[2024-01-25 17:43:50,456] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:43:50,461] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:43:50,461] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ae90cdb-8252-406a-8972-fdae26163f0c/dqc_reference
[2024-01-25 17:43:51,628] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:43:51,629] [INFO] Task started: Prodigal
[2024-01-25 17:43:51,629] [INFO] Running command: gunzip -c /var/lib/cwl/stg14e221c1-6948-4b8d-9149-89dedf5d88d2/GCF_002102265.1_ASM210226v1_genomic.fna.gz | prodigal -d GCF_002102265.1_ASM210226v1_genomic.fna/cds.fna -a GCF_002102265.1_ASM210226v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:44:04,866] [INFO] Task succeeded: Prodigal
[2024-01-25 17:44:04,867] [INFO] Task started: HMMsearch
[2024-01-25 17:44:04,867] [INFO] Running command: hmmsearch --tblout GCF_002102265.1_ASM210226v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ae90cdb-8252-406a-8972-fdae26163f0c/dqc_reference/reference_markers.hmm GCF_002102265.1_ASM210226v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:44:05,192] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:44:05,193] [INFO] Found 6/6 markers.
[2024-01-25 17:44:05,236] [INFO] Query marker FASTA was written to GCF_002102265.1_ASM210226v1_genomic.fna/markers.fasta
[2024-01-25 17:44:05,237] [INFO] Task started: Blastn
[2024-01-25 17:44:05,237] [INFO] Running command: blastn -query GCF_002102265.1_ASM210226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ae90cdb-8252-406a-8972-fdae26163f0c/dqc_reference/reference_markers.fasta -out GCF_002102265.1_ASM210226v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:06,428] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:06,432] [INFO] Selected 21 target genomes.
[2024-01-25 17:44:06,432] [INFO] Target genome list was writen to GCF_002102265.1_ASM210226v1_genomic.fna/target_genomes.txt
[2024-01-25 17:44:06,445] [INFO] Task started: fastANI
[2024-01-25 17:44:06,445] [INFO] Running command: fastANI --query /var/lib/cwl/stg14e221c1-6948-4b8d-9149-89dedf5d88d2/GCF_002102265.1_ASM210226v1_genomic.fna.gz --refList GCF_002102265.1_ASM210226v1_genomic.fna/target_genomes.txt --output GCF_002102265.1_ASM210226v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:44:30,653] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:30,653] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ae90cdb-8252-406a-8972-fdae26163f0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:44:30,654] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ae90cdb-8252-406a-8972-fdae26163f0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:44:30,666] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:44:30,666] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:44:30,666] [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 longobardus	strain=DSM 45394	GCA_002102265.1	1108812	1108812	type	True	100.0	1575	1577	95	conclusive
Mycolicibacter terrae	strain=CIP 104321	GCA_002101955.1	1788	1788	type	True	86.5576	1131	1577	95	below_threshold
Mycolicibacter terrae	strain=JCM 12143	GCA_010727125.1	1788	1788	type	True	86.4163	1153	1577	95	below_threshold
Mycolicibacter kumamotonensis	strain=DSM 45093	GCA_002086285.1	354243	354243	type	True	86.1895	1155	1577	95	below_threshold
Mycolicibacter senuensis	strain=JCM 16017	GCA_010723225.1	386913	386913	type	True	86.0508	1167	1577	95	below_threshold
Mycolicibacter kumamotonensis	strain=CST 7247	GCA_010093495.1	354243	354243	type	True	86.0421	1114	1577	95	below_threshold
Mycolicibacter senuensis	strain=DSM 44999	GCA_002101885.1	386913	386913	type	True	86.003	1162	1577	95	below_threshold
Mycolicibacter nonchromogenicus	strain=DSM 44164	GCA_002101775.1	1782	1782	type	True	85.7434	1122	1577	95	below_threshold
Mycolicibacter engbaekii	strain=ATCC 27353	GCA_002101585.1	188915	188915	type	True	85.2734	1132	1577	95	below_threshold
Mycolicibacter hiberniae	strain=JCM 13571	GCA_010729485.1	29314	29314	type	True	85.1922	1135	1577	95	below_threshold
Mycolicibacter arupensis	strain=DSM 44942	GCA_002086515.1	342002	342002	type	True	85.166	1067	1577	95	below_threshold
Mycolicibacter hiberniae	strain=ATCC 49874	GCA_002101655.1	29314	29314	type	True	85.1069	1129	1577	95	below_threshold
Mycolicibacter minnesotensis	strain=DSM 45633	GCA_002086405.1	1118379	1118379	type	True	84.6898	1057	1577	95	below_threshold
Mycolicibacter minnesotensis	strain=JCM 17932	GCA_010731755.1	1118379	1118379	type	True	84.64	1063	1577	95	below_threshold
Mycobacterium nebraskense	strain=DSM 44803	GCA_002102255.1	244292	244292	type	True	79.6721	726	1577	95	below_threshold
Mycobacterium mantenii	strain=DSM 45255	GCA_002086335.1	560555	560555	type	True	79.6015	730	1577	95	below_threshold
Mycobacterium mantenii	strain=JCM 18113	GCA_010731775.1	560555	560555	type	True	79.5019	751	1577	95	below_threshold
Mycobacterium shigaense	strain=JCM 32072	GCA_002356315.1	722731	722731	type	True	79.4065	694	1577	95	below_threshold
Mycobacterium shigaense	strain=UN-152	GCA_002983495.1	722731	722731	type	True	79.3731	687	1577	95	below_threshold
Mycolicibacterium helvum	strain=JCM 30396	GCA_010731895.1	1534349	1534349	type	True	79.0276	649	1577	95	below_threshold
Mycobacterium simulans	strain=FI-09026	GCA_900232995.1	627089	627089	type	True	78.6283	606	1577	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:44:30,668] [INFO] DFAST Taxonomy check result was written to GCF_002102265.1_ASM210226v1_genomic.fna/tc_result.tsv
[2024-01-25 17:44:30,668] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:44:30,669] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:44:30,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ae90cdb-8252-406a-8972-fdae26163f0c/dqc_reference/checkm_data
[2024-01-25 17:44:30,669] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:44:30,714] [INFO] Task started: CheckM
[2024-01-25 17:44:30,714] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002102265.1_ASM210226v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002102265.1_ASM210226v1_genomic.fna/checkm_input GCF_002102265.1_ASM210226v1_genomic.fna/checkm_result
[2024-01-25 17:45:12,633] [INFO] Task succeeded: CheckM
[2024-01-25 17:45:12,634] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:45:12,652] [INFO] ===== Completeness check finished =====
[2024-01-25 17:45:12,652] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:45:12,652] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002102265.1_ASM210226v1_genomic.fna/markers.fasta)
[2024-01-25 17:45:12,653] [INFO] Task started: Blastn
[2024-01-25 17:45:12,653] [INFO] Running command: blastn -query GCF_002102265.1_ASM210226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ae90cdb-8252-406a-8972-fdae26163f0c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002102265.1_ASM210226v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:45:14,329] [INFO] Task succeeded: Blastn
[2024-01-25 17:45:14,331] [INFO] Selected 19 target genomes.
[2024-01-25 17:45:14,332] [INFO] Target genome list was writen to GCF_002102265.1_ASM210226v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:45:14,346] [INFO] Task started: fastANI
[2024-01-25 17:45:14,346] [INFO] Running command: fastANI --query /var/lib/cwl/stg14e221c1-6948-4b8d-9149-89dedf5d88d2/GCF_002102265.1_ASM210226v1_genomic.fna.gz --refList GCF_002102265.1_ASM210226v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002102265.1_ASM210226v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:45:37,777] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:37,789] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:45:37,789] [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_002102265.1	s__Mycobacterium longobardum	100.0	1575	1577	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_001021505.1	s__Mycobacterium heraklionense_B	87.4369	1219	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003284925.1	s__Mycobacterium algericum_A	86.584	1072	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001673105.1	s__Mycobacterium heraklionense_A	86.5815	1207	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.02	95.09	0.92	0.90	5	-
GCF_010727125.1	s__Mycobacterium terrae	86.4492	1149	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	99.99	1.00	1.00	3	-
GCF_000455125.1	s__Mycobacterium sp000455125	86.3173	1138	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.70	98.55	0.90	0.88	3	-
GCF_002086285.1	s__Mycobacterium kumamotonense	86.1862	1154	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.55	98.48	0.89	0.87	4	-
GCF_002086455.1	s__Mycobacterium algericum	86.1217	1148	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.66	97.92	0.93	0.90	4	-
GCF_001667375.1	s__Mycobacterium sinense_A	86.0576	1131	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.51	95.04	0.94	0.89	3	-
GCF_002101885.1	s__Mycobacterium senuense	86.0065	1161	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002101775.1	s__Mycobacterium nonchromogenicum	85.7522	1120	1577	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	85.2774	1130	1577	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	85.1567	1139	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.4017	97.81	95.62	0.96	0.92	3	-
GCF_002086515.1	s__Mycobacterium arupense	85.1388	1071	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.89	98.19	0.91	0.89	5	-
GCA_004354905.1	s__Mycobacterium eburneum	81.556	931	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.68	99.68	0.92	0.92	2	-
GCF_001673535.1	s__Mycobacterium sp001673535	79.8583	772	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731775.1	s__Mycobacterium mantenii	79.5275	747	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.19	95.22	0.92	0.90	6	-
GCF_001666835.1	s__Mycobacterium sp001666835	79.4152	726	1577	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	99.01	0.94	0.94	3	-
GCA_011334635.1	s__Mycobacterium sp011334635	78.9595	515	1577	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 17:45:37,791] [INFO] GTDB search result was written to GCF_002102265.1_ASM210226v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:45:37,792] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:45:37,795] [INFO] DFAST_QC result json was written to GCF_002102265.1_ASM210226v1_genomic.fna/dqc_result.json
[2024-01-25 17:45:37,796] [INFO] DFAST_QC completed!
[2024-01-25 17:45:37,796] [INFO] Total running time: 0h1m47s