[2024-01-24 13:22:00,415] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:00,416] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:00,417] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb6bd4b6-c8c1-47ee-9126-af28e4893932/dqc_reference
[2024-01-24 13:22:01,746] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:01,747] [INFO] Task started: Prodigal
[2024-01-24 13:22:01,747] [INFO] Running command: gunzip -c /var/lib/cwl/stga92067eb-4841-452a-85b8-bab5319f9d35/GCF_010731655.1_ASM1073165v1_genomic.fna.gz | prodigal -d GCF_010731655.1_ASM1073165v1_genomic.fna/cds.fna -a GCF_010731655.1_ASM1073165v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:21,887] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:21,888] [INFO] Task started: HMMsearch
[2024-01-24 13:22:21,888] [INFO] Running command: hmmsearch --tblout GCF_010731655.1_ASM1073165v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb6bd4b6-c8c1-47ee-9126-af28e4893932/dqc_reference/reference_markers.hmm GCF_010731655.1_ASM1073165v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:22,286] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:22,287] [INFO] Found 6/6 markers.
[2024-01-24 13:22:22,386] [INFO] Query marker FASTA was written to GCF_010731655.1_ASM1073165v1_genomic.fna/markers.fasta
[2024-01-24 13:22:22,387] [INFO] Task started: Blastn
[2024-01-24 13:22:22,387] [INFO] Running command: blastn -query GCF_010731655.1_ASM1073165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb6bd4b6-c8c1-47ee-9126-af28e4893932/dqc_reference/reference_markers.fasta -out GCF_010731655.1_ASM1073165v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:23,632] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:23,635] [INFO] Selected 11 target genomes.
[2024-01-24 13:22:23,636] [INFO] Target genome list was writen to GCF_010731655.1_ASM1073165v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:23,651] [INFO] Task started: fastANI
[2024-01-24 13:22:23,652] [INFO] Running command: fastANI --query /var/lib/cwl/stga92067eb-4841-452a-85b8-bab5319f9d35/GCF_010731655.1_ASM1073165v1_genomic.fna.gz --refList GCF_010731655.1_ASM1073165v1_genomic.fna/target_genomes.txt --output GCF_010731655.1_ASM1073165v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:41,021] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:41,022] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb6bd4b6-c8c1-47ee-9126-af28e4893932/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:41,022] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb6bd4b6-c8c1-47ee-9126-af28e4893932/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:41,032] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:22:41,033] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:41,033] [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 paraseoulense	strain=JCM 16952	GCA_010731655.1	590652	590652	type	True	100.0	2028	2028	95	conclusive
Mycobacterium paraseoulense	strain=DSM 45000	GCA_002086475.1	590652	590652	type	True	99.959	1945	2028	95	conclusive
Mycobacterium seoulense	strain=JCM 16018	GCA_010731595.1	386911	386911	type	True	94.7644	1702	2028	95	below_threshold
Mycobacterium nebraskense	strain=DSM 44803	GCA_002102255.1	244292	244292	type	True	89.3639	1548	2028	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	84.3946	1319	2028	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000277125.1	1767	1767	suspected-type	True	84.1751	1353	2028	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	84.1741	1352	2028	95	below_threshold
Mycobacterium mantenii	strain=JCM 18113	GCA_010731775.1	560555	560555	type	True	83.9891	1429	2028	95	below_threshold
Mycobacterium helveticum	strain=16-83	GCA_007714205.1	2592811	2592811	type	True	83.261	1091	2028	95	below_threshold
Mycobacterium saskatchewanense	strain=DSM 44616	GCA_002101875.1	220927	220927	type	True	83.1868	1241	2028	95	below_threshold
Mycobacterium saskatchewanense	strain=JCM 13016	GCA_010729105.1	220927	220927	type	True	83.1506	1276	2028	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:41,034] [INFO] DFAST Taxonomy check result was written to GCF_010731655.1_ASM1073165v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:41,035] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:41,035] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:41,035] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb6bd4b6-c8c1-47ee-9126-af28e4893932/dqc_reference/checkm_data
[2024-01-24 13:22:41,036] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:41,105] [INFO] Task started: CheckM
[2024-01-24 13:22:41,105] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010731655.1_ASM1073165v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010731655.1_ASM1073165v1_genomic.fna/checkm_input GCF_010731655.1_ASM1073165v1_genomic.fna/checkm_result
[2024-01-24 13:23:45,695] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:45,696] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:45,715] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:45,716] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:45,716] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010731655.1_ASM1073165v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:45,716] [INFO] Task started: Blastn
[2024-01-24 13:23:45,717] [INFO] Running command: blastn -query GCF_010731655.1_ASM1073165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb6bd4b6-c8c1-47ee-9126-af28e4893932/dqc_reference/reference_markers_gtdb.fasta -out GCF_010731655.1_ASM1073165v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:47,430] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:47,433] [INFO] Selected 12 target genomes.
[2024-01-24 13:23:47,434] [INFO] Target genome list was writen to GCF_010731655.1_ASM1073165v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:47,450] [INFO] Task started: fastANI
[2024-01-24 13:23:47,451] [INFO] Running command: fastANI --query /var/lib/cwl/stga92067eb-4841-452a-85b8-bab5319f9d35/GCF_010731655.1_ASM1073165v1_genomic.fna.gz --refList GCF_010731655.1_ASM1073165v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010731655.1_ASM1073165v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:05,950] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:05,966] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:05,966] [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_010731655.1	s__Mycobacterium paraseoulense	100.0	2028	2028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_010731595.1	s__Mycobacterium seoulense	94.7671	1701	2028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900240975.1	s__Mycobacterium sp900240975	89.5611	1581	2028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.65	95.35	0.92	0.88	4	-
GCF_002102155.1	s__Mycobacterium europaeum	89.5591	1543	2028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.26	99.26	0.97	0.97	2	-
GCF_002102255.1	s__Mycobacterium nebraskense	89.3817	1546	2028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.58	99.42	0.93	0.92	4	-
GCF_001665605.1	s__Mycobacterium sp001665605	89.0095	1546	2028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.77	98.77	0.96	0.96	2	-
GCF_001667075.1	s__Mycobacterium sp001667075	88.6971	1568	2028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.41	99.38	0.97	0.97	3	-
GCF_000164135.1	s__Mycobacterium parascrofulaceum	88.5556	1543	2028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.18	96.53	0.89	0.85	6	-
GCF_001666835.1	s__Mycobacterium sp001666835	88.5332	1553	2028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	99.01	0.94	0.94	3	-
GCF_001667585.1	s__Mycobacterium sp001667585	88.4845	1522	2028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086735.1	s__Mycobacterium scrofulaceum	88.2932	1537	2028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001907675.1	s__Mycobacterium paraffinicum	87.9172	1546	2028	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 13:24:05,968] [INFO] GTDB search result was written to GCF_010731655.1_ASM1073165v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:05,969] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:05,972] [INFO] DFAST_QC result json was written to GCF_010731655.1_ASM1073165v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:05,972] [INFO] DFAST_QC completed!
[2024-01-24 13:24:05,972] [INFO] Total running time: 0h2m6s