[2024-01-24 13:33:11,012] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:33:11,014] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:33:11,014] [INFO] DQC Reference Directory: /var/lib/cwl/stg715e52ed-e953-46fe-b578-298ccb085576/dqc_reference
[2024-01-24 13:33:12,302] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:33:12,303] [INFO] Task started: Prodigal
[2024-01-24 13:33:12,303] [INFO] Running command: gunzip -c /var/lib/cwl/stgf996ee1f-2cfa-4969-a9d6-35e53b09223e/GCF_025345615.1_ASM2534561v1_genomic.fna.gz | prodigal -d GCF_025345615.1_ASM2534561v1_genomic.fna/cds.fna -a GCF_025345615.1_ASM2534561v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:30,254] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:30,254] [INFO] Task started: HMMsearch
[2024-01-24 13:33:30,255] [INFO] Running command: hmmsearch --tblout GCF_025345615.1_ASM2534561v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg715e52ed-e953-46fe-b578-298ccb085576/dqc_reference/reference_markers.hmm GCF_025345615.1_ASM2534561v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:30,591] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:30,592] [INFO] Found 6/6 markers.
[2024-01-24 13:33:30,659] [INFO] Query marker FASTA was written to GCF_025345615.1_ASM2534561v1_genomic.fna/markers.fasta
[2024-01-24 13:33:30,659] [INFO] Task started: Blastn
[2024-01-24 13:33:30,660] [INFO] Running command: blastn -query GCF_025345615.1_ASM2534561v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg715e52ed-e953-46fe-b578-298ccb085576/dqc_reference/reference_markers.fasta -out GCF_025345615.1_ASM2534561v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:31,821] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:31,825] [INFO] Selected 24 target genomes.
[2024-01-24 13:33:31,826] [INFO] Target genome list was writen to GCF_025345615.1_ASM2534561v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:31,837] [INFO] Task started: fastANI
[2024-01-24 13:33:31,837] [INFO] Running command: fastANI --query /var/lib/cwl/stgf996ee1f-2cfa-4969-a9d6-35e53b09223e/GCF_025345615.1_ASM2534561v1_genomic.fna.gz --refList GCF_025345615.1_ASM2534561v1_genomic.fna/target_genomes.txt --output GCF_025345615.1_ASM2534561v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:59,277] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:59,278] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg715e52ed-e953-46fe-b578-298ccb085576/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:59,279] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg715e52ed-e953-46fe-b578-298ccb085576/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:59,300] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:33:59,300] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:33:59,301] [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 rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	81.8252	1189	1872	95	below_threshold
Mycolicibacterium celeriflavum	strain=JCM 18439	GCA_010731795.1	1249101	1249101	type	True	81.5644	1078	1872	95	below_threshold
Mycolicibacterium celeriflavum	strain=DSM 46765	GCA_002086175.1	1249101	1249101	type	True	81.5203	1080	1872	95	below_threshold
Mycolicibacterium malmesburyense	strain=WCM 7299	GCA_001050015.1	1566886	1566886	type	True	81.4866	1085	1872	95	below_threshold
Mycolicibacterium komanii	strain=GPK 1020	GCA_001050035.1	1566885	1566885	type	True	81.3795	1117	1872	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	81.3493	1083	1872	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	81.3476	1079	1872	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	81.3255	1082	1872	95	below_threshold
Mycobacterium neumannii	strain=CECT 8766	GCA_002245615.1	2048551	2048551	type	True	81.1378	1088	1872	95	below_threshold
Mycobacterium lehmannii	strain=CECT 8763	GCA_002245535.1	2048550	2048550	type	True	81.091	1049	1872	95	below_threshold
Mycolicibacterium pulveris	strain=JCM 6370	GCA_010725725.1	36813	36813	type	True	80.9514	1102	1872	95	below_threshold
Mycolicibacterium moriokaense	strain=JCM 6375	GCA_010726085.1	39691	39691	type	True	80.8533	1084	1872	95	below_threshold
Mycolicibacterium moriokaense	strain=CIP105393	GCA_002086395.1	39691	39691	type	True	80.8484	1083	1872	95	below_threshold
Mycolicibacterium agri	strain=CCUG37673	GCA_002553505.1	36811	36811	type	True	80.3941	985	1872	95	below_threshold
Mycolicibacterium agri	strain=JCM 6377	GCA_010722915.1	36811	36811	type	True	80.353	1018	1872	95	below_threshold
Mycolicibacterium chubuense	strain=NCTC10819	GCA_900453455.1	1800	1800	type	True	80.3516	960	1872	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_002086595.1	1800	1800	type	True	80.3224	959	1872	95	below_threshold
Mycolicibacterium houstonense	strain=type strain: ATCC 49403	GCA_900078665.2	146021	146021	type	True	79.7008	874	1872	95	below_threshold
Mycolicibacterium conceptionense	strain=CCUG 50187	GCA_002102065.1	451644	451644	suspected-type	True	79.469	844	1872	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.0994	714	1872	95	below_threshold
Mycobacterium paraintracellulare	strain=KCTC 29084	GCA_002104735.1	1138383	1138383	suspected-type	True	79.0983	723	1872	95	below_threshold
Mycobacterium paraintracellulare	strain=MOTT64	GCA_000276825.1	1138383	1138383	suspected-type	True	79.0779	742	1872	95	below_threshold
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	79.0386	747	1872	95	below_threshold
Mycolicibacterium sphagni	strain=ATCC 33027	GCA_002250655.1	1786	1786	type	True	79.0218	746	1872	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:59,302] [INFO] DFAST Taxonomy check result was written to GCF_025345615.1_ASM2534561v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:59,303] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:59,303] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:59,303] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg715e52ed-e953-46fe-b578-298ccb085576/dqc_reference/checkm_data
[2024-01-24 13:33:59,304] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:59,355] [INFO] Task started: CheckM
[2024-01-24 13:33:59,356] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025345615.1_ASM2534561v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025345615.1_ASM2534561v1_genomic.fna/checkm_input GCF_025345615.1_ASM2534561v1_genomic.fna/checkm_result
[2024-01-24 13:34:53,672] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:53,674] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:53,711] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:53,711] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:53,712] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025345615.1_ASM2534561v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:53,713] [INFO] Task started: Blastn
[2024-01-24 13:34:53,713] [INFO] Running command: blastn -query GCF_025345615.1_ASM2534561v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg715e52ed-e953-46fe-b578-298ccb085576/dqc_reference/reference_markers_gtdb.fasta -out GCF_025345615.1_ASM2534561v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:55,424] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:55,428] [INFO] Selected 24 target genomes.
[2024-01-24 13:34:55,428] [INFO] Target genome list was writen to GCF_025345615.1_ASM2534561v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:55,464] [INFO] Task started: fastANI
[2024-01-24 13:34:55,464] [INFO] Running command: fastANI --query /var/lib/cwl/stgf996ee1f-2cfa-4969-a9d6-35e53b09223e/GCF_025345615.1_ASM2534561v1_genomic.fna.gz --refList GCF_025345615.1_ASM2534561v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025345615.1_ASM2534561v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:35:25,095] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:25,124] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:35:25,125] [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_010731795.1	s__Mycobacterium celeriflavum	81.558	1079	1872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.07	98.14	0.96	0.92	3	-
GCF_001500065.1	s__Mycobacterium sp001500065	81.5445	1096	1872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050015.1	s__Mycobacterium malmesburyense	81.4853	1086	1872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050035.1	s__Mycobacterium komanii	81.3851	1115	1872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665535.1	s__Mycobacterium sp001665535	81.3365	1110	1872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.97	96.97	0.90	0.90	2	-
GCF_001583415.1	s__Mycobacterium phlei	81.3255	1083	1872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_002245535.1	s__Mycobacterium lehmannii	81.1099	1046	1872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.2034	97.95	97.72	0.91	0.88	6	-
GCA_900637135.1	s__Mycobacterium flavescens	81.0903	1101	1872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.2034	98.19	96.77	0.93	0.88	4	-
GCF_001500025.1	s__Mycobacterium sp001500025	81.0185	1088	1872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010725725.1	s__Mycobacterium pulveris	80.9458	1103	1872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010726085.1	s__Mycobacterium moriokaense	80.855	1084	1872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010726765.1	s__Mycobacterium gallinarum	80.7921	1115	1872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900240945.1	s__Mycobacterium sp900240945	80.7671	1131	1872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002591975.1	s__Mycobacterium neglectum	80.575	1048	1872	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	80.5233	1028	1872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667505.1	s__Mycobacterium sp001667505	80.5103	1079	1872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003347205.1	s__Mycobacterium moriokaense_B	80.4895	994	1872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873705.1	s__Mycobacterium sp014873705	80.4164	1124	1872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.28	98.28	0.92	0.92	2	-
GCF_002553505.1	s__Mycobacterium agri	80.392	985	1872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCA_000762985.1	s__Mycobacterium rufum_A	80.3366	946	1872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001500125.1	s__Mycobacterium sp001500125	80.3098	1002	1872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078665.2	s__Mycobacterium houstonense	79.7282	868	1872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667315.1	s__Mycobacterium sp001667315	78.8656	677	1872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001666835.1	s__Mycobacterium sp001666835	78.6926	691	1872	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	99.01	0.94	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:35:25,127] [INFO] GTDB search result was written to GCF_025345615.1_ASM2534561v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:35:25,127] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:35:25,132] [INFO] DFAST_QC result json was written to GCF_025345615.1_ASM2534561v1_genomic.fna/dqc_result.json
[2024-01-24 13:35:25,132] [INFO] DFAST_QC completed!
[2024-01-24 13:35:25,132] [INFO] Total running time: 0h2m14s