[2024-01-24 12:13:56,656] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:56,659] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:56,659] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e94c61a-bd59-4b83-980f-56b1701fb566/dqc_reference
[2024-01-24 12:13:57,949] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:57,950] [INFO] Task started: Prodigal
[2024-01-24 12:13:57,950] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f874d92-f22d-4ed5-8aae-ea09f57c9bca/GCF_002104765.1_ASM210476v1_genomic.fna.gz | prodigal -d GCF_002104765.1_ASM210476v1_genomic.fna/cds.fna -a GCF_002104765.1_ASM210476v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:19,999] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:20,000] [INFO] Task started: HMMsearch
[2024-01-24 12:14:20,000] [INFO] Running command: hmmsearch --tblout GCF_002104765.1_ASM210476v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e94c61a-bd59-4b83-980f-56b1701fb566/dqc_reference/reference_markers.hmm GCF_002104765.1_ASM210476v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:20,410] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:20,412] [INFO] Found 6/6 markers.
[2024-01-24 12:14:20,463] [INFO] Query marker FASTA was written to GCF_002104765.1_ASM210476v1_genomic.fna/markers.fasta
[2024-01-24 12:14:20,464] [INFO] Task started: Blastn
[2024-01-24 12:14:20,464] [INFO] Running command: blastn -query GCF_002104765.1_ASM210476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e94c61a-bd59-4b83-980f-56b1701fb566/dqc_reference/reference_markers.fasta -out GCF_002104765.1_ASM210476v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:21,741] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:21,744] [INFO] Selected 8 target genomes.
[2024-01-24 12:14:21,745] [INFO] Target genome list was writen to GCF_002104765.1_ASM210476v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:21,748] [INFO] Task started: fastANI
[2024-01-24 12:14:21,749] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f874d92-f22d-4ed5-8aae-ea09f57c9bca/GCF_002104765.1_ASM210476v1_genomic.fna.gz --refList GCF_002104765.1_ASM210476v1_genomic.fna/target_genomes.txt --output GCF_002104765.1_ASM210476v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:34,493] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:34,494] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e94c61a-bd59-4b83-980f-56b1701fb566/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:34,494] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e94c61a-bd59-4b83-980f-56b1701fb566/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:34,503] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:14:34,504] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:14:34,504] [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 colombiense	strain=CECT 3035	GCA_000222105.4	339268	339268	suspected-type	True	92.1451	1509	2042	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	92.143	1519	2042	95	below_threshold
Mycobacterium mantenii	strain=DSM 45255	GCA_002086335.1	560555	560555	type	True	89.6977	1596	2042	95	below_threshold
Mycobacterium mantenii	strain=JCM 18113	GCA_010731775.1	560555	560555	type	True	89.6643	1620	2042	95	below_threshold
Mycobacterium arosiense	strain=DSM 45069	GCA_002086125.1	425468	425468	type	True	88.5166	1415	2042	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000277125.1	1767	1767	suspected-type	True	87.7344	1485	2042	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	87.7183	1484	2042	95	below_threshold
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	87.0089	1447	2042	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:34,508] [INFO] DFAST Taxonomy check result was written to GCF_002104765.1_ASM210476v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:34,511] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:34,511] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:34,512] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e94c61a-bd59-4b83-980f-56b1701fb566/dqc_reference/checkm_data
[2024-01-24 12:14:34,513] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:34,593] [INFO] Task started: CheckM
[2024-01-24 12:14:34,594] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002104765.1_ASM210476v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002104765.1_ASM210476v1_genomic.fna/checkm_input GCF_002104765.1_ASM210476v1_genomic.fna/checkm_result
[2024-01-24 12:15:35,330] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:35,331] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:35,356] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:35,356] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:35,356] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002104765.1_ASM210476v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:35,357] [INFO] Task started: Blastn
[2024-01-24 12:15:35,357] [INFO] Running command: blastn -query GCF_002104765.1_ASM210476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e94c61a-bd59-4b83-980f-56b1701fb566/dqc_reference/reference_markers_gtdb.fasta -out GCF_002104765.1_ASM210476v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:37,236] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:37,240] [INFO] Selected 8 target genomes.
[2024-01-24 12:15:37,240] [INFO] Target genome list was writen to GCF_002104765.1_ASM210476v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:37,247] [INFO] Task started: fastANI
[2024-01-24 12:15:37,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f874d92-f22d-4ed5-8aae-ea09f57c9bca/GCF_002104765.1_ASM210476v1_genomic.fna.gz --refList GCF_002104765.1_ASM210476v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002104765.1_ASM210476v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:49,648] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:49,663] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:49,663] [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_002104765.1	s__Mycobacterium vulneris	100.0	2035	2042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001672755.1	s__Mycobacterium colombiense_C	94.5424	1521	2042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953985.1	s__Mycobacterium colombiense_B	93.7601	1516	2042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.54	96.91	0.93	0.88	12	-
GCF_001665835.1	s__Mycobacterium colombiense_A	93.6344	1500	2042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105755.1	s__Mycobacterium colombiense	92.123	1521	2042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.60	97.75	0.94	0.91	4	-
GCF_010731775.1	s__Mycobacterium mantenii	89.6643	1620	2042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.19	95.22	0.92	0.90	6	-
GCF_003284935.1	s__Mycobacterium arosiense_A	89.2835	1390	2042	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001673555.1	s__Mycobacterium sp001673555	89.1369	1250	2042	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 12:15:49,665] [INFO] GTDB search result was written to GCF_002104765.1_ASM210476v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:49,666] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:49,669] [INFO] DFAST_QC result json was written to GCF_002104765.1_ASM210476v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:49,670] [INFO] DFAST_QC completed!
[2024-01-24 12:15:49,670] [INFO] Total running time: 0h1m53s