[2024-01-24 14:22:04,527] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:04,529] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:04,529] [INFO] DQC Reference Directory: /var/lib/cwl/stg62339a6f-7468-42db-8ee5-eb10a8d87cda/dqc_reference
[2024-01-24 14:22:05,931] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:05,932] [INFO] Task started: Prodigal
[2024-01-24 14:22:05,932] [INFO] Running command: gunzip -c /var/lib/cwl/stg0239ff1e-2e64-414b-8bbb-978a2fad1dae/GCF_010731755.1_ASM1073175v1_genomic.fna.gz | prodigal -d GCF_010731755.1_ASM1073175v1_genomic.fna/cds.fna -a GCF_010731755.1_ASM1073175v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:20,844] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:20,845] [INFO] Task started: HMMsearch
[2024-01-24 14:22:20,845] [INFO] Running command: hmmsearch --tblout GCF_010731755.1_ASM1073175v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62339a6f-7468-42db-8ee5-eb10a8d87cda/dqc_reference/reference_markers.hmm GCF_010731755.1_ASM1073175v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:21,162] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:21,164] [INFO] Found 6/6 markers.
[2024-01-24 14:22:21,210] [INFO] Query marker FASTA was written to GCF_010731755.1_ASM1073175v1_genomic.fna/markers.fasta
[2024-01-24 14:22:21,210] [INFO] Task started: Blastn
[2024-01-24 14:22:21,211] [INFO] Running command: blastn -query GCF_010731755.1_ASM1073175v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62339a6f-7468-42db-8ee5-eb10a8d87cda/dqc_reference/reference_markers.fasta -out GCF_010731755.1_ASM1073175v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:22,421] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:22,426] [INFO] Selected 9 target genomes.
[2024-01-24 14:22:22,427] [INFO] Target genome list was writen to GCF_010731755.1_ASM1073175v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:22,432] [INFO] Task started: fastANI
[2024-01-24 14:22:22,432] [INFO] Running command: fastANI --query /var/lib/cwl/stg0239ff1e-2e64-414b-8bbb-978a2fad1dae/GCF_010731755.1_ASM1073175v1_genomic.fna.gz --refList GCF_010731755.1_ASM1073175v1_genomic.fna/target_genomes.txt --output GCF_010731755.1_ASM1073175v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:33,683] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:33,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62339a6f-7468-42db-8ee5-eb10a8d87cda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:33,684] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62339a6f-7468-42db-8ee5-eb10a8d87cda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:33,693] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:22:33,694] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:33,694] [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
Mycolicibacter minnesotensis	strain=JCM 17932	GCA_010731755.1	1118379	1118379	type	True	100.0	1408	1408	95	conclusive
Mycolicibacter minnesotensis	strain=DSM 45633	GCA_002086405.1	1118379	1118379	type	True	99.9731	1370	1408	95	conclusive
Mycolicibacter arupensis	strain=DSM 44942	GCA_002086515.1	342002	342002	type	True	90.6872	1224	1408	95	below_threshold
Mycolicibacter nonchromogenicus	strain=DSM 44164	GCA_002101775.1	1782	1782	type	True	85.292	1094	1408	95	below_threshold
Mycolicibacter engbaekii	strain=ATCC 27353	GCA_002101585.1	188915	188915	type	True	84.7889	1084	1408	95	below_threshold
Mycolicibacter longobardus	strain=DSM 45394	GCA_002102265.1	1108812	1108812	type	True	84.7644	1063	1408	95	below_threshold
Mycolicibacter hiberniae	strain=JCM 13571	GCA_010729485.1	29314	29314	type	True	84.6835	1083	1408	95	below_threshold
Mycolicibacter hiberniae	strain=ATCC 49874	GCA_002101655.1	29314	29314	type	True	84.6796	1075	1408	95	below_threshold
Mycolicibacter senuensis	strain=DSM 44999	GCA_002101885.1	386913	386913	type	True	83.2888	1023	1408	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:33,695] [INFO] DFAST Taxonomy check result was written to GCF_010731755.1_ASM1073175v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:33,696] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:33,696] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:33,696] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62339a6f-7468-42db-8ee5-eb10a8d87cda/dqc_reference/checkm_data
[2024-01-24 14:22:33,697] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:33,744] [INFO] Task started: CheckM
[2024-01-24 14:22:33,744] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010731755.1_ASM1073175v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010731755.1_ASM1073175v1_genomic.fna/checkm_input GCF_010731755.1_ASM1073175v1_genomic.fna/checkm_result
[2024-01-24 14:23:20,002] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:20,004] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:20,025] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:20,026] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:20,026] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010731755.1_ASM1073175v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:20,027] [INFO] Task started: Blastn
[2024-01-24 14:23:20,027] [INFO] Running command: blastn -query GCF_010731755.1_ASM1073175v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62339a6f-7468-42db-8ee5-eb10a8d87cda/dqc_reference/reference_markers_gtdb.fasta -out GCF_010731755.1_ASM1073175v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:21,675] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:21,680] [INFO] Selected 10 target genomes.
[2024-01-24 14:23:21,680] [INFO] Target genome list was writen to GCF_010731755.1_ASM1073175v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:21,692] [INFO] Task started: fastANI
[2024-01-24 14:23:21,692] [INFO] Running command: fastANI --query /var/lib/cwl/stg0239ff1e-2e64-414b-8bbb-978a2fad1dae/GCF_010731755.1_ASM1073175v1_genomic.fna.gz --refList GCF_010731755.1_ASM1073175v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010731755.1_ASM1073175v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:34,293] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:34,311] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:34,311] [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_010731755.1	s__Mycobacterium minnesotense	100.0	1408	1408	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_002086515.1	s__Mycobacterium arupense	90.6872	1224	1408	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.89	98.19	0.91	0.89	5	-
GCF_001021505.1	s__Mycobacterium heraklionense_B	86.4735	1171	1408	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455125.1	s__Mycobacterium sp000455125	86.0021	1126	1408	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.70	98.55	0.90	0.88	3	-
GCF_001673105.1	s__Mycobacterium heraklionense_A	86.0015	1180	1408	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.02	95.09	0.92	0.90	5	-
GCF_900078685.2	s__Mycobacterium icosiumassiliensis	85.9578	1124	1408	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101775.1	s__Mycobacterium nonchromogenicum	85.3204	1091	1408	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.25	96.26	0.92	0.92	3	-
GCF_002101585.1	s__Mycobacterium engbaekii	84.7826	1085	1408	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.4017	N/A	N/A	N/A	N/A	1	-
GCF_002102265.1	s__Mycobacterium longobardum	84.782	1061	1408	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010729485.1	s__Mycobacterium hiberniae	84.6891	1081	1408	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.4017	97.81	95.62	0.96	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:34,313] [INFO] GTDB search result was written to GCF_010731755.1_ASM1073175v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:34,314] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:34,316] [INFO] DFAST_QC result json was written to GCF_010731755.1_ASM1073175v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:34,317] [INFO] DFAST_QC completed!
[2024-01-24 14:23:34,317] [INFO] Total running time: 0h1m30s