[2024-01-25 17:37:50,643] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:37:50,645] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:37:50,645] [INFO] DQC Reference Directory: /var/lib/cwl/stg42e4c1c7-0a7e-4ef9-a0bb-ae84a8d7953a/dqc_reference
[2024-01-25 17:37:51,732] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:37:51,733] [INFO] Task started: Prodigal
[2024-01-25 17:37:51,733] [INFO] Running command: gunzip -c /var/lib/cwl/stg790753c0-879c-43fa-8d5b-7ace681658a4/GCF_001050015.1_Mycobacterium_malmesburii_WCM_7299_genomic.fna.gz | prodigal -d GCF_001050015.1_Mycobacterium_malmesburii_WCM_7299_genomic.fna/cds.fna -a GCF_001050015.1_Mycobacterium_malmesburii_WCM_7299_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:38:13,515] [INFO] Task succeeded: Prodigal
[2024-01-25 17:38:13,515] [INFO] Task started: HMMsearch
[2024-01-25 17:38:13,515] [INFO] Running command: hmmsearch --tblout GCF_001050015.1_Mycobacterium_malmesburii_WCM_7299_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42e4c1c7-0a7e-4ef9-a0bb-ae84a8d7953a/dqc_reference/reference_markers.hmm GCF_001050015.1_Mycobacterium_malmesburii_WCM_7299_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:38:13,794] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:38:13,797] [INFO] Found 6/6 markers.
[2024-01-25 17:38:13,841] [INFO] Query marker FASTA was written to GCF_001050015.1_Mycobacterium_malmesburii_WCM_7299_genomic.fna/markers.fasta
[2024-01-25 17:38:13,841] [INFO] Task started: Blastn
[2024-01-25 17:38:13,841] [INFO] Running command: blastn -query GCF_001050015.1_Mycobacterium_malmesburii_WCM_7299_genomic.fna/markers.fasta -db /var/lib/cwl/stg42e4c1c7-0a7e-4ef9-a0bb-ae84a8d7953a/dqc_reference/reference_markers.fasta -out GCF_001050015.1_Mycobacterium_malmesburii_WCM_7299_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:14,986] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:14,989] [INFO] Selected 11 target genomes.
[2024-01-25 17:38:14,989] [INFO] Target genome list was writen to GCF_001050015.1_Mycobacterium_malmesburii_WCM_7299_genomic.fna/target_genomes.txt
[2024-01-25 17:38:14,993] [INFO] Task started: fastANI
[2024-01-25 17:38:14,993] [INFO] Running command: fastANI --query /var/lib/cwl/stg790753c0-879c-43fa-8d5b-7ace681658a4/GCF_001050015.1_Mycobacterium_malmesburii_WCM_7299_genomic.fna.gz --refList GCF_001050015.1_Mycobacterium_malmesburii_WCM_7299_genomic.fna/target_genomes.txt --output GCF_001050015.1_Mycobacterium_malmesburii_WCM_7299_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:38:29,144] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:29,144] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42e4c1c7-0a7e-4ef9-a0bb-ae84a8d7953a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:38:29,144] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42e4c1c7-0a7e-4ef9-a0bb-ae84a8d7953a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:38:29,152] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:38:29,153] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:38:29,153] [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 malmesburyense	strain=WCM 7299	GCA_001050015.1	1566886	1566886	type	True	100.0	1715	1726	95	conclusive
Mycolicibacterium komanii	strain=GPK 1020	GCA_001050035.1	1566885	1566885	type	True	89.4824	1472	1726	95	below_threshold
Mycobacterium neumannii	strain=CECT 8766	GCA_002245615.1	2048551	2048551	type	True	87.7403	1394	1726	95	below_threshold
Mycobacterium lehmannii	strain=CECT 8763	GCA_002245535.1	2048550	2048550	type	True	87.6429	1377	1726	95	below_threshold
Mycolicibacterium celeriflavum	strain=DSM 46765	GCA_002086175.1	1249101	1249101	type	True	84.8359	1214	1726	95	below_threshold
Mycolicibacterium celeriflavum	strain=JCM 18439	GCA_010731795.1	1249101	1249101	type	True	84.79	1237	1726	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	84.4461	1277	1726	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	83.474	1170	1726	95	below_threshold
Mycolicibacterium elephantis	strain=DSM 44368	GCA_004014805.1	81858	81858	type	True	82.4339	1170	1726	95	below_threshold
Mycolicibacterium pulveris	strain=JCM 6370	GCA_010725725.1	36813	36813	type	True	82.3965	1176	1726	95	below_threshold
Mycolicibacterium moriokaense	strain=CIP105393	GCA_002086395.1	39691	39691	type	True	81.3769	1132	1726	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:38:29,154] [INFO] DFAST Taxonomy check result was written to GCF_001050015.1_Mycobacterium_malmesburii_WCM_7299_genomic.fna/tc_result.tsv
[2024-01-25 17:38:29,154] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:38:29,155] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:38:29,155] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42e4c1c7-0a7e-4ef9-a0bb-ae84a8d7953a/dqc_reference/checkm_data
[2024-01-25 17:38:29,155] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:38:29,208] [INFO] Task started: CheckM
[2024-01-25 17:38:29,209] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001050015.1_Mycobacterium_malmesburii_WCM_7299_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001050015.1_Mycobacterium_malmesburii_WCM_7299_genomic.fna/checkm_input GCF_001050015.1_Mycobacterium_malmesburii_WCM_7299_genomic.fna/checkm_result
[2024-01-25 17:39:33,145] [INFO] Task succeeded: CheckM
[2024-01-25 17:39:33,146] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:39:33,169] [INFO] ===== Completeness check finished =====
[2024-01-25 17:39:33,170] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:39:33,171] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001050015.1_Mycobacterium_malmesburii_WCM_7299_genomic.fna/markers.fasta)
[2024-01-25 17:39:33,171] [INFO] Task started: Blastn
[2024-01-25 17:39:33,171] [INFO] Running command: blastn -query GCF_001050015.1_Mycobacterium_malmesburii_WCM_7299_genomic.fna/markers.fasta -db /var/lib/cwl/stg42e4c1c7-0a7e-4ef9-a0bb-ae84a8d7953a/dqc_reference/reference_markers_gtdb.fasta -out GCF_001050015.1_Mycobacterium_malmesburii_WCM_7299_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:34,985] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:34,988] [INFO] Selected 12 target genomes.
[2024-01-25 17:39:34,988] [INFO] Target genome list was writen to GCF_001050015.1_Mycobacterium_malmesburii_WCM_7299_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:39:35,011] [INFO] Task started: fastANI
[2024-01-25 17:39:35,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg790753c0-879c-43fa-8d5b-7ace681658a4/GCF_001050015.1_Mycobacterium_malmesburii_WCM_7299_genomic.fna.gz --refList GCF_001050015.1_Mycobacterium_malmesburii_WCM_7299_genomic.fna/target_genomes_gtdb.txt --output GCF_001050015.1_Mycobacterium_malmesburii_WCM_7299_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:39:50,829] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:50,838] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:39:50,838] [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_001050015.1	s__Mycobacterium malmesburyense	100.0	1715	1726	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_001050035.1	s__Mycobacterium komanii	89.4824	1472	1726	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	89.255	1463	1726	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.97	96.97	0.90	0.90	2	-
GCF_001668575.1	s__Mycobacterium sp001668575	88.6853	1428	1726	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	88.0759	1470	1726	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900637135.1	s__Mycobacterium flavescens	87.7431	1416	1726	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.2034	98.19	96.77	0.93	0.88	4	-
GCF_002245535.1	s__Mycobacterium lehmannii	87.6351	1378	1726	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.2034	97.95	97.72	0.91	0.88	6	-
GCF_001499905.1	s__Mycobacterium sp001499905	87.2973	1307	1726	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108565.1	s__Mycobacterium rutilum	84.4534	1276	1726	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	82.4516	1167	1726	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	82.4138	1174	1726	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727325.1	s__Mycobacterium alvei	79.8282	846	1726	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 17:39:50,840] [INFO] GTDB search result was written to GCF_001050015.1_Mycobacterium_malmesburii_WCM_7299_genomic.fna/result_gtdb.tsv
[2024-01-25 17:39:50,842] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:39:50,847] [INFO] DFAST_QC result json was written to GCF_001050015.1_Mycobacterium_malmesburii_WCM_7299_genomic.fna/dqc_result.json
[2024-01-25 17:39:50,848] [INFO] DFAST_QC completed!
[2024-01-25 17:39:50,848] [INFO] Total running time: 0h2m0s