[2024-01-24 13:22:55,513] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:55,516] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:55,516] [INFO] DQC Reference Directory: /var/lib/cwl/stg079c1aab-fb3c-46d9-8027-a7451030e6c1/dqc_reference
[2024-01-24 13:22:56,811] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:56,812] [INFO] Task started: Prodigal
[2024-01-24 13:22:56,812] [INFO] Running command: gunzip -c /var/lib/cwl/stg7de104d5-f0f3-4851-bd12-19530bdadd5b/GCF_000691525.1_ATCC25795_good_1_paired_assembly_genomic.fna.gz | prodigal -d GCF_000691525.1_ATCC25795_good_1_paired_assembly_genomic.fna/cds.fna -a GCF_000691525.1_ATCC25795_good_1_paired_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:15,096] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:15,097] [INFO] Task started: HMMsearch
[2024-01-24 13:23:15,097] [INFO] Running command: hmmsearch --tblout GCF_000691525.1_ATCC25795_good_1_paired_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg079c1aab-fb3c-46d9-8027-a7451030e6c1/dqc_reference/reference_markers.hmm GCF_000691525.1_ATCC25795_good_1_paired_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:15,412] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:15,413] [INFO] Found 6/6 markers.
[2024-01-24 13:23:15,460] [INFO] Query marker FASTA was written to GCF_000691525.1_ATCC25795_good_1_paired_assembly_genomic.fna/markers.fasta
[2024-01-24 13:23:15,460] [INFO] Task started: Blastn
[2024-01-24 13:23:15,460] [INFO] Running command: blastn -query GCF_000691525.1_ATCC25795_good_1_paired_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg079c1aab-fb3c-46d9-8027-a7451030e6c1/dqc_reference/reference_markers.fasta -out GCF_000691525.1_ATCC25795_good_1_paired_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:16,631] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:16,634] [INFO] Selected 14 target genomes.
[2024-01-24 13:23:16,635] [INFO] Target genome list was writen to GCF_000691525.1_ATCC25795_good_1_paired_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:23:16,657] [INFO] Task started: fastANI
[2024-01-24 13:23:16,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg7de104d5-f0f3-4851-bd12-19530bdadd5b/GCF_000691525.1_ATCC25795_good_1_paired_assembly_genomic.fna.gz --refList GCF_000691525.1_ATCC25795_good_1_paired_assembly_genomic.fna/target_genomes.txt --output GCF_000691525.1_ATCC25795_good_1_paired_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:34,922] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:34,923] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg079c1aab-fb3c-46d9-8027-a7451030e6c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:34,924] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg079c1aab-fb3c-46d9-8027-a7451030e6c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:34,939] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:23:34,939] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:34,939] [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 neoaurum	strain=ATCC 25795	GCA_000691525.1	1795	1795	type	True	100.0	1799	1803	95	conclusive
Mycolicibacterium neoaurum	strain=DSM 44074	GCA_005670605.1	1795	1795	type	True	99.9967	1801	1803	95	conclusive
Mycolicibacterium neoaurum	strain=DSM 44074	GCA_000724065.1	1795	1795	type	True	99.9434	1796	1803	95	conclusive
Mycolicibacterium bacteremicum	strain=DSM 45578	GCA_002086115.1	564198	564198	type	True	85.4338	1416	1803	95	below_threshold
Mycolicibacterium cosmeticum	strain=DSM 44829	GCA_005670675.1	258533	258533	type	True	81.3296	1086	1803	95	below_threshold
Mycolicibacterium canariasense	strain=JCM15298	GCA_001570445.1	228230	228230	type	True	81.1948	995	1803	95	below_threshold
Mycolicibacterium fluoranthenivorans	strain=DSM 44556	GCA_011758805.1	258505	258505	type	True	80.8391	1042	1803	95	below_threshold
Mycolicibacterium nivoides	strain=DL90	GCA_003855255.1	2487344	2487344	type	True	79.9962	895	1803	95	below_threshold
Mycolicibacterium peregrinum	strain=DSM 43271	GCA_002102345.1	43304	43304	type	True	79.859	865	1803	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	79.7469	844	1803	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.4697	734	1803	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.2222	746	1803	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.1511	759	1803	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.1319	752	1803	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:34,941] [INFO] DFAST Taxonomy check result was written to GCF_000691525.1_ATCC25795_good_1_paired_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:23:34,941] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:34,941] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:34,942] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg079c1aab-fb3c-46d9-8027-a7451030e6c1/dqc_reference/checkm_data
[2024-01-24 13:23:34,942] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:34,992] [INFO] Task started: CheckM
[2024-01-24 13:23:34,992] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000691525.1_ATCC25795_good_1_paired_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000691525.1_ATCC25795_good_1_paired_assembly_genomic.fna/checkm_input GCF_000691525.1_ATCC25795_good_1_paired_assembly_genomic.fna/checkm_result
[2024-01-24 13:24:33,007] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:33,008] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:33,028] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:33,028] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:33,028] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000691525.1_ATCC25795_good_1_paired_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:24:33,029] [INFO] Task started: Blastn
[2024-01-24 13:24:33,029] [INFO] Running command: blastn -query GCF_000691525.1_ATCC25795_good_1_paired_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg079c1aab-fb3c-46d9-8027-a7451030e6c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000691525.1_ATCC25795_good_1_paired_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:34,735] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:34,739] [INFO] Selected 12 target genomes.
[2024-01-24 13:24:34,740] [INFO] Target genome list was writen to GCF_000691525.1_ATCC25795_good_1_paired_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:34,769] [INFO] Task started: fastANI
[2024-01-24 13:24:34,769] [INFO] Running command: fastANI --query /var/lib/cwl/stg7de104d5-f0f3-4851-bd12-19530bdadd5b/GCF_000691525.1_ATCC25795_good_1_paired_assembly_genomic.fna.gz --refList GCF_000691525.1_ATCC25795_good_1_paired_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_000691525.1_ATCC25795_good_1_paired_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:50,863] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:50,878] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:50,878] [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_000691525.1	s__Mycobacterium neoaurum	100.0	1799	1803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.16	98.36	0.96	0.91	6	conclusive
GCF_000317305.3	s__Mycobacterium neoaurum_A	92.9721	1588	1803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.30	95.79	0.98	0.90	7	-
GCF_002086115.1	s__Mycobacterium bacteremicum	85.4402	1416	1803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078775.1	s__Mycobacterium aurum_A	82.603	1194	1803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428895.1	s__Mycobacterium sp001428895	82.3616	1282	1803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001644575.1	s__Mycobacterium sp001644575	82.3547	1216	1803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.69	99.69	0.98	0.98	2	-
GCF_008329585.1	s__Mycobacterium sp008329585	82.2624	1240	1803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001907655.1	s__Mycobacterium diernhoferi	82.1812	1169	1803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.97	99.94	1.00	1.00	3	-
GCF_000613185.1	s__Mycobacterium cosmeticum	81.3366	1085	1803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.89	98.33	0.93	0.89	4	-
GCF_002101555.1	s__Mycobacterium canariasense	81.1535	1006	1803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900078665.2	s__Mycobacterium houstonense	79.9898	871	1803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552615.1	s__Millisia brevis	77.7174	372	1803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Millisia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:50,887] [INFO] GTDB search result was written to GCF_000691525.1_ATCC25795_good_1_paired_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:50,887] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:50,891] [INFO] DFAST_QC result json was written to GCF_000691525.1_ATCC25795_good_1_paired_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:24:50,891] [INFO] DFAST_QC completed!
[2024-01-24 13:24:50,891] [INFO] Total running time: 0h1m55s