[2024-01-24 13:33:10,923] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:33:10,924] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:33:10,925] [INFO] DQC Reference Directory: /var/lib/cwl/stg8cd30594-0f75-42f9-a93c-5d463a92b78e/dqc_reference
[2024-01-24 13:33:12,240] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:33:12,241] [INFO] Task started: Prodigal
[2024-01-24 13:33:12,241] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ac9c822-0766-4d92-8da2-0fa72254f93d/GCF_009192875.1_ASM919287v1_genomic.fna.gz | prodigal -d GCF_009192875.1_ASM919287v1_genomic.fna/cds.fna -a GCF_009192875.1_ASM919287v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:28,495] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:28,495] [INFO] Task started: HMMsearch
[2024-01-24 13:33:28,496] [INFO] Running command: hmmsearch --tblout GCF_009192875.1_ASM919287v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8cd30594-0f75-42f9-a93c-5d463a92b78e/dqc_reference/reference_markers.hmm GCF_009192875.1_ASM919287v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:28,749] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:28,751] [INFO] Found 6/6 markers.
[2024-01-24 13:33:28,797] [INFO] Query marker FASTA was written to GCF_009192875.1_ASM919287v1_genomic.fna/markers.fasta
[2024-01-24 13:33:28,798] [INFO] Task started: Blastn
[2024-01-24 13:33:28,798] [INFO] Running command: blastn -query GCF_009192875.1_ASM919287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cd30594-0f75-42f9-a93c-5d463a92b78e/dqc_reference/reference_markers.fasta -out GCF_009192875.1_ASM919287v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:30,182] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:30,186] [INFO] Selected 16 target genomes.
[2024-01-24 13:33:30,186] [INFO] Target genome list was writen to GCF_009192875.1_ASM919287v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:30,191] [INFO] Task started: fastANI
[2024-01-24 13:33:30,191] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ac9c822-0766-4d92-8da2-0fa72254f93d/GCF_009192875.1_ASM919287v1_genomic.fna.gz --refList GCF_009192875.1_ASM919287v1_genomic.fna/target_genomes.txt --output GCF_009192875.1_ASM919287v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:51,581] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:51,581] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8cd30594-0f75-42f9-a93c-5d463a92b78e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:51,582] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8cd30594-0f75-42f9-a93c-5d463a92b78e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:51,594] [INFO] Found 16 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:33:51,594] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:51,594] [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 phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	100.0	1749	1750	95	conclusive
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	99.9815	1728	1750	95	conclusive
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	99.9811	1744	1750	95	conclusive
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	85.0012	1341	1750	95	below_threshold
Mycolicibacterium hassiacum	strain=DSM 44199	GCA_000300375.1	46351	46351	type	True	83.6926	1148	1750	95	below_threshold
Mycolicibacterium hassiacum	strain=DSM 44199	GCA_000379865.1	46351	46351	type	True	83.6437	1172	1750	95	below_threshold
Mycolicibacterium komanii	strain=GPK 1020	GCA_001050035.1	1566885	1566885	type	True	83.2842	1204	1750	95	below_threshold
Mycolicibacterium elephantis	strain=DSM 44368	GCA_004014805.1	81858	81858	type	True	82.7449	1126	1750	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	81.8582	1103	1750	95	below_threshold
Mycolicibacterium moriokaense	strain=CIP105393	GCA_002086395.1	39691	39691	type	True	81.6484	1090	1750	95	below_threshold
Mycolicibacterium boenickei	strain=JCM 15653	GCA_010731295.1	146017	146017	type	True	80.8533	1059	1750	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	80.5248	889	1750	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	80.5001	994	1750	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	80.4379	953	1750	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	80.2842	966	1750	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	80.1544	959	1750	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:51,595] [INFO] DFAST Taxonomy check result was written to GCF_009192875.1_ASM919287v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:51,596] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:51,596] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:51,596] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8cd30594-0f75-42f9-a93c-5d463a92b78e/dqc_reference/checkm_data
[2024-01-24 13:33:51,597] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:51,644] [INFO] Task started: CheckM
[2024-01-24 13:33:51,644] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009192875.1_ASM919287v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009192875.1_ASM919287v1_genomic.fna/checkm_input GCF_009192875.1_ASM919287v1_genomic.fna/checkm_result
[2024-01-24 13:34:39,689] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:39,690] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:39,705] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:39,705] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:39,705] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009192875.1_ASM919287v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:39,706] [INFO] Task started: Blastn
[2024-01-24 13:34:39,706] [INFO] Running command: blastn -query GCF_009192875.1_ASM919287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cd30594-0f75-42f9-a93c-5d463a92b78e/dqc_reference/reference_markers_gtdb.fasta -out GCF_009192875.1_ASM919287v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:41,840] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:41,843] [INFO] Selected 21 target genomes.
[2024-01-24 13:34:41,843] [INFO] Target genome list was writen to GCF_009192875.1_ASM919287v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:41,882] [INFO] Task started: fastANI
[2024-01-24 13:34:41,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ac9c822-0766-4d92-8da2-0fa72254f93d/GCF_009192875.1_ASM919287v1_genomic.fna.gz --refList GCF_009192875.1_ASM919287v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009192875.1_ASM919287v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:35:09,172] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:09,189] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:35:09,189] [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_001583415.1	s__Mycobacterium phlei	99.9811	1744	1750	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	conclusive
GCF_900108565.1	s__Mycobacterium rutilum	85.0028	1341	1750	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001722335.1	s__Mycobacterium flavescens_A	84.8375	1332	1750	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900603025.1	s__Mycobacterium hassiacum	83.599	1201	1750	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCF_001665535.1	s__Mycobacterium sp001665535	83.0404	1188	1750	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.97	96.97	0.90	0.90	2	-
GCF_001570485.1	s__Mycobacterium novocastrense	82.9481	1179	1750	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.10	95.11	0.87	0.87	5	-
GCF_001668575.1	s__Mycobacterium sp001668575	82.9374	1165	1750	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001500025.1	s__Mycobacterium sp001500025	82.8727	1175	1750	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004014805.1	s__Mycobacterium elephantis	82.7362	1125	1750	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.23	96.21	0.87	0.85	6	-
GCF_002086815.1	s__Mycobacterium parafortuitum	82.0275	1163	1750	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010731695.1	s__Mycobacterium litorale	82.0171	1101	1750	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000762985.1	s__Mycobacterium rufum_A	81.9889	1064	1750	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014218295.1	s__Mycobacterium litorale_B	81.8058	1113	1750	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187505.1	s__Mycobacterium goodii_B	81.7342	1114	1750	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001457595.1	s__Mycobacterium smegmatis	81.7	1148	1750	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.06	0.95	0.91	32	-
GCF_010726085.1	s__Mycobacterium moriokaense	81.6443	1108	1750	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002553505.1	s__Mycobacterium agri	81.5837	1078	1750	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002798385.1	s__Mycobacterium goodii	81.1817	1024	1750	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.16	99.12	0.92	0.89	7	-
GCF_002086835.1	s__Mycobacterium porcinum	80.8444	1051	1750	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.47	97.32	0.92	0.87	9	-
GCF_002723835.1	s__Mycobacterium sp002723835	80.7961	975	1750	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010729895.1	s__Mycobacterium confluentis	80.6141	957	1750	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:35:09,197] [INFO] GTDB search result was written to GCF_009192875.1_ASM919287v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:35:09,197] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:35:09,201] [INFO] DFAST_QC result json was written to GCF_009192875.1_ASM919287v1_genomic.fna/dqc_result.json
[2024-01-24 13:35:09,201] [INFO] DFAST_QC completed!
[2024-01-24 13:35:09,201] [INFO] Total running time: 0h1m58s