[2024-01-24 14:30:34,059] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:34,061] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:34,061] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c83e9fe-644c-4d5a-89a3-98378a19a059/dqc_reference
[2024-01-24 14:30:35,397] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:35,398] [INFO] Task started: Prodigal
[2024-01-24 14:30:35,398] [INFO] Running command: gunzip -c /var/lib/cwl/stgd093e673-011f-459b-800a-7b562b45cc9d/GCF_010730055.1_ASM1073005v1_genomic.fna.gz | prodigal -d GCF_010730055.1_ASM1073005v1_genomic.fna/cds.fna -a GCF_010730055.1_ASM1073005v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:54,902] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:54,903] [INFO] Task started: HMMsearch
[2024-01-24 14:30:54,903] [INFO] Running command: hmmsearch --tblout GCF_010730055.1_ASM1073005v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c83e9fe-644c-4d5a-89a3-98378a19a059/dqc_reference/reference_markers.hmm GCF_010730055.1_ASM1073005v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:55,192] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:55,194] [INFO] Found 6/6 markers.
[2024-01-24 14:30:55,241] [INFO] Query marker FASTA was written to GCF_010730055.1_ASM1073005v1_genomic.fna/markers.fasta
[2024-01-24 14:30:55,242] [INFO] Task started: Blastn
[2024-01-24 14:30:55,242] [INFO] Running command: blastn -query GCF_010730055.1_ASM1073005v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c83e9fe-644c-4d5a-89a3-98378a19a059/dqc_reference/reference_markers.fasta -out GCF_010730055.1_ASM1073005v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:56,308] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:56,312] [INFO] Selected 17 target genomes.
[2024-01-24 14:30:56,312] [INFO] Target genome list was writen to GCF_010730055.1_ASM1073005v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:56,328] [INFO] Task started: fastANI
[2024-01-24 14:30:56,329] [INFO] Running command: fastANI --query /var/lib/cwl/stgd093e673-011f-459b-800a-7b562b45cc9d/GCF_010730055.1_ASM1073005v1_genomic.fna.gz --refList GCF_010730055.1_ASM1073005v1_genomic.fna/target_genomes.txt --output GCF_010730055.1_ASM1073005v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:20,478] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:20,479] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c83e9fe-644c-4d5a-89a3-98378a19a059/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:20,479] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c83e9fe-644c-4d5a-89a3-98378a19a059/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:20,494] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:31:20,494] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:20,494] [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 shinjukuense	strain=JCM 14233	GCA_010730055.1	398694	398694	type	True	100.0	1501	1501	95	conclusive
Mycobacterium shinjukuense	strain=CCUG 53584	GCA_002086755.1	398694	398694	type	True	99.915	1382	1501	95	conclusive
Mycobacterium tuberculosis	strain=H37Rv	GCA_000195955.2	1773	1773	type	True	83.5147	1081	1501	95	below_threshold
Mycobacterium lacus	strain=DSM 44577	GCA_002102215.1	169765	169765	type	True	83.4611	1102	1501	95	below_threshold
Mycobacterium lacus	strain=JCM 15657	GCA_010731535.1	169765	169765	type	True	83.3745	1160	1501	95	below_threshold
Mycobacterium heidelbergense	strain=JCM 14842	GCA_010730745.1	53376	53376	type	True	82.7352	929	1501	95	below_threshold
Mycobacterium riyadhense	strain=DSM 45176	GCA_002101845.1	486698	486698	type	True	82.5813	1099	1501	95	below_threshold
Mycobacterium simulans	strain=FI-09026	GCA_900232995.1	627089	627089	type	True	82.4219	1071	1501	95	below_threshold
Mycobacterium innocens	strain=MK13	GCA_900566055.1	2341083	2341083	type	True	82.1933	1049	1501	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	82.1059	934	1501	95	below_threshold
Mycobacterium avium subsp. avium	strain=ATCC 25291	GCA_000174035.1	44454	1764	type	True	82.0335	824	1501	95	below_threshold
Mycobacterium angelicum	strain=DSM 45057	GCA_002086155.1	470074	470074	type	True	81.9897	1052	1501	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	81.96	892	1501	95	below_threshold
Mycobacterium szulgai	strain=DSM 44166	GCA_002116635.1	1787	1787	type	True	81.8159	1037	1501	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	81.4421	878	1501	95	below_threshold
Mycobacterium haemophilum	strain=ATCC 29548	GCA_000340435.3	29311	29311	type	True	81.3163	854	1501	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_001053185.1	56425	56425	type	True	81.2893	852	1501	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:20,500] [INFO] DFAST Taxonomy check result was written to GCF_010730055.1_ASM1073005v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:20,501] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:20,501] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:20,501] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c83e9fe-644c-4d5a-89a3-98378a19a059/dqc_reference/checkm_data
[2024-01-24 14:31:20,504] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:20,549] [INFO] Task started: CheckM
[2024-01-24 14:31:20,550] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010730055.1_ASM1073005v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010730055.1_ASM1073005v1_genomic.fna/checkm_input GCF_010730055.1_ASM1073005v1_genomic.fna/checkm_result
[2024-01-24 14:32:15,455] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:15,460] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:15,483] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:15,483] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:15,483] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010730055.1_ASM1073005v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:15,484] [INFO] Task started: Blastn
[2024-01-24 14:32:15,484] [INFO] Running command: blastn -query GCF_010730055.1_ASM1073005v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c83e9fe-644c-4d5a-89a3-98378a19a059/dqc_reference/reference_markers_gtdb.fasta -out GCF_010730055.1_ASM1073005v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:16,935] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:16,939] [INFO] Selected 19 target genomes.
[2024-01-24 14:32:16,939] [INFO] Target genome list was writen to GCF_010730055.1_ASM1073005v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:16,969] [INFO] Task started: fastANI
[2024-01-24 14:32:16,970] [INFO] Running command: fastANI --query /var/lib/cwl/stgd093e673-011f-459b-800a-7b562b45cc9d/GCF_010730055.1_ASM1073005v1_genomic.fna.gz --refList GCF_010730055.1_ASM1073005v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010730055.1_ASM1073005v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:43,303] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:43,321] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:43,321] [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_010730055.1	s__Mycobacterium shinjukuense	100.0	1501	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_000195955.2	s__Mycobacterium tuberculosis	83.526	1078	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.92	97.88	0.99	0.91	6836	-
GCF_010731535.1	s__Mycobacterium lacus	83.408	1156	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002086305.1	s__Mycobacterium malmoense_B	82.8588	916	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.01	99.01	0.95	0.95	2	-
GCF_010730745.1	s__Mycobacterium heidelbergense	82.7065	933	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002104675.1	s__Mycobacterium decipiens	82.67	1022	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101845.1	s__Mycobacterium riyadhense	82.5964	1096	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.42	99.30	0.97	0.96	10	-
GCF_900232995.1	s__Mycobacterium simulans	82.4015	1074	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.78	97.78	0.92	0.92	2	-
GCF_900566055.1	s__Mycobacterium innocens	82.2289	1043	1501	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	82.0971	936	1501	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	82.0708	909	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001672915.1	s__Mycobacterium sp001672915	82.032	906	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086155.1	s__Mycobacterium angelicum	81.9875	1052	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900157385.1	s__Mycobacterium terramassiliense	81.9717	950	1501	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	81.806	927	1501	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	81.7986	1044	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000340435.2	s__Mycobacterium haemophilum	81.3224	854	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.07	99.06	0.94	0.94	5	-
GCF_001053185.1	s__Mycobacterium bohemicum	81.2734	854	1501	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	-
GCF_008370645.1	s__Mycobacterium simiae_A	80.9623	915	1501	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 14:32:43,323] [INFO] GTDB search result was written to GCF_010730055.1_ASM1073005v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:43,324] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:43,328] [INFO] DFAST_QC result json was written to GCF_010730055.1_ASM1073005v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:43,328] [INFO] DFAST_QC completed!
[2024-01-24 14:32:43,328] [INFO] Total running time: 0h2m9s