[2024-01-24 11:44:05,456] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:05,458] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:05,458] [INFO] DQC Reference Directory: /var/lib/cwl/stge39f7525-c43f-4a7f-820c-a954380bc77c/dqc_reference
[2024-01-24 11:44:08,838] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:08,838] [INFO] Task started: Prodigal
[2024-01-24 11:44:08,839] [INFO] Running command: gunzip -c /var/lib/cwl/stg5756008b-1cd3-49db-8033-ee4e4f000364/GCF_019456655.1_ASM1945665v1_genomic.fna.gz | prodigal -d GCF_019456655.1_ASM1945665v1_genomic.fna/cds.fna -a GCF_019456655.1_ASM1945665v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:28,164] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:28,164] [INFO] Task started: HMMsearch
[2024-01-24 11:44:28,164] [INFO] Running command: hmmsearch --tblout GCF_019456655.1_ASM1945665v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge39f7525-c43f-4a7f-820c-a954380bc77c/dqc_reference/reference_markers.hmm GCF_019456655.1_ASM1945665v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:28,476] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:28,477] [INFO] Found 6/6 markers.
[2024-01-24 11:44:28,532] [INFO] Query marker FASTA was written to GCF_019456655.1_ASM1945665v1_genomic.fna/markers.fasta
[2024-01-24 11:44:28,532] [INFO] Task started: Blastn
[2024-01-24 11:44:28,532] [INFO] Running command: blastn -query GCF_019456655.1_ASM1945665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge39f7525-c43f-4a7f-820c-a954380bc77c/dqc_reference/reference_markers.fasta -out GCF_019456655.1_ASM1945665v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:29,740] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:29,745] [INFO] Selected 19 target genomes.
[2024-01-24 11:44:29,745] [INFO] Target genome list was writen to GCF_019456655.1_ASM1945665v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:29,767] [INFO] Task started: fastANI
[2024-01-24 11:44:29,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg5756008b-1cd3-49db-8033-ee4e4f000364/GCF_019456655.1_ASM1945665v1_genomic.fna.gz --refList GCF_019456655.1_ASM1945665v1_genomic.fna/target_genomes.txt --output GCF_019456655.1_ASM1945665v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:53,017] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:53,018] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge39f7525-c43f-4a7f-820c-a954380bc77c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:53,018] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge39f7525-c43f-4a7f-820c-a954380bc77c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:53,032] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:44:53,032] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:44:53,033] [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
Mycolicibacterium bacteremicum	strain=DSM 45578	GCA_002086115.1	564198	564198	type	True	83.2514	1318	1999	95	below_threshold
Mycolicibacterium neoaurum	strain=DSM 44074	GCA_005670605.1	1795	1795	type	True	82.2377	1184	1999	95	below_threshold
Mycolicibacterium neoaurum	strain=ATCC 25795	GCA_000691525.1	1795	1795	type	True	82.216	1154	1999	95	below_threshold
Mycolicibacterium neoaurum	strain=DSM 44074	GCA_000724065.1	1795	1795	type	True	82.2144	1177	1999	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_000613185.1	258533	258533	type	True	82.0621	1165	1999	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_005670675.1	258533	258533	type	True	82.0388	1155	1999	95	below_threshold
Mycolicibacterium canariasense	strain=CCUG 47953	GCA_002101555.1	228230	228230	type	True	81.8123	1075	1999	95	below_threshold
Mycolicibacterium canariasense	strain=JCM15298	GCA_001570445.1	228230	228230	type	True	81.8017	1068	1999	95	below_threshold
Mycolicibacterium fluoranthenivorans	strain=DSM 44556	GCA_011758805.1	258505	258505	type	True	81.6913	1127	1999	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	81.1691	1036	1999	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	81.1148	1052	1999	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	81.0936	1054	1999	95	below_threshold
Mycolicibacterium nivoides	strain=DL90	GCA_003855255.1	2487344	2487344	type	True	80.6725	1072	1999	95	below_threshold
Mycolicibacterium peregrinum	strain=DSM 43271	GCA_002102345.1	43304	43304	type	True	80.5208	1016	1999	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	80.4585	956	1999	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	80.0218	835	1999	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.6731	884	1999	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.6554	884	1999	95	below_threshold
Mycolicibacterium mengxianglii	strain=Z-34	GCA_015710575.2	2736649	2736649	type	True	79.5842	862	1999	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:53,037] [INFO] DFAST Taxonomy check result was written to GCF_019456655.1_ASM1945665v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:53,043] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:53,043] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:53,043] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge39f7525-c43f-4a7f-820c-a954380bc77c/dqc_reference/checkm_data
[2024-01-24 11:44:53,045] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:53,101] [INFO] Task started: CheckM
[2024-01-24 11:44:53,101] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019456655.1_ASM1945665v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019456655.1_ASM1945665v1_genomic.fna/checkm_input GCF_019456655.1_ASM1945665v1_genomic.fna/checkm_result
[2024-01-24 11:46:06,263] [INFO] Task succeeded: CheckM
[2024-01-24 11:46:06,264] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:46:06,287] [INFO] ===== Completeness check finished =====
[2024-01-24 11:46:06,289] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:46:06,289] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019456655.1_ASM1945665v1_genomic.fna/markers.fasta)
[2024-01-24 11:46:06,290] [INFO] Task started: Blastn
[2024-01-24 11:46:06,290] [INFO] Running command: blastn -query GCF_019456655.1_ASM1945665v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge39f7525-c43f-4a7f-820c-a954380bc77c/dqc_reference/reference_markers_gtdb.fasta -out GCF_019456655.1_ASM1945665v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:46:08,068] [INFO] Task succeeded: Blastn
[2024-01-24 11:46:08,072] [INFO] Selected 15 target genomes.
[2024-01-24 11:46:08,072] [INFO] Target genome list was writen to GCF_019456655.1_ASM1945665v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:46:08,083] [INFO] Task started: fastANI
[2024-01-24 11:46:08,083] [INFO] Running command: fastANI --query /var/lib/cwl/stg5756008b-1cd3-49db-8033-ee4e4f000364/GCF_019456655.1_ASM1945665v1_genomic.fna.gz --refList GCF_019456655.1_ASM1945665v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019456655.1_ASM1945665v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:29,084] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:29,103] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:29,104] [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_001907655.1	s__Mycobacterium diernhoferi	99.9768	1974	1999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.97	99.94	1.00	1.00	3	conclusive
GCF_900078775.1	s__Mycobacterium aurum_A	89.9974	1681	1999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428895.1	s__Mycobacterium sp001428895	84.7183	1434	1999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012223425.1	s__Mycobacterium frederiksbergense	84.5737	1354	1999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.39	95.39	0.91	0.91	2	-
GCF_008329585.1	s__Mycobacterium sp008329585	84.4053	1393	1999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001644575.1	s__Mycobacterium sp001644575	84.2818	1339	1999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.69	99.69	0.98	0.98	2	-
GCF_002086115.1	s__Mycobacterium bacteremicum	83.2272	1322	1999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317305.3	s__Mycobacterium neoaurum_A	82.4208	1144	1999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.30	95.79	0.98	0.90	7	-
GCF_000691525.1	s__Mycobacterium neoaurum	82.2116	1154	1999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.16	98.36	0.96	0.91	6	-
GCF_000613185.1	s__Mycobacterium cosmeticum	82.0751	1163	1999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.89	98.33	0.93	0.89	4	-
GCF_002101555.1	s__Mycobacterium canariasense	81.8061	1076	1999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCA_016197365.1	s__Mycobacterium cosmeticum_A	81.697	1044	1999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637205.1	s__Mycobacterium chitae	80.7116	998	1999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000612725.1	s__Mycobacterium austroafricanum	80.3868	1022	1999	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.53	98.42	0.88	0.88	3	-
GCF_000426065.1	s__Mycobacterium sp000426065	80.3781	991	1999	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 11:46:29,105] [INFO] GTDB search result was written to GCF_019456655.1_ASM1945665v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:29,106] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:29,110] [INFO] DFAST_QC result json was written to GCF_019456655.1_ASM1945665v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:29,111] [INFO] DFAST_QC completed!
[2024-01-24 11:46:29,111] [INFO] Total running time: 0h2m24s