[2024-01-25 17:53:50,478] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:53:50,480] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:53:50,480] [INFO] DQC Reference Directory: /var/lib/cwl/stg897b2dbd-86b6-4a6c-a082-9a719aef7823/dqc_reference
[2024-01-25 17:53:51,618] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:53:51,619] [INFO] Task started: Prodigal
[2024-01-25 17:53:51,619] [INFO] Running command: gunzip -c /var/lib/cwl/stg195f2d7c-d559-4024-b72b-7f4d89eb2bbb/GCF_025822555.1_ASM2582255v1_genomic.fna.gz | prodigal -d GCF_025822555.1_ASM2582255v1_genomic.fna/cds.fna -a GCF_025822555.1_ASM2582255v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:54:12,004] [INFO] Task succeeded: Prodigal
[2024-01-25 17:54:12,005] [INFO] Task started: HMMsearch
[2024-01-25 17:54:12,005] [INFO] Running command: hmmsearch --tblout GCF_025822555.1_ASM2582255v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg897b2dbd-86b6-4a6c-a082-9a719aef7823/dqc_reference/reference_markers.hmm GCF_025822555.1_ASM2582255v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:54:12,265] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:54:12,267] [INFO] Found 6/6 markers.
[2024-01-25 17:54:12,319] [INFO] Query marker FASTA was written to GCF_025822555.1_ASM2582255v1_genomic.fna/markers.fasta
[2024-01-25 17:54:12,319] [INFO] Task started: Blastn
[2024-01-25 17:54:12,319] [INFO] Running command: blastn -query GCF_025822555.1_ASM2582255v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg897b2dbd-86b6-4a6c-a082-9a719aef7823/dqc_reference/reference_markers.fasta -out GCF_025822555.1_ASM2582255v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:13,429] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:13,432] [INFO] Selected 20 target genomes.
[2024-01-25 17:54:13,432] [INFO] Target genome list was writen to GCF_025822555.1_ASM2582255v1_genomic.fna/target_genomes.txt
[2024-01-25 17:54:13,444] [INFO] Task started: fastANI
[2024-01-25 17:54:13,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg195f2d7c-d559-4024-b72b-7f4d89eb2bbb/GCF_025822555.1_ASM2582255v1_genomic.fna.gz --refList GCF_025822555.1_ASM2582255v1_genomic.fna/target_genomes.txt --output GCF_025822555.1_ASM2582255v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:54:38,820] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:38,820] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg897b2dbd-86b6-4a6c-a082-9a719aef7823/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:54:38,821] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg897b2dbd-86b6-4a6c-a082-9a719aef7823/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:54:38,833] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:54:38,834] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:54:38,834] [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 fluoranthenivorans	strain=DSM 44556	GCA_011758805.1	258505	258505	type	True	96.0204	1813	2218	95	conclusive
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_000613185.1	258533	258533	type	True	85.0286	1558	2218	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_005670675.1	258533	258533	type	True	85.0108	1538	2218	95	below_threshold
Mycolicibacterium canariasense	strain=JCM15298	GCA_001570445.1	228230	228230	type	True	84.9376	1467	2218	95	below_threshold
Mycolicibacterium canariasense	strain=CCUG 47953	GCA_002101555.1	228230	228230	type	True	84.8671	1485	2218	95	below_threshold
Mycolicibacterium bacteremicum	strain=DSM 45578	GCA_002086115.1	564198	564198	type	True	81.4336	1156	2218	95	below_threshold
Mycolicibacterium neoaurum	strain=DSM 44074	GCA_005670605.1	1795	1795	type	True	80.774	1068	2218	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	80.449	964	2218	95	below_threshold
Mycolicibacterium boenickei	strain=JCM 15653	GCA_010731295.1	146017	146017	type	True	80.3484	1061	2218	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	80.1305	956	2218	95	below_threshold
Mycobacterium dioxanotrophicus	strain=PH-06	GCA_002157835.1	482462	482462	type	True	79.9719	1043	2218	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	79.966	749	2218	95	below_threshold
Mycolicibacterium arabiense	strain=JCM 18538	GCA_010731815.2	1286181	1286181	type	True	79.781	965	2218	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	79.7209	996	2218	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.578	867	2218	95	below_threshold
Mycolicibacterium stellerae	strain=CECT 8783	GCA_003719305.1	2358193	2358193	type	True	79.1271	877	2218	95	below_threshold
Mycobacterium arosiense	strain=DSM 45069	GCA_002086125.1	425468	425468	type	True	78.7242	662	2218	95	below_threshold
Mycolicibacter hiberniae	strain=ATCC 49874	GCA_002101655.1	29314	29314	type	True	78.7095	638	2218	95	below_threshold
Mycolicibacter hiberniae	strain=JCM 13571	GCA_010729485.1	29314	29314	type	True	78.6934	635	2218	95	below_threshold
Mycobacteroides chelonae	strain=CCUG 47445	GCA_001632805.1	1774	1774	suspected-type	True	78.2116	454	2218	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:54:38,835] [INFO] DFAST Taxonomy check result was written to GCF_025822555.1_ASM2582255v1_genomic.fna/tc_result.tsv
[2024-01-25 17:54:38,836] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:54:38,836] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:54:38,836] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg897b2dbd-86b6-4a6c-a082-9a719aef7823/dqc_reference/checkm_data
[2024-01-25 17:54:38,837] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:54:38,902] [INFO] Task started: CheckM
[2024-01-25 17:54:38,902] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025822555.1_ASM2582255v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025822555.1_ASM2582255v1_genomic.fna/checkm_input GCF_025822555.1_ASM2582255v1_genomic.fna/checkm_result
[2024-01-25 17:55:56,505] [INFO] Task succeeded: CheckM
[2024-01-25 17:55:56,506] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:55:56,527] [INFO] ===== Completeness check finished =====
[2024-01-25 17:55:56,527] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:55:56,528] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025822555.1_ASM2582255v1_genomic.fna/markers.fasta)
[2024-01-25 17:55:56,529] [INFO] Task started: Blastn
[2024-01-25 17:55:56,529] [INFO] Running command: blastn -query GCF_025822555.1_ASM2582255v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg897b2dbd-86b6-4a6c-a082-9a719aef7823/dqc_reference/reference_markers_gtdb.fasta -out GCF_025822555.1_ASM2582255v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:55:58,225] [INFO] Task succeeded: Blastn
[2024-01-25 17:55:58,228] [INFO] Selected 21 target genomes.
[2024-01-25 17:55:58,228] [INFO] Target genome list was writen to GCF_025822555.1_ASM2582255v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:55:58,244] [INFO] Task started: fastANI
[2024-01-25 17:55:58,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg195f2d7c-d559-4024-b72b-7f4d89eb2bbb/GCF_025822555.1_ASM2582255v1_genomic.fna.gz --refList GCF_025822555.1_ASM2582255v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025822555.1_ASM2582255v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:56:27,571] [INFO] Task succeeded: fastANI
[2024-01-25 17:56:27,584] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:56:27,584] [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_011758805.1	s__Mycobacterium fluoranthenivorans	96.0086	1814	2218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.15	95.95	0.85	0.84	4	conclusive
GCA_016197365.1	s__Mycobacterium cosmeticum_A	85.9798	1407	2218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613185.1	s__Mycobacterium cosmeticum	85.0151	1560	2218	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	84.8644	1485	2218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900078775.1	s__Mycobacterium aurum_A	81.8599	1175	2218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008329585.1	s__Mycobacterium sp008329585	81.6534	1213	2218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001907655.1	s__Mycobacterium diernhoferi	81.6246	1133	2218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.97	99.94	1.00	1.00	3	-
GCF_012223425.1	s__Mycobacterium frederiksbergense	81.5972	1158	2218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.39	95.39	0.91	0.91	2	-
GCF_001644575.1	s__Mycobacterium sp001644575	81.5123	1141	2218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.69	99.69	0.98	0.98	2	-
GCF_000317305.3	s__Mycobacterium neoaurum_A	80.8961	1041	2218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.30	95.79	0.98	0.90	7	-
GCF_010731295.1	s__Mycobacterium boenickei	80.353	1061	2218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.96	1.00	1.00	3	-
GCF_001044235.1	s__Mycobacterium chlorophenolicum	80.2602	1081	2218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	98.88	97.93	0.94	0.90	4	-
GCF_004762045.1	s__Mycobacterium sp004762045	80.2529	1022	2218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570425.1	s__Mycobacterium brisbanense	80.1229	1001	2218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.59	97.59	0.86	0.86	2	-
GCF_002157835.1	s__Mycobacterium dioxanotrophicus	79.9797	1041	2218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000612725.1	s__Mycobacterium austroafricanum	79.9415	959	2218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.53	98.42	0.88	0.88	3	-
GCF_000382405.1	s__Mycobacterium sp000382405	79.8948	723	2218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002798385.1	s__Mycobacterium goodii	79.8492	946	2218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.16	99.12	0.92	0.89	7	-
GCF_002723835.1	s__Mycobacterium sp002723835	79.7437	884	2218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000328565.1	s__Mycobacterium sp000328565	79.5775	903	2218	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000243415.2	s__Mycobacterium tusciae_A	79.0254	805	2218	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 17:56:27,585] [INFO] GTDB search result was written to GCF_025822555.1_ASM2582255v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:56:27,586] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:56:27,589] [INFO] DFAST_QC result json was written to GCF_025822555.1_ASM2582255v1_genomic.fna/dqc_result.json
[2024-01-25 17:56:27,590] [INFO] DFAST_QC completed!
[2024-01-25 17:56:27,590] [INFO] Total running time: 0h2m37s