[2024-01-25 19:36:35,625] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:36:35,626] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:36:35,626] [INFO] DQC Reference Directory: /var/lib/cwl/stg04ba087c-1651-4621-8e1d-cf0b1ef2c53e/dqc_reference
[2024-01-25 19:36:36,751] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:36:36,755] [INFO] Task started: Prodigal
[2024-01-25 19:36:36,755] [INFO] Running command: gunzip -c /var/lib/cwl/stg445d0b61-dce2-4d34-9198-0028106175da/GCF_022374875.2_ASM2237487v3_genomic.fna.gz | prodigal -d GCF_022374875.2_ASM2237487v3_genomic.fna/cds.fna -a GCF_022374875.2_ASM2237487v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:37:04,128] [INFO] Task succeeded: Prodigal
[2024-01-25 19:37:04,129] [INFO] Task started: HMMsearch
[2024-01-25 19:37:04,129] [INFO] Running command: hmmsearch --tblout GCF_022374875.2_ASM2237487v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04ba087c-1651-4621-8e1d-cf0b1ef2c53e/dqc_reference/reference_markers.hmm GCF_022374875.2_ASM2237487v3_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:37:04,455] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:37:04,456] [INFO] Found 6/6 markers.
[2024-01-25 19:37:04,506] [INFO] Query marker FASTA was written to GCF_022374875.2_ASM2237487v3_genomic.fna/markers.fasta
[2024-01-25 19:37:04,506] [INFO] Task started: Blastn
[2024-01-25 19:37:04,506] [INFO] Running command: blastn -query GCF_022374875.2_ASM2237487v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg04ba087c-1651-4621-8e1d-cf0b1ef2c53e/dqc_reference/reference_markers.fasta -out GCF_022374875.2_ASM2237487v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:05,646] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:05,649] [INFO] Selected 13 target genomes.
[2024-01-25 19:37:05,649] [INFO] Target genome list was writen to GCF_022374875.2_ASM2237487v3_genomic.fna/target_genomes.txt
[2024-01-25 19:37:05,673] [INFO] Task started: fastANI
[2024-01-25 19:37:05,673] [INFO] Running command: fastANI --query /var/lib/cwl/stg445d0b61-dce2-4d34-9198-0028106175da/GCF_022374875.2_ASM2237487v3_genomic.fna.gz --refList GCF_022374875.2_ASM2237487v3_genomic.fna/target_genomes.txt --output GCF_022374875.2_ASM2237487v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:37:25,176] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:25,176] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04ba087c-1651-4621-8e1d-cf0b1ef2c53e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:37:25,177] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04ba087c-1651-4621-8e1d-cf0b1ef2c53e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:37:25,186] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:37:25,186] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:37:25,186] [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 chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	89.4078	1686	2034	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=DSM 43826	GCA_001044235.1	37916	37916	type	True	89.3946	1696	2034	95	below_threshold
Mycolicibacterium chubuense	strain=NCTC10819	GCA_900453455.1	1800	1800	type	True	89.3322	1681	2034	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_001044255.1	1800	1800	type	True	89.327	1661	2034	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_002086595.1	1800	1800	type	True	89.3073	1670	2034	95	below_threshold
Mycolicibacterium psychrotolerans	strain=JCM 13323	GCA_010729305.1	216929	216929	type	True	89.1042	1575	2034	95	below_threshold
Mycolicibacterium aurum	strain=NCTC10437	GCA_900637195.1	1791	1791	type	True	81.9898	1263	2034	95	below_threshold
Mycolicibacterium aurum	strain=NCTC 10437	GCA_001049355.1	1791	1791	type	True	81.9767	1248	2034	95	below_threshold
Mycolicibacterium arabiense	strain=JCM 18538	GCA_010731815.2	1286181	1286181	type	True	80.8629	1086	2034	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	80.6451	1088	2034	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	80.2518	918	2034	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	80.2491	892	2034	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.9134	940	2034	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:37:25,187] [INFO] DFAST Taxonomy check result was written to GCF_022374875.2_ASM2237487v3_genomic.fna/tc_result.tsv
[2024-01-25 19:37:25,189] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:37:25,189] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:37:25,189] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04ba087c-1651-4621-8e1d-cf0b1ef2c53e/dqc_reference/checkm_data
[2024-01-25 19:37:25,190] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:37:25,245] [INFO] Task started: CheckM
[2024-01-25 19:37:25,245] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022374875.2_ASM2237487v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022374875.2_ASM2237487v3_genomic.fna/checkm_input GCF_022374875.2_ASM2237487v3_genomic.fna/checkm_result
[2024-01-25 19:39:17,488] [INFO] Task succeeded: CheckM
[2024-01-25 19:39:17,490] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:39:17,518] [INFO] ===== Completeness check finished =====
[2024-01-25 19:39:17,518] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:39:17,521] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022374875.2_ASM2237487v3_genomic.fna/markers.fasta)
[2024-01-25 19:39:17,521] [INFO] Task started: Blastn
[2024-01-25 19:39:17,522] [INFO] Running command: blastn -query GCF_022374875.2_ASM2237487v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg04ba087c-1651-4621-8e1d-cf0b1ef2c53e/dqc_reference/reference_markers_gtdb.fasta -out GCF_022374875.2_ASM2237487v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:19,344] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:19,348] [INFO] Selected 11 target genomes.
[2024-01-25 19:39:19,348] [INFO] Target genome list was writen to GCF_022374875.2_ASM2237487v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:39:19,355] [INFO] Task started: fastANI
[2024-01-25 19:39:19,355] [INFO] Running command: fastANI --query /var/lib/cwl/stg445d0b61-dce2-4d34-9198-0028106175da/GCF_022374875.2_ASM2237487v3_genomic.fna.gz --refList GCF_022374875.2_ASM2237487v3_genomic.fna/target_genomes_gtdb.txt --output GCF_022374875.2_ASM2237487v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:39:36,402] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:36,410] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:39:36,410] [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
GCA_000762985.1	s__Mycobacterium rufum_A	99.9997	2034	2034	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_001044235.1	s__Mycobacterium chlorophenolicum	89.3908	1696	2034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	98.88	97.93	0.94	0.90	4	-
GCF_001044255.1	s__Mycobacterium chubuense	89.3397	1659	2034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	99.98	99.97	0.99	0.98	3	-
GCF_010729305.1	s__Mycobacterium psychrotolerans	89.099	1576	2034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.53	96.53	0.90	0.90	2	-
GCF_007096635.1	s__Mycobacterium sp007096635	84.363	1319	2034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001044245.1	s__Mycobacterium obuense	84.3561	1358	2034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.74	96.27	0.88	0.86	5	-
GCF_014190915.1	s__Mycobacterium iranicum_B	82.3814	1217	2034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900454025.1	s__Mycobacterium gilvum	82.355	1206	2034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.87	97.81	0.88	0.86	5	-
GCF_010728325.1	s__Mycobacterium poriferae	82.1238	1197	2034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.01	98.01	0.88	0.88	2	-
GCF_900637195.1	s__Mycobacterium aurum	81.9948	1264	2034	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001050015.1	s__Mycobacterium malmesburyense	80.9981	961	2034	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 19:39:36,412] [INFO] GTDB search result was written to GCF_022374875.2_ASM2237487v3_genomic.fna/result_gtdb.tsv
[2024-01-25 19:39:36,412] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:39:36,415] [INFO] DFAST_QC result json was written to GCF_022374875.2_ASM2237487v3_genomic.fna/dqc_result.json
[2024-01-25 19:39:36,415] [INFO] DFAST_QC completed!
[2024-01-25 19:39:36,415] [INFO] Total running time: 0h3m1s