[2024-01-24 13:58:41,095] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:41,097] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:41,097] [INFO] DQC Reference Directory: /var/lib/cwl/stg466db2b0-d0ee-4cdc-9519-db617f103a1f/dqc_reference
[2024-01-24 13:58:42,479] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:42,482] [INFO] Task started: Prodigal
[2024-01-24 13:58:42,483] [INFO] Running command: gunzip -c /var/lib/cwl/stg43730bac-785e-4891-89ac-370a89a6b074/GCF_013404075.1_ASM1340407v1_genomic.fna.gz | prodigal -d GCF_013404075.1_ASM1340407v1_genomic.fna/cds.fna -a GCF_013404075.1_ASM1340407v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:59:05,932] [INFO] Task succeeded: Prodigal
[2024-01-24 13:59:05,933] [INFO] Task started: HMMsearch
[2024-01-24 13:59:05,933] [INFO] Running command: hmmsearch --tblout GCF_013404075.1_ASM1340407v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg466db2b0-d0ee-4cdc-9519-db617f103a1f/dqc_reference/reference_markers.hmm GCF_013404075.1_ASM1340407v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:59:06,276] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:59:06,277] [INFO] Found 6/6 markers.
[2024-01-24 13:59:06,345] [INFO] Query marker FASTA was written to GCF_013404075.1_ASM1340407v1_genomic.fna/markers.fasta
[2024-01-24 13:59:06,346] [INFO] Task started: Blastn
[2024-01-24 13:59:06,346] [INFO] Running command: blastn -query GCF_013404075.1_ASM1340407v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg466db2b0-d0ee-4cdc-9519-db617f103a1f/dqc_reference/reference_markers.fasta -out GCF_013404075.1_ASM1340407v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:07,686] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:07,689] [INFO] Selected 13 target genomes.
[2024-01-24 13:59:07,690] [INFO] Target genome list was writen to GCF_013404075.1_ASM1340407v1_genomic.fna/target_genomes.txt
[2024-01-24 13:59:07,697] [INFO] Task started: fastANI
[2024-01-24 13:59:07,698] [INFO] Running command: fastANI --query /var/lib/cwl/stg43730bac-785e-4891-89ac-370a89a6b074/GCF_013404075.1_ASM1340407v1_genomic.fna.gz --refList GCF_013404075.1_ASM1340407v1_genomic.fna/target_genomes.txt --output GCF_013404075.1_ASM1340407v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:26,439] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:26,439] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg466db2b0-d0ee-4cdc-9519-db617f103a1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:26,440] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg466db2b0-d0ee-4cdc-9519-db617f103a1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:26,451] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:59:26,451] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:26,451] [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 vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	100.0	2280	2288	95	conclusive
Mycolicibacterium helvum	strain=JCM 30396	GCA_010731895.1	1534349	1534349	type	True	85.8057	1505	2288	95	below_threshold
Mycolicibacterium sarraceniae	strain=JCM 30395	GCA_010731875.1	1534348	1534348	type	True	84.9035	1245	2288	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	84.8125	1485	2288	95	below_threshold
Mycolicibacterium sphagni	strain=ATCC 33027	GCA_002250655.1	1786	1786	type	True	84.7884	1451	2288	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	84.743	1523	2288	95	below_threshold
Mycolicibacterium aromaticivorans	strain=JS19b1	GCA_000559085.2	318425	318425	type	True	84.4065	1483	2288	95	below_threshold
Mycolicibacterium rhodesiae	strain=DSM 44223	GCA_002086695.1	36814	36814	type	True	84.3154	1500	2288	95	below_threshold
Mycolicibacterium aichiense	strain=JCM 6376	GCA_010726245.1	1799	1799	type	True	84.2717	1490	2288	95	below_threshold
Mycolicibacterium aichiense	strain=NCTC10820	GCA_900453085.1	1799	1799	type	True	84.2085	1483	2288	95	below_threshold
Candidatus Mycolicibacterium alkanivorans		GCA_022760805.1	2954114	2954114	type	True	82.2008	840	2288	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	81.5739	1161	2288	95	below_threshold
Mycolicibacterium llatzerense	strain=MG13	GCA_025331195.1	280871	280871	type	True	79.4657	794	2288	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:26,453] [INFO] DFAST Taxonomy check result was written to GCF_013404075.1_ASM1340407v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:26,453] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:26,453] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:26,454] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg466db2b0-d0ee-4cdc-9519-db617f103a1f/dqc_reference/checkm_data
[2024-01-24 13:59:26,455] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:26,523] [INFO] Task started: CheckM
[2024-01-24 13:59:26,524] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013404075.1_ASM1340407v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013404075.1_ASM1340407v1_genomic.fna/checkm_input GCF_013404075.1_ASM1340407v1_genomic.fna/checkm_result
[2024-01-24 14:00:33,001] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:33,002] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:33,028] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:33,028] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:33,029] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013404075.1_ASM1340407v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:33,029] [INFO] Task started: Blastn
[2024-01-24 14:00:33,029] [INFO] Running command: blastn -query GCF_013404075.1_ASM1340407v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg466db2b0-d0ee-4cdc-9519-db617f103a1f/dqc_reference/reference_markers_gtdb.fasta -out GCF_013404075.1_ASM1340407v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:35,015] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:35,019] [INFO] Selected 13 target genomes.
[2024-01-24 14:00:35,019] [INFO] Target genome list was writen to GCF_013404075.1_ASM1340407v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:35,045] [INFO] Task started: fastANI
[2024-01-24 14:00:35,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg43730bac-785e-4891-89ac-370a89a6b074/GCF_013404075.1_ASM1340407v1_genomic.fna.gz --refList GCF_013404075.1_ASM1340407v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013404075.1_ASM1340407v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:57,605] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:57,619] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:57,619] [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_013404075.1	s__Mycobacterium sp013404075	100.0	2280	2288	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_000230935.1	s__Mycobacterium rhodesiae_B	94.7654	1821	2288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362315.1	s__Mycobacterium sp004362315	87.6532	1768	2288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.02	98.99	0.96	0.96	6	-
GCF_013337765.1	s__Mycobacterium sp003053865	86.7526	1621	2288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.43	95.41	0.83	0.83	3	-
GCA_900078375.1	s__Mycobacterium sp900078375	86.5673	1577	2288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731895.1	s__Mycobacterium helvum	85.7872	1508	2288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723835.1	s__Mycobacterium sp002723835	85.0072	1524	2288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886515.1	s__Mycobacterium sp001886515	84.7772	1497	2288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.54	98.54	0.94	0.94	2	-
GCF_008329905.1	s__Mycobacterium sp008329905	84.5578	1520	2288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086695.1	s__Mycobacterium rhodesiae	84.3007	1502	2288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001021385.1	s__Mycobacterium sp001021385	84.1223	1463	2288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008329565.1	s__Mycobacterium sp008329565	83.9022	1364	2288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002007745.1	s__Mycobacterium litorale_A	82.6941	1270	2288	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:57,621] [INFO] GTDB search result was written to GCF_013404075.1_ASM1340407v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:57,621] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:57,625] [INFO] DFAST_QC result json was written to GCF_013404075.1_ASM1340407v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:57,625] [INFO] DFAST_QC completed!
[2024-01-24 14:00:57,625] [INFO] Total running time: 0h2m17s