[2024-01-24 14:07:15,030] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:07:15,032] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:07:15,032] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb08c109-d655-4c32-8205-d74dc2420ed1/dqc_reference
[2024-01-24 14:07:16,366] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:16,367] [INFO] Task started: Prodigal
[2024-01-24 14:07:16,367] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0efe369-031b-4dd0-b07c-62917acabc0c/GCF_000613245.1_PRJEB5743_assembly_1_genomic.fna.gz | prodigal -d GCF_000613245.1_PRJEB5743_assembly_1_genomic.fna/cds.fna -a GCF_000613245.1_PRJEB5743_assembly_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:37,184] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:37,184] [INFO] Task started: HMMsearch
[2024-01-24 14:07:37,184] [INFO] Running command: hmmsearch --tblout GCF_000613245.1_PRJEB5743_assembly_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb08c109-d655-4c32-8205-d74dc2420ed1/dqc_reference/reference_markers.hmm GCF_000613245.1_PRJEB5743_assembly_1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:37,515] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:37,517] [INFO] Found 6/6 markers.
[2024-01-24 14:07:37,571] [INFO] Query marker FASTA was written to GCF_000613245.1_PRJEB5743_assembly_1_genomic.fna/markers.fasta
[2024-01-24 14:07:37,572] [INFO] Task started: Blastn
[2024-01-24 14:07:37,572] [INFO] Running command: blastn -query GCF_000613245.1_PRJEB5743_assembly_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb08c109-d655-4c32-8205-d74dc2420ed1/dqc_reference/reference_markers.fasta -out GCF_000613245.1_PRJEB5743_assembly_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:38,656] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:38,661] [INFO] Selected 14 target genomes.
[2024-01-24 14:07:38,661] [INFO] Target genome list was writen to GCF_000613245.1_PRJEB5743_assembly_1_genomic.fna/target_genomes.txt
[2024-01-24 14:07:38,676] [INFO] Task started: fastANI
[2024-01-24 14:07:38,677] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0efe369-031b-4dd0-b07c-62917acabc0c/GCF_000613245.1_PRJEB5743_assembly_1_genomic.fna.gz --refList GCF_000613245.1_PRJEB5743_assembly_1_genomic.fna/target_genomes.txt --output GCF_000613245.1_PRJEB5743_assembly_1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:58,117] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:58,117] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb08c109-d655-4c32-8205-d74dc2420ed1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:58,118] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb08c109-d655-4c32-8205-d74dc2420ed1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:58,130] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:07:58,130] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:58,130] [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 asiaticum	strain=DSM 44297	GCA_000613245.1	1790	1790	suspected-type	True	100.0	1973	1976	95	conclusive
Mycobacterium asiaticum	strain=DSM 44297	GCA_002086545.1	1790	1790	suspected-type	True	99.9312	1911	1976	95	conclusive
Mycobacterium paragordonae	strain=49061	GCA_003614435.1	1389713	1389713	type	True	81.8993	1422	1976	95	below_threshold
Mycobacterium paragordonae	strain=JCM 18565	GCA_010723415.1	1389713	1389713	type	True	81.8964	1433	1976	95	below_threshold
Mycobacterium gordonae	strain=DSM 44160	GCA_002101675.1	1778	1778	type	True	81.5988	1337	1976	95	below_threshold
Mycobacterium avium subsp. avium	strain=DSM 44156	GCA_009741445.1	44454	1764	type	True	81.0804	1057	1976	95	below_threshold
Mycobacterium avium subsp. avium	strain=ATCC 25291	GCA_000174035.1	44454	1764	type	True	81.0627	994	1976	95	below_threshold
Mycobacterium palustre	strain=DSM 44572	GCA_002101785.1	153971	153971	type	True	80.8175	1053	1976	95	below_threshold
Mycobacterium kubicae	strain=CIP 106428	GCA_002101745.1	120959	120959	type	True	80.6286	1139	1976	95	below_threshold
Mycobacterium kubicae	strain=JCM 13573	GCA_010723135.1	120959	120959	type	True	80.6281	1120	1976	95	below_threshold
Mycobacterium kubicae	strain=JCM 13573	GCA_015689175.1	120959	120959	type	True	80.606	1132	1976	95	below_threshold
Mycobacterium bohemicum	strain=DSM 44277	GCA_002102025.1	56425	56425	type	True	80.569	1065	1976	95	below_threshold
Mycobacterium conspicuum	strain=DSM 44136	GCA_002102095.1	44010	44010	type	True	80.5127	1116	1976	95	below_threshold
Mycobacterium conspicuum	strain=JCM 14738	GCA_010730195.1	44010	44010	type	True	80.448	1125	1976	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:58,301] [INFO] DFAST Taxonomy check result was written to GCF_000613245.1_PRJEB5743_assembly_1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:58,302] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:58,302] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:58,303] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb08c109-d655-4c32-8205-d74dc2420ed1/dqc_reference/checkm_data
[2024-01-24 14:07:58,305] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:58,364] [INFO] Task started: CheckM
[2024-01-24 14:07:58,365] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000613245.1_PRJEB5743_assembly_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000613245.1_PRJEB5743_assembly_1_genomic.fna/checkm_input GCF_000613245.1_PRJEB5743_assembly_1_genomic.fna/checkm_result
[2024-01-24 14:08:56,917] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:56,918] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:56,939] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:56,939] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:56,940] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000613245.1_PRJEB5743_assembly_1_genomic.fna/markers.fasta)
[2024-01-24 14:08:56,940] [INFO] Task started: Blastn
[2024-01-24 14:08:56,940] [INFO] Running command: blastn -query GCF_000613245.1_PRJEB5743_assembly_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb08c109-d655-4c32-8205-d74dc2420ed1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000613245.1_PRJEB5743_assembly_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:58,452] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:58,456] [INFO] Selected 12 target genomes.
[2024-01-24 14:08:58,457] [INFO] Target genome list was writen to GCF_000613245.1_PRJEB5743_assembly_1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:58,469] [INFO] Task started: fastANI
[2024-01-24 14:08:58,469] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0efe369-031b-4dd0-b07c-62917acabc0c/GCF_000613245.1_PRJEB5743_assembly_1_genomic.fna.gz --refList GCF_000613245.1_PRJEB5743_assembly_1_genomic.fna/target_genomes_gtdb.txt --output GCF_000613245.1_PRJEB5743_assembly_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:09:17,331] [INFO] Task succeeded: fastANI
[2024-01-24 14:09:17,347] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:09:17,347] [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_000613245.1	s__Mycobacterium asiaticum	100.0	1973	1976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.95	98.52	0.95	0.93	5	conclusive
GCF_001673635.1	s__Mycobacterium asiaticum_C	91.9916	1783	1976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.07	99.07	0.94	0.94	2	-
GCF_001668675.1	s__Mycobacterium asiaticum_D	91.9054	1647	1976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001673315.1	s__Mycobacterium asiaticum_B	84.2254	1456	1976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003614435.1	s__Mycobacterium paragordonae	81.8737	1426	1976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.23	97.83	0.93	0.88	9	-
GCF_001417955.2	s__Mycobacterium gordonae_B	81.8008	1402	1976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001673365.1	s__Mycobacterium asiaticum_A	81.62	1274	1976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017086405.1	s__Mycobacterium gordonae_D	81.4215	1325	1976	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	80.7841	1101	1976	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	80.6279	1151	1976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015689175.1	s__Mycobacterium kubicae	80.6129	1130	1976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.05	97.98	0.96	0.92	7	-
GCF_002086275.1	s__Mycobacterium intermedium	80.359	1178	1976	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.91	99.88	0.97	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:09:17,349] [INFO] GTDB search result was written to GCF_000613245.1_PRJEB5743_assembly_1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:09:17,350] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:09:17,355] [INFO] DFAST_QC result json was written to GCF_000613245.1_PRJEB5743_assembly_1_genomic.fna/dqc_result.json
[2024-01-24 14:09:17,355] [INFO] DFAST_QC completed!
[2024-01-24 14:09:17,355] [INFO] Total running time: 0h2m2s