[2024-01-25 18:17:05,747] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:17:05,751] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:17:05,751] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ca8ec9b-1a5c-40bb-99ec-389f47067ad4/dqc_reference
[2024-01-25 18:17:06,938] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:17:06,938] [INFO] Task started: Prodigal
[2024-01-25 18:17:06,939] [INFO] Running command: gunzip -c /var/lib/cwl/stg5bed33e5-11bc-4f3a-bf3d-5711e56433bc/GCF_002101775.1_ASM210177v1_genomic.fna.gz | prodigal -d GCF_002101775.1_ASM210177v1_genomic.fna/cds.fna -a GCF_002101775.1_ASM210177v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:17:19,572] [INFO] Task succeeded: Prodigal
[2024-01-25 18:17:19,572] [INFO] Task started: HMMsearch
[2024-01-25 18:17:19,572] [INFO] Running command: hmmsearch --tblout GCF_002101775.1_ASM210177v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ca8ec9b-1a5c-40bb-99ec-389f47067ad4/dqc_reference/reference_markers.hmm GCF_002101775.1_ASM210177v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:17:19,832] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:17:19,833] [INFO] Found 6/6 markers.
[2024-01-25 18:17:19,873] [INFO] Query marker FASTA was written to GCF_002101775.1_ASM210177v1_genomic.fna/markers.fasta
[2024-01-25 18:17:19,873] [INFO] Task started: Blastn
[2024-01-25 18:17:19,873] [INFO] Running command: blastn -query GCF_002101775.1_ASM210177v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ca8ec9b-1a5c-40bb-99ec-389f47067ad4/dqc_reference/reference_markers.fasta -out GCF_002101775.1_ASM210177v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:17:20,965] [INFO] Task succeeded: Blastn
[2024-01-25 18:17:20,967] [INFO] Selected 11 target genomes.
[2024-01-25 18:17:20,968] [INFO] Target genome list was writen to GCF_002101775.1_ASM210177v1_genomic.fna/target_genomes.txt
[2024-01-25 18:17:20,977] [INFO] Task started: fastANI
[2024-01-25 18:17:20,977] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bed33e5-11bc-4f3a-bf3d-5711e56433bc/GCF_002101775.1_ASM210177v1_genomic.fna.gz --refList GCF_002101775.1_ASM210177v1_genomic.fna/target_genomes.txt --output GCF_002101775.1_ASM210177v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:17:34,180] [INFO] Task succeeded: fastANI
[2024-01-25 18:17:34,180] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ca8ec9b-1a5c-40bb-99ec-389f47067ad4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:17:34,180] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ca8ec9b-1a5c-40bb-99ec-389f47067ad4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:17:34,189] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:17:34,189] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:17:34,190] [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 nonchromogenicus	strain=DSM 44164	GCA_002101775.1	1782	1782	type	True	100.0	1439	1443	95	conclusive
Mycolicibacter engbaekii	strain=ATCC 27353	GCA_002101585.1	188915	188915	type	True	86.2282	1206	1443	95	below_threshold
Mycolicibacter hiberniae	strain=ATCC 49874	GCA_002101655.1	29314	29314	type	True	86.0243	1215	1443	95	below_threshold
Mycolicibacter longobardus	strain=DSM 45394	GCA_002102265.1	1108812	1108812	type	True	85.7416	1133	1443	95	below_threshold
Mycolicibacter arupensis	strain=DSM 44942	GCA_002086515.1	342002	342002	type	True	85.516	1080	1443	95	below_threshold
Mycolicibacter minnesotensis	strain=DSM 45633	GCA_002086405.1	1118379	1118379	type	True	85.3677	1089	1443	95	below_threshold
Mycolicibacter minnesotensis	strain=JCM 17932	GCA_010731755.1	1118379	1118379	type	True	85.3301	1087	1443	95	below_threshold
Mycolicibacter kumamotonensis	strain=DSM 45093	GCA_002086285.1	354243	354243	type	True	84.7348	1121	1443	95	below_threshold
Mycolicibacter kumamotonensis	strain=CST 7247	GCA_010093495.1	354243	354243	type	True	84.7235	1093	1443	95	below_threshold
Mycolicibacter terrae	strain=CIP 104321	GCA_002101955.1	1788	1788	type	True	84.6073	1117	1443	95	below_threshold
Mycolicibacter terrae	strain=JCM 12143	GCA_010727125.1	1788	1788	type	True	84.5321	1136	1443	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:17:34,191] [INFO] DFAST Taxonomy check result was written to GCF_002101775.1_ASM210177v1_genomic.fna/tc_result.tsv
[2024-01-25 18:17:34,192] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:17:34,192] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:17:34,192] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ca8ec9b-1a5c-40bb-99ec-389f47067ad4/dqc_reference/checkm_data
[2024-01-25 18:17:34,193] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:17:34,258] [INFO] Task started: CheckM
[2024-01-25 18:17:34,258] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002101775.1_ASM210177v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002101775.1_ASM210177v1_genomic.fna/checkm_input GCF_002101775.1_ASM210177v1_genomic.fna/checkm_result
[2024-01-25 18:18:15,791] [INFO] Task succeeded: CheckM
[2024-01-25 18:18:15,792] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:18:15,811] [INFO] ===== Completeness check finished =====
[2024-01-25 18:18:15,811] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:18:15,812] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002101775.1_ASM210177v1_genomic.fna/markers.fasta)
[2024-01-25 18:18:15,813] [INFO] Task started: Blastn
[2024-01-25 18:18:15,813] [INFO] Running command: blastn -query GCF_002101775.1_ASM210177v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ca8ec9b-1a5c-40bb-99ec-389f47067ad4/dqc_reference/reference_markers_gtdb.fasta -out GCF_002101775.1_ASM210177v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:18:17,441] [INFO] Task succeeded: Blastn
[2024-01-25 18:18:17,443] [INFO] Selected 8 target genomes.
[2024-01-25 18:18:17,443] [INFO] Target genome list was writen to GCF_002101775.1_ASM210177v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:18:17,450] [INFO] Task started: fastANI
[2024-01-25 18:18:17,450] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bed33e5-11bc-4f3a-bf3d-5711e56433bc/GCF_002101775.1_ASM210177v1_genomic.fna.gz --refList GCF_002101775.1_ASM210177v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002101775.1_ASM210177v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:18:27,439] [INFO] Task succeeded: fastANI
[2024-01-25 18:18:27,445] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:18:27,445] [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_002101775.1	s__Mycobacterium nonchromogenicum	100.0	1439	1443	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.25	96.26	0.92	0.92	3	conclusive
GCF_001673105.1	s__Mycobacterium heraklionense_A	89.1137	1200	1443	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.02	95.09	0.92	0.90	5	-
GCF_000455125.1	s__Mycobacterium sp000455125	89.0506	1174	1443	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.70	98.55	0.90	0.88	3	-
GCF_001021505.1	s__Mycobacterium heraklionense_B	88.7388	1228	1443	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078685.2	s__Mycobacterium icosiumassiliensis	88.6105	1103	1443	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101585.1	s__Mycobacterium engbaekii	86.2231	1206	1443	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.4017	N/A	N/A	N/A	N/A	1	-
GCF_010729485.1	s__Mycobacterium hiberniae	86.0346	1222	1443	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.4017	97.81	95.62	0.96	0.92	3	-
GCF_002102265.1	s__Mycobacterium longobardum	85.7642	1130	1443	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 18:18:27,447] [INFO] GTDB search result was written to GCF_002101775.1_ASM210177v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:18:27,447] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:18:27,450] [INFO] DFAST_QC result json was written to GCF_002101775.1_ASM210177v1_genomic.fna/dqc_result.json
[2024-01-25 18:18:27,450] [INFO] DFAST_QC completed!
[2024-01-25 18:18:27,450] [INFO] Total running time: 0h1m22s