[2024-01-25 18:54:50,803] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:54:50,804] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:54:50,804] [INFO] DQC Reference Directory: /var/lib/cwl/stg83afa5ad-88da-4ff3-bd43-81d0bf32dd3e/dqc_reference
[2024-01-25 18:54:51,966] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:54:51,967] [INFO] Task started: Prodigal
[2024-01-25 18:54:51,967] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf35df03-9350-44e9-b5ca-acb459582aff/GCF_025822705.1_ASM2582270v1_genomic.fna.gz | prodigal -d GCF_025822705.1_ASM2582270v1_genomic.fna/cds.fna -a GCF_025822705.1_ASM2582270v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:55:08,317] [INFO] Task succeeded: Prodigal
[2024-01-25 18:55:08,317] [INFO] Task started: HMMsearch
[2024-01-25 18:55:08,317] [INFO] Running command: hmmsearch --tblout GCF_025822705.1_ASM2582270v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83afa5ad-88da-4ff3-bd43-81d0bf32dd3e/dqc_reference/reference_markers.hmm GCF_025822705.1_ASM2582270v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:55:08,590] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:55:08,591] [INFO] Found 6/6 markers.
[2024-01-25 18:55:08,643] [INFO] Query marker FASTA was written to GCF_025822705.1_ASM2582270v1_genomic.fna/markers.fasta
[2024-01-25 18:55:08,643] [INFO] Task started: Blastn
[2024-01-25 18:55:08,643] [INFO] Running command: blastn -query GCF_025822705.1_ASM2582270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83afa5ad-88da-4ff3-bd43-81d0bf32dd3e/dqc_reference/reference_markers.fasta -out GCF_025822705.1_ASM2582270v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:09,770] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:09,772] [INFO] Selected 26 target genomes.
[2024-01-25 18:55:09,772] [INFO] Target genome list was writen to GCF_025822705.1_ASM2582270v1_genomic.fna/target_genomes.txt
[2024-01-25 18:55:09,778] [INFO] Task started: fastANI
[2024-01-25 18:55:09,778] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf35df03-9350-44e9-b5ca-acb459582aff/GCF_025822705.1_ASM2582270v1_genomic.fna.gz --refList GCF_025822705.1_ASM2582270v1_genomic.fna/target_genomes.txt --output GCF_025822705.1_ASM2582270v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:55:42,938] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:42,939] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83afa5ad-88da-4ff3-bd43-81d0bf32dd3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:55:42,939] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83afa5ad-88da-4ff3-bd43-81d0bf32dd3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:55:42,953] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:55:42,953] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:55:42,954] [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	88.2001	1558	1970	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	84.9243	1343	1970	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	84.8921	1343	1970	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	84.8773	1335	1970	95	below_threshold
Mycobacterium lehmannii	strain=CECT 8763	GCA_002245535.1	2048550	2048550	type	True	84.1471	1296	1970	95	below_threshold
Mycolicibacterium malmesburyense	strain=WCM 7299	GCA_001050015.1	1566886	1566886	type	True	84.0389	1267	1970	95	below_threshold
Mycolicibacterium komanii	strain=GPK 1020	GCA_001050035.1	1566885	1566885	type	True	84.0098	1303	1970	95	below_threshold
Mycobacterium neumannii	strain=CECT 8766	GCA_002245615.1	2048551	2048551	type	True	83.8724	1277	1970	95	below_threshold
Mycolicibacterium celeriflavum	strain=DSM 46765	GCA_002086175.1	1249101	1249101	type	True	83.8667	1184	1970	95	below_threshold
Mycolicibacterium celeriflavum	strain=JCM 18439	GCA_010731795.1	1249101	1249101	type	True	83.813	1228	1970	95	below_threshold
Mycolicibacterium elephantis	strain=DSM 44368	GCA_004014805.1	81858	81858	type	True	82.7732	1176	1970	95	below_threshold
Mycolicibacterium moriokaense	strain=CIP105393	GCA_002086395.1	39691	39691	type	True	81.5219	1113	1970	95	below_threshold
Mycolicibacterium moriokaense	strain=JCM 6375	GCA_010726085.1	39691	39691	type	True	81.4983	1129	1970	95	below_threshold
Mycolicibacterium gadium	strain=JCM 12688	GCA_010728925.1	1794	1794	type	True	81.2419	1111	1970	95	below_threshold
Mycolicibacterium thermoresistibile	strain=ATCC 19527	GCA_000234585.2	1797	1797	type	True	81.0004	990	1970	95	below_threshold
Mycolicibacterium thermoresistibile	strain=NCTC10409	GCA_900187065.1	1797	1797	type	True	80.9683	1002	1970	95	below_threshold
Mycolicibacterium neworleansense	strain=type strain: ATCC 49404	GCA_001245615.1	146018	146018	type	True	80.591	1031	1970	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	80.5856	1033	1970	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	80.5741	973	1970	95	below_threshold
Mycolicibacterium mageritense	strain=JCM 12375	GCA_010727475.1	53462	53462	type	True	80.545	1037	1970	95	below_threshold
Mycobacterium dioxanotrophicus	strain=PH-06	GCA_002157835.1	482462	482462	type	True	80.391	1019	1970	95	below_threshold
Mycobacterium aquaticum	strain=RW6	GCA_002086485.1	1927124	1927124	type	True	80.2864	1018	1970	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	80.26	970	1970	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	80.2356	973	1970	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	80.0923	869	1970	95	below_threshold
Mycolicibacterium mengxianglii	strain=Z-34	GCA_015710575.2	2736649	2736649	type	True	79.4148	887	1970	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:55:42,955] [INFO] DFAST Taxonomy check result was written to GCF_025822705.1_ASM2582270v1_genomic.fna/tc_result.tsv
[2024-01-25 18:55:42,956] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:55:42,956] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:55:42,956] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83afa5ad-88da-4ff3-bd43-81d0bf32dd3e/dqc_reference/checkm_data
[2024-01-25 18:55:42,957] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:55:43,015] [INFO] Task started: CheckM
[2024-01-25 18:55:43,015] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025822705.1_ASM2582270v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025822705.1_ASM2582270v1_genomic.fna/checkm_input GCF_025822705.1_ASM2582270v1_genomic.fna/checkm_result
[2024-01-25 18:56:42,528] [INFO] Task succeeded: CheckM
[2024-01-25 18:56:42,529] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:56:42,549] [INFO] ===== Completeness check finished =====
[2024-01-25 18:56:42,549] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:56:42,550] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025822705.1_ASM2582270v1_genomic.fna/markers.fasta)
[2024-01-25 18:56:42,550] [INFO] Task started: Blastn
[2024-01-25 18:56:42,550] [INFO] Running command: blastn -query GCF_025822705.1_ASM2582270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83afa5ad-88da-4ff3-bd43-81d0bf32dd3e/dqc_reference/reference_markers_gtdb.fasta -out GCF_025822705.1_ASM2582270v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:44,205] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:44,208] [INFO] Selected 20 target genomes.
[2024-01-25 18:56:44,208] [INFO] Target genome list was writen to GCF_025822705.1_ASM2582270v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:56:44,230] [INFO] Task started: fastANI
[2024-01-25 18:56:44,230] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf35df03-9350-44e9-b5ca-acb459582aff/GCF_025822705.1_ASM2582270v1_genomic.fna.gz --refList GCF_025822705.1_ASM2582270v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025822705.1_ASM2582270v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:57:12,353] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:12,365] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:57:12,365] [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_001722335.1	s__Mycobacterium flavescens_A	99.9829	1953	1970	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_900108565.1	s__Mycobacterium rutilum	88.1969	1559	1970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001583415.1	s__Mycobacterium phlei	84.8892	1344	1970	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	84.1495	1295	1970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.2034	97.95	97.72	0.91	0.88	6	-
GCF_001050015.1	s__Mycobacterium malmesburyense	84.0616	1264	1970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570485.1	s__Mycobacterium novocastrense	83.9712	1328	1970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.10	95.11	0.87	0.87	5	-
GCA_900637135.1	s__Mycobacterium flavescens	83.9217	1286	1970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.2034	98.19	96.77	0.93	0.88	4	-
GCF_001665535.1	s__Mycobacterium sp001665535	83.8393	1275	1970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.97	96.97	0.90	0.90	2	-
GCF_001500025.1	s__Mycobacterium sp001500025	83.7815	1297	1970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001668575.1	s__Mycobacterium sp001668575	83.6708	1249	1970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499905.1	s__Mycobacterium sp001499905	83.6256	1160	1970	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	82.7751	1176	1970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.23	96.21	0.87	0.85	6	-
GCF_010725725.1	s__Mycobacterium pulveris	82.6545	1187	1970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010726645.1	s__Mycobacterium duvalii	82.309	1094	1970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900240945.1	s__Mycobacterium sp900240945	81.6189	1196	1970	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	81.5107	1127	1970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001667505.1	s__Mycobacterium sp001667505	81.4878	1130	1970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727475.1	s__Mycobacterium mageritense	80.5199	1041	1970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.33	0.91	0.85	5	-
GCF_002157835.1	s__Mycobacterium dioxanotrophicus	80.3961	1018	1970	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086485.1	s__Mycobacterium aquaticum	80.2889	1018	1970	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 18:57:12,368] [INFO] GTDB search result was written to GCF_025822705.1_ASM2582270v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:57:12,369] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:57:12,373] [INFO] DFAST_QC result json was written to GCF_025822705.1_ASM2582270v1_genomic.fna/dqc_result.json
[2024-01-25 18:57:12,373] [INFO] DFAST_QC completed!
[2024-01-25 18:57:12,373] [INFO] Total running time: 0h2m22s