[2024-01-24 14:46:33,948] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:33,950] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:33,951] [INFO] DQC Reference Directory: /var/lib/cwl/stg2548307c-a138-420a-acd3-0bb65136049c/dqc_reference
[2024-01-24 14:46:35,293] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:35,295] [INFO] Task started: Prodigal
[2024-01-24 14:46:35,296] [INFO] Running command: gunzip -c /var/lib/cwl/stg4135caf5-2e3a-4e99-97c4-ae189bd1a896/GCF_001044245.1_ASM104424v1_genomic.fna.gz | prodigal -d GCF_001044245.1_ASM104424v1_genomic.fna/cds.fna -a GCF_001044245.1_ASM104424v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:46:54,343] [INFO] Task succeeded: Prodigal
[2024-01-24 14:46:54,344] [INFO] Task started: HMMsearch
[2024-01-24 14:46:54,344] [INFO] Running command: hmmsearch --tblout GCF_001044245.1_ASM104424v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2548307c-a138-420a-acd3-0bb65136049c/dqc_reference/reference_markers.hmm GCF_001044245.1_ASM104424v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:46:54,703] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:46:54,705] [INFO] Found 6/6 markers.
[2024-01-24 14:46:54,763] [INFO] Query marker FASTA was written to GCF_001044245.1_ASM104424v1_genomic.fna/markers.fasta
[2024-01-24 14:46:54,763] [INFO] Task started: Blastn
[2024-01-24 14:46:54,763] [INFO] Running command: blastn -query GCF_001044245.1_ASM104424v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2548307c-a138-420a-acd3-0bb65136049c/dqc_reference/reference_markers.fasta -out GCF_001044245.1_ASM104424v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:46:55,974] [INFO] Task succeeded: Blastn
[2024-01-24 14:46:55,978] [INFO] Selected 15 target genomes.
[2024-01-24 14:46:55,979] [INFO] Target genome list was writen to GCF_001044245.1_ASM104424v1_genomic.fna/target_genomes.txt
[2024-01-24 14:46:55,985] [INFO] Task started: fastANI
[2024-01-24 14:46:55,985] [INFO] Running command: fastANI --query /var/lib/cwl/stg4135caf5-2e3a-4e99-97c4-ae189bd1a896/GCF_001044245.1_ASM104424v1_genomic.fna.gz --refList GCF_001044245.1_ASM104424v1_genomic.fna/target_genomes.txt --output GCF_001044245.1_ASM104424v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:15,802] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:15,803] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2548307c-a138-420a-acd3-0bb65136049c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:15,803] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2548307c-a138-420a-acd3-0bb65136049c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:15,817] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:47:15,818] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:47:15,818] [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	84.5002	1401	1879	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=DSM 43826	GCA_001044235.1	37916	37916	type	True	84.4655	1401	1879	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_002086595.1	1800	1800	type	True	84.3706	1353	1879	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_001044255.1	1800	1800	type	True	84.3202	1347	1879	95	below_threshold
Mycolicibacterium chubuense	strain=NCTC10819	GCA_900453455.1	1800	1800	type	True	84.2749	1400	1879	95	below_threshold
Mycolicibacterium psychrotolerans	strain=JCM 13323	GCA_010729305.1	216929	216929	type	True	84.2268	1273	1879	95	below_threshold
Mycolicibacterium aurum	strain=NCTC 10437	GCA_001049355.1	1791	1791	type	True	81.1103	1114	1879	95	below_threshold
Mycolicibacterium aurum	strain=NCTC10437	GCA_900637195.1	1791	1791	type	True	81.0588	1131	1879	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	80.8928	988	1879	95	below_threshold
Mycolicibacterium bacteremicum	strain=DSM 45578	GCA_002086115.1	564198	564198	type	True	80.0698	893	1879	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.8032	832	1879	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	79.7346	794	1879	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.7036	833	1879	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.6399	791	1879	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	79.6293	829	1879	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:15,820] [INFO] DFAST Taxonomy check result was written to GCF_001044245.1_ASM104424v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:15,821] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:15,821] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:15,821] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2548307c-a138-420a-acd3-0bb65136049c/dqc_reference/checkm_data
[2024-01-24 14:47:15,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:15,884] [INFO] Task started: CheckM
[2024-01-24 14:47:15,884] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001044245.1_ASM104424v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001044245.1_ASM104424v1_genomic.fna/checkm_input GCF_001044245.1_ASM104424v1_genomic.fna/checkm_result
[2024-01-24 14:48:23,225] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:23,226] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:23,252] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:23,252] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:23,253] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001044245.1_ASM104424v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:23,253] [INFO] Task started: Blastn
[2024-01-24 14:48:23,253] [INFO] Running command: blastn -query GCF_001044245.1_ASM104424v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2548307c-a138-420a-acd3-0bb65136049c/dqc_reference/reference_markers_gtdb.fasta -out GCF_001044245.1_ASM104424v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:25,177] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:25,181] [INFO] Selected 15 target genomes.
[2024-01-24 14:48:25,181] [INFO] Target genome list was writen to GCF_001044245.1_ASM104424v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:25,194] [INFO] Task started: fastANI
[2024-01-24 14:48:25,195] [INFO] Running command: fastANI --query /var/lib/cwl/stg4135caf5-2e3a-4e99-97c4-ae189bd1a896/GCF_001044245.1_ASM104424v1_genomic.fna.gz --refList GCF_001044245.1_ASM104424v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001044245.1_ASM104424v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:46,575] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:46,593] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:46,593] [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_001044245.1	s__Mycobacterium obuense	100.0	1875	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.74	96.27	0.88	0.86	5	conclusive
GCF_007096635.1	s__Mycobacterium sp007096635	87.0676	1463	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001044235.1	s__Mycobacterium chlorophenolicum	84.447	1406	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.8643	98.88	97.93	0.94	0.90	4	-
GCA_000762985.1	s__Mycobacterium rufum_A	84.3607	1372	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001044255.1	s__Mycobacterium chubuense	84.3424	1344	1879	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	84.2298	1274	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.53	96.53	0.90	0.90	2	-
GCF_000266905.1	s__Mycobacterium chubuense_A	82.0907	1155	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001545925.1	s__Mycobacterium sp001545925	81.8247	912	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014190915.1	s__Mycobacterium iranicum_B	81.6293	1092	1879	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	81.3638	1031	1879	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	80.9051	985	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086115.1	s__Mycobacterium bacteremicum	80.0452	897	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001494595.1	s__Mycobacterium sp001494595	79.859	855	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731855.1	s__Mycobacterium anyangense	79.6219	830	1879	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	79.5716	868	1879	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.02	98.99	0.96	0.96	6	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:46,596] [INFO] GTDB search result was written to GCF_001044245.1_ASM104424v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:46,597] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:46,604] [INFO] DFAST_QC result json was written to GCF_001044245.1_ASM104424v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:46,605] [INFO] DFAST_QC completed!
[2024-01-24 14:48:46,605] [INFO] Total running time: 0h2m13s