	98.84	0.96	0.92	3	conclusive
GCF_001668625.1	s__Mycobacterium sp001668625	84.0395	902	1385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002102395.1	s__Mycobacterium triviale	83.6229	962	1385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004354905.1	s__Mycobacterium eburneum	81.5254	820	1385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.68	99.68	0.92	0.92	2	-
GCF_018455725.1	s__Mycobacterium sp018455725	80.8083	776	1385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086455.1	s__Mycobacterium algericum	80.708	745	1385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.66	97.92	0.93	0.90	4	-
GCF_002101885.1	s__Mycobacterium senuense	80.5907	761	1385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002102265.1	s__Mycobacterium longobardum	80.5401	746	1385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727125.1	s__Mycobacterium terrae	80.4911	739	1385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	99.99	1.00	1.00	3	-
GCF_010726955.1	s__Mycobacterium fallax	80.4776	680	1385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.97	0.97	2	-
GCF_003284935.1	s__Mycobacterium arosiense_A	80.0801	662	1385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001021505.1	s__Mycobacterium heraklionense_B	80.0334	733	1385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187065.1	s__Mycobacterium thermoresistibile	79.9824	681	1385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.97	1.00	1.00	3	-
GCF_000613185.1	s__Mycobacterium cosmeticum	79.7284	657	1385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.89	98.33	0.93	0.89	4	-
GCF_004570325.1	s__Mycobacterium sp004570325	79.7141	670	1385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731755.1	s__Mycobacterium minnesotense	79.5974	621	1385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015689175.1	s__Mycobacterium kubicae	79.4121	596	1385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.05	97.98	0.96	0.92	7	-
GCF_001673155.1	s__Mycobacterium sp001673155	79.0981	545	1385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019245755.1	s__Mycobacterium sp019245755	78.8597	544	1385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.79	99.79	0.94	0.94	2	-
GCA_018401645.1	s__Mycobacterium sp018401645	77.8864	325	1385	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:58,826] [INFO] GTDB search result was written to GCF_010731835.1_ASM1073183v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:58,827] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:58,831] [INFO] DFAST_QC result json was written to GCF_010731835.1_ASM1073183v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:58,832] [INFO] DFAST_QC completed!
[2024-01-24 12:46:58,832] [INFO] Total running time: 0h1m48s