[2024-01-25 19:46:50,589] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:46:50,591] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:46:50,591] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a366c71-a5b5-4456-bfe1-e2e804822b32/dqc_reference
[2024-01-25 19:46:51,707] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:46:51,708] [INFO] Task started: Prodigal
[2024-01-25 19:46:51,708] [INFO] Running command: gunzip -c /var/lib/cwl/stgae481691-19ff-447f-8d4f-577ed244c144/GCF_025822105.1_ASM2582210v1_genomic.fna.gz | prodigal -d GCF_025822105.1_ASM2582210v1_genomic.fna/cds.fna -a GCF_025822105.1_ASM2582210v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:07,438] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:07,438] [INFO] Task started: HMMsearch
[2024-01-25 19:47:07,438] [INFO] Running command: hmmsearch --tblout GCF_025822105.1_ASM2582210v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a366c71-a5b5-4456-bfe1-e2e804822b32/dqc_reference/reference_markers.hmm GCF_025822105.1_ASM2582210v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:07,783] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:07,786] [INFO] Found 6/6 markers.
[2024-01-25 19:47:07,842] [INFO] Query marker FASTA was written to GCF_025822105.1_ASM2582210v1_genomic.fna/markers.fasta
[2024-01-25 19:47:07,842] [INFO] Task started: Blastn
[2024-01-25 19:47:07,842] [INFO] Running command: blastn -query GCF_025822105.1_ASM2582210v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a366c71-a5b5-4456-bfe1-e2e804822b32/dqc_reference/reference_markers.fasta -out GCF_025822105.1_ASM2582210v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:09,027] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:09,029] [INFO] Selected 13 target genomes.
[2024-01-25 19:47:09,029] [INFO] Target genome list was writen to GCF_025822105.1_ASM2582210v1_genomic.fna/target_genomes.txt
[2024-01-25 19:47:09,035] [INFO] Task started: fastANI
[2024-01-25 19:47:09,036] [INFO] Running command: fastANI --query /var/lib/cwl/stgae481691-19ff-447f-8d4f-577ed244c144/GCF_025822105.1_ASM2582210v1_genomic.fna.gz --refList GCF_025822105.1_ASM2582210v1_genomic.fna/target_genomes.txt --output GCF_025822105.1_ASM2582210v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:47:25,014] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:25,015] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a366c71-a5b5-4456-bfe1-e2e804822b32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:47:25,015] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a366c71-a5b5-4456-bfe1-e2e804822b32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:47:25,023] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:47:25,024] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:47:25,024] [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 pulveris	strain=JCM 6370	GCA_010725725.1	36813	36813	type	True	99.9938	1813	1819	95	conclusive
Mycolicibacterium elephantis	strain=DSM 44368	GCA_004014805.1	81858	81858	type	True	92.1112	1536	1819	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	82.7558	1153	1819	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	82.7264	1151	1819	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	82.6485	1176	1819	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	82.6446	1158	1819	95	below_threshold
Mycolicibacterium malmesburyense	strain=WCM 7299	GCA_001050015.1	1566886	1566886	type	True	82.3765	1188	1819	95	below_threshold
Mycolicibacterium komanii	strain=GPK 1020	GCA_001050035.1	1566885	1566885	type	True	82.1556	1151	1819	95	below_threshold
Mycobacterium lehmannii	strain=CECT 8763	GCA_002245535.1	2048550	2048550	type	True	81.9724	1148	1819	95	below_threshold
Mycolicibacterium moriokaense	strain=JCM 6375	GCA_010726085.1	39691	39691	type	True	81.1659	1130	1819	95	below_threshold
Mycolicibacterium moriokaense	strain=CIP105393	GCA_002086395.1	39691	39691	type	True	81.1264	1124	1819	95	below_threshold
Mycobacterium helveticum	strain=16-83	GCA_007714205.1	2592811	2592811	type	True	79.6647	729	1819	95	below_threshold
Mycobacterium marseillense	strain=JCM 17324	GCA_010731675.1	701042	701042	type	True	79.4101	787	1819	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:47:25,025] [INFO] DFAST Taxonomy check result was written to GCF_025822105.1_ASM2582210v1_genomic.fna/tc_result.tsv
[2024-01-25 19:47:25,025] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:47:25,026] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:47:25,026] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a366c71-a5b5-4456-bfe1-e2e804822b32/dqc_reference/checkm_data
[2024-01-25 19:47:25,027] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:47:25,077] [INFO] Task started: CheckM
[2024-01-25 19:47:25,078] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025822105.1_ASM2582210v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025822105.1_ASM2582210v1_genomic.fna/checkm_input GCF_025822105.1_ASM2582210v1_genomic.fna/checkm_result
[2024-01-25 19:48:15,342] [INFO] Task succeeded: CheckM
[2024-01-25 19:48:15,343] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:48:15,367] [INFO] ===== Completeness check finished =====
[2024-01-25 19:48:15,368] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:48:15,368] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025822105.1_ASM2582210v1_genomic.fna/markers.fasta)
[2024-01-25 19:48:15,369] [INFO] Task started: Blastn
[2024-01-25 19:48:15,369] [INFO] Running command: blastn -query GCF_025822105.1_ASM2582210v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a366c71-a5b5-4456-bfe1-e2e804822b32/dqc_reference/reference_markers_gtdb.fasta -out GCF_025822105.1_ASM2582210v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:17,022] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:17,024] [INFO] Selected 16 target genomes.
[2024-01-25 19:48:17,025] [INFO] Target genome list was writen to GCF_025822105.1_ASM2582210v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:48:17,064] [INFO] Task started: fastANI
[2024-01-25 19:48:17,064] [INFO] Running command: fastANI --query /var/lib/cwl/stgae481691-19ff-447f-8d4f-577ed244c144/GCF_025822105.1_ASM2582210v1_genomic.fna.gz --refList GCF_025822105.1_ASM2582210v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025822105.1_ASM2582210v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:48:37,926] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:37,936] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:48:37,937] [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_010725725.1	s__Mycobacterium pulveris	99.9938	1813	1819	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_004014805.1	s__Mycobacterium elephantis	92.1112	1536	1819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.23	96.21	0.87	0.85	6	-
GCF_001722355.1	s__Mycobacterium holsaticum	86.8981	1296	1819	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	82.7075	1153	1819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_900108565.1	s__Mycobacterium rutilum	82.6655	1174	1819	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	82.3781	1188	1819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001500065.1	s__Mycobacterium sp001500065	82.2466	1125	1819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001672895.1	s__Mycobacterium sp001672895	82.1689	994	1819	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	82.1686	1149	1819	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	81.9884	1177	1819	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	80.7173	962	1819	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	80.6928	1027	1819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.28	98.28	0.92	0.92	2	-
GCF_000266905.1	s__Mycobacterium chubuense_A	80.6415	980	1819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010723735.1	s__Mycobacterium hippocampi_B	80.2085	961	1819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455325.1	s__Mycobacterium septicum	79.9255	939	1819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.04	95.11	0.88	0.83	8	-
GCF_007714205.1	s__Mycobacterium helveticum	79.6689	731	1819	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:48:37,938] [INFO] GTDB search result was written to GCF_025822105.1_ASM2582210v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:48:37,939] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:48:37,941] [INFO] DFAST_QC result json was written to GCF_025822105.1_ASM2582210v1_genomic.fna/dqc_result.json
[2024-01-25 19:48:37,942] [INFO] DFAST_QC completed!
[2024-01-25 19:48:37,942] [INFO] Total running time: 0h1m47s