[2024-01-25 20:21:35,332] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:21:35,334] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:21:35,334] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd240a9f-c9b7-414b-9d5c-1e69100d1ff7/dqc_reference
[2024-01-25 20:21:36,465] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:21:36,465] [INFO] Task started: Prodigal
[2024-01-25 20:21:36,466] [INFO] Running command: gunzip -c /var/lib/cwl/stgad82a192-c050-4aac-bbc2-38d29977935d/GCF_002101845.1_ASM210184v1_genomic.fna.gz | prodigal -d GCF_002101845.1_ASM210184v1_genomic.fna/cds.fna -a GCF_002101845.1_ASM210184v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:21:57,507] [INFO] Task succeeded: Prodigal
[2024-01-25 20:21:57,508] [INFO] Task started: HMMsearch
[2024-01-25 20:21:57,508] [INFO] Running command: hmmsearch --tblout GCF_002101845.1_ASM210184v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd240a9f-c9b7-414b-9d5c-1e69100d1ff7/dqc_reference/reference_markers.hmm GCF_002101845.1_ASM210184v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:21:57,796] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:21:57,797] [INFO] Found 6/6 markers.
[2024-01-25 20:21:57,845] [INFO] Query marker FASTA was written to GCF_002101845.1_ASM210184v1_genomic.fna/markers.fasta
[2024-01-25 20:21:57,846] [INFO] Task started: Blastn
[2024-01-25 20:21:57,846] [INFO] Running command: blastn -query GCF_002101845.1_ASM210184v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd240a9f-c9b7-414b-9d5c-1e69100d1ff7/dqc_reference/reference_markers.fasta -out GCF_002101845.1_ASM210184v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:58,832] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:58,834] [INFO] Selected 16 target genomes.
[2024-01-25 20:21:58,835] [INFO] Target genome list was writen to GCF_002101845.1_ASM210184v1_genomic.fna/target_genomes.txt
[2024-01-25 20:21:58,843] [INFO] Task started: fastANI
[2024-01-25 20:21:58,844] [INFO] Running command: fastANI --query /var/lib/cwl/stgad82a192-c050-4aac-bbc2-38d29977935d/GCF_002101845.1_ASM210184v1_genomic.fna.gz --refList GCF_002101845.1_ASM210184v1_genomic.fna/target_genomes.txt --output GCF_002101845.1_ASM210184v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:22:22,583] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:22,583] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd240a9f-c9b7-414b-9d5c-1e69100d1ff7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:22:22,585] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd240a9f-c9b7-414b-9d5c-1e69100d1ff7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:22:22,595] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:22:22,596] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:22:22,596] [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 riyadhense	strain=DSM 45176	GCA_002101845.1	486698	486698	type	True	100.0	1945	1961	95	conclusive
Mycobacterium simulans	strain=FI-09026	GCA_900232995.1	627089	627089	type	True	91.6972	1586	1961	95	below_threshold
Mycobacterium lacus	strain=DSM 44577	GCA_002102215.1	169765	169765	type	True	83.0903	1198	1961	95	below_threshold
Mycobacterium lacus	strain=JCM 15657	GCA_010731535.1	169765	169765	type	True	82.9403	1264	1961	95	below_threshold
Mycobacterium angelicum	strain=DSM 45057	GCA_002086155.1	470074	470074	type	True	82.7319	1315	1961	95	below_threshold
Mycobacterium szulgai	strain=DSM 44166	GCA_002116635.1	1787	1787	type	True	82.5004	1327	1961	95	below_threshold
Mycobacterium shinjukuense	strain=JCM 14233	GCA_010730055.1	398694	398694	type	True	82.4849	1111	1961	95	below_threshold
Mycobacterium shinjukuense	strain=CCUG 53584	GCA_002086755.1	398694	398694	type	True	82.4719	1077	1961	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	81.8459	1014	1961	95	below_threshold
Mycobacterium tuberculosis variant pinnipedii	strain=ATCC BAA-688	GCA_002982275.1	194542	1773	type	True	81.7148	996	1961	95	below_threshold
Mycobacterium tuberculosis	strain=H37Rv	GCA_000195955.2	1773	1773	type	True	81.6401	1050	1961	95	below_threshold
Mycobacterium tuberculosis variant microti	strain=ATCC 19422	GCA_002982215.1	1806	1773	type	True	81.5547	956	1961	95	below_threshold
Mycobacterium innocens	strain=MK13	GCA_900566055.1	2341083	2341083	type	True	81.4168	1121	1961	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	81.1911	1037	1961	95	below_threshold
Mycobacterium haemophilum	strain=ATCC 29548	GCA_000340435.3	29311	29311	type	True	80.7983	905	1961	95	below_threshold
Mycobacterium helveticum	strain=16-83	GCA_007714205.1	2592811	2592811	type	True	80.6722	899	1961	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:22:22,597] [INFO] DFAST Taxonomy check result was written to GCF_002101845.1_ASM210184v1_genomic.fna/tc_result.tsv
[2024-01-25 20:22:22,597] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:22:22,598] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:22:22,598] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd240a9f-c9b7-414b-9d5c-1e69100d1ff7/dqc_reference/checkm_data
[2024-01-25 20:22:22,598] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:22:22,658] [INFO] Task started: CheckM
[2024-01-25 20:22:22,658] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002101845.1_ASM210184v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002101845.1_ASM210184v1_genomic.fna/checkm_input GCF_002101845.1_ASM210184v1_genomic.fna/checkm_result
[2024-01-25 20:23:20,494] [INFO] Task succeeded: CheckM
[2024-01-25 20:23:20,496] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:23:20,527] [INFO] ===== Completeness check finished =====
[2024-01-25 20:23:20,527] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:23:20,528] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002101845.1_ASM210184v1_genomic.fna/markers.fasta)
[2024-01-25 20:23:20,529] [INFO] Task started: Blastn
[2024-01-25 20:23:20,529] [INFO] Running command: blastn -query GCF_002101845.1_ASM210184v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd240a9f-c9b7-414b-9d5c-1e69100d1ff7/dqc_reference/reference_markers_gtdb.fasta -out GCF_002101845.1_ASM210184v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:21,941] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:21,945] [INFO] Selected 18 target genomes.
[2024-01-25 20:23:21,945] [INFO] Target genome list was writen to GCF_002101845.1_ASM210184v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:23:21,954] [INFO] Task started: fastANI
[2024-01-25 20:23:21,955] [INFO] Running command: fastANI --query /var/lib/cwl/stgad82a192-c050-4aac-bbc2-38d29977935d/GCF_002101845.1_ASM210184v1_genomic.fna.gz --refList GCF_002101845.1_ASM210184v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002101845.1_ASM210184v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:23:49,399] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:49,411] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:23:49,411] [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_002101845.1	s__Mycobacterium riyadhense	100.0	1945	1961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.42	99.30	0.97	0.96	10	conclusive
GCF_900232995.1	s__Mycobacterium simulans	91.6762	1588	1961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.78	97.78	0.92	0.92	2	-
GCF_010731535.1	s__Mycobacterium lacus	82.935	1266	1961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002086155.1	s__Mycobacterium angelicum	82.7723	1309	1961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002116635.1	s__Mycobacterium szulgai	82.5225	1322	1961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010730055.1	s__Mycobacterium shinjukuense	82.4941	1109	1961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002104675.1	s__Mycobacterium decipiens	81.9205	1164	1961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010730745.1	s__Mycobacterium heidelbergense	81.8072	1020	1961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000195955.2	s__Mycobacterium tuberculosis	81.6347	1054	1961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.92	97.88	0.99	0.91	6836	-
GCF_002705925.1	s__Mycobacterium ostraviense	81.4344	1165	1961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.87	99.87	0.99	0.99	2	-
GCF_900566055.1	s__Mycobacterium innocens	81.4192	1118	1961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.27	98.57	0.94	0.90	3	-
GCF_002101815.1	s__Mycobacterium paraense	81.184	1038	1961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_001667015.1	s__Mycobacterium sp001667015	81.1422	985	1961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086635.1	s__Mycobacterium alsense	81.1037	1025	1961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.76	96.71	0.91	0.90	3	-
GCF_001668725.1	s__Mycobacterium sp001668725	81.0588	997	1961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.46	99.46	0.97	0.97	2	-
GCF_000340435.2	s__Mycobacterium haemophilum	80.8021	904	1961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.07	99.06	0.94	0.94	5	-
GCF_007714205.1	s__Mycobacterium helveticum	80.6788	898	1961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_008370645.1	s__Mycobacterium simiae_A	80.386	906	1961	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:23:49,413] [INFO] GTDB search result was written to GCF_002101845.1_ASM210184v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:23:49,413] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:23:49,416] [INFO] DFAST_QC result json was written to GCF_002101845.1_ASM210184v1_genomic.fna/dqc_result.json
[2024-01-25 20:23:49,416] [INFO] DFAST_QC completed!
[2024-01-25 20:23:49,417] [INFO] Total running time: 0h2m14s