[2024-01-25 20:04:05,454] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:04:05,455] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:04:05,455] [INFO] DQC Reference Directory: /var/lib/cwl/stg3acff39a-5486-4949-a72e-ede52747b574/dqc_reference
[2024-01-25 20:04:06,614] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:04:06,614] [INFO] Task started: Prodigal
[2024-01-25 20:04:06,615] [INFO] Running command: gunzip -c /var/lib/cwl/stge43a4bd7-b2fa-4594-8776-73d14148f2a1/GCF_002591975.1_ASM259197v1_genomic.fna.gz | prodigal -d GCF_002591975.1_ASM259197v1_genomic.fna/cds.fna -a GCF_002591975.1_ASM259197v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:04:24,196] [INFO] Task succeeded: Prodigal
[2024-01-25 20:04:24,197] [INFO] Task started: HMMsearch
[2024-01-25 20:04:24,197] [INFO] Running command: hmmsearch --tblout GCF_002591975.1_ASM259197v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3acff39a-5486-4949-a72e-ede52747b574/dqc_reference/reference_markers.hmm GCF_002591975.1_ASM259197v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:04:24,598] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:04:24,599] [INFO] Found 6/6 markers.
[2024-01-25 20:04:24,673] [INFO] Query marker FASTA was written to GCF_002591975.1_ASM259197v1_genomic.fna/markers.fasta
[2024-01-25 20:04:24,675] [INFO] Task started: Blastn
[2024-01-25 20:04:24,675] [INFO] Running command: blastn -query GCF_002591975.1_ASM259197v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3acff39a-5486-4949-a72e-ede52747b574/dqc_reference/reference_markers.fasta -out GCF_002591975.1_ASM259197v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:25,803] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:25,806] [INFO] Selected 17 target genomes.
[2024-01-25 20:04:25,806] [INFO] Target genome list was writen to GCF_002591975.1_ASM259197v1_genomic.fna/target_genomes.txt
[2024-01-25 20:04:25,822] [INFO] Task started: fastANI
[2024-01-25 20:04:25,822] [INFO] Running command: fastANI --query /var/lib/cwl/stge43a4bd7-b2fa-4594-8776-73d14148f2a1/GCF_002591975.1_ASM259197v1_genomic.fna.gz --refList GCF_002591975.1_ASM259197v1_genomic.fna/target_genomes.txt --output GCF_002591975.1_ASM259197v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:04:45,467] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:45,468] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3acff39a-5486-4949-a72e-ede52747b574/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:04:45,468] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3acff39a-5486-4949-a72e-ede52747b574/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:04:45,479] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:04:45,479] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:04:45,479] [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 tusciae	strain=DSM 44338	GCA_002086795.1	75922	75922	type	True	85.71	1572	2014	95	below_threshold
Mycolicibacterium gadium	strain=JCM 12688	GCA_010728925.1	1794	1794	type	True	85.4695	1535	2014	95	below_threshold
Mycolicibacterium moriokaense	strain=CIP105393	GCA_002086395.1	39691	39691	type	True	83.8194	1368	2014	95	below_threshold
Mycolicibacterium moriokaense	strain=JCM 6375	GCA_010726085.1	39691	39691	type	True	83.7852	1391	2014	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	81.1351	1133	2014	95	below_threshold
Mycobacterium lehmannii	strain=CECT 8763	GCA_002245535.1	2048550	2048550	type	True	80.4975	1053	2014	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	80.4306	1028	2014	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	80.4187	1034	2014	95	below_threshold
Mycolicibacterium komanii	strain=GPK 1020	GCA_001050035.1	1566885	1566885	type	True	80.4051	1049	2014	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	80.3764	1030	2014	95	below_threshold
Mycolicibacterium monacense	strain=JCM 15658	GCA_010731575.1	85693	85693	type	True	80.1238	932	2014	95	below_threshold
Mycolicibacterium monacense	strain=DSM 44395	GCA_002086655.1	85693	85693	type	True	80.0828	925	2014	95	below_threshold
Mycolicibacterium monacense	strain=DSM 44395	GCA_009931355.1	85693	85693	type	True	80.064	945	2014	95	below_threshold
Mycolicibacterium psychrotolerans	strain=JCM 13323	GCA_010729305.1	216929	216929	type	True	79.853	907	2014	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	79.8105	885	2014	95	below_threshold
Mycobacterium branderi	strain=JCM 12687	GCA_010728725.1	43348	43348	type	True	78.6501	674	2014	95	below_threshold
Mycobacterium branderi	strain=DSM 44624	GCA_002086575.1	43348	43348	type	True	78.6237	679	2014	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:04:45,481] [INFO] DFAST Taxonomy check result was written to GCF_002591975.1_ASM259197v1_genomic.fna/tc_result.tsv
[2024-01-25 20:04:45,481] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:04:45,481] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:04:45,482] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3acff39a-5486-4949-a72e-ede52747b574/dqc_reference/checkm_data
[2024-01-25 20:04:45,482] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:04:45,540] [INFO] Task started: CheckM
[2024-01-25 20:04:45,540] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002591975.1_ASM259197v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002591975.1_ASM259197v1_genomic.fna/checkm_input GCF_002591975.1_ASM259197v1_genomic.fna/checkm_result
[2024-01-25 20:05:40,039] [INFO] Task succeeded: CheckM
[2024-01-25 20:05:40,041] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:05:40,059] [INFO] ===== Completeness check finished =====
[2024-01-25 20:05:40,059] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:05:40,060] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002591975.1_ASM259197v1_genomic.fna/markers.fasta)
[2024-01-25 20:05:40,060] [INFO] Task started: Blastn
[2024-01-25 20:05:40,060] [INFO] Running command: blastn -query GCF_002591975.1_ASM259197v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3acff39a-5486-4949-a72e-ede52747b574/dqc_reference/reference_markers_gtdb.fasta -out GCF_002591975.1_ASM259197v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:41,692] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:41,696] [INFO] Selected 10 target genomes.
[2024-01-25 20:05:41,697] [INFO] Target genome list was writen to GCF_002591975.1_ASM259197v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:05:41,709] [INFO] Task started: fastANI
[2024-01-25 20:05:41,709] [INFO] Running command: fastANI --query /var/lib/cwl/stge43a4bd7-b2fa-4594-8776-73d14148f2a1/GCF_002591975.1_ASM259197v1_genomic.fna.gz --refList GCF_002591975.1_ASM259197v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002591975.1_ASM259197v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:05:56,016] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:56,023] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:05:56,026] [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_002591975.1	s__Mycobacterium neglectum	100.0	2011	2014	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_000243415.2	s__Mycobacterium tusciae_A	89.7491	1624	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086795.1	s__Mycobacterium tusciae	85.7199	1570	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010726765.1	s__Mycobacterium gallinarum	85.4974	1527	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010728925.1	s__Mycobacterium gadium	85.4763	1534	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000230895.2	s__Mycobacterium rhodesiae_A	84.2915	1484	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010726085.1	s__Mycobacterium moriokaense	83.8143	1385	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002245535.1	s__Mycobacterium lehmannii	80.4867	1054	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.2034	97.95	97.72	0.91	0.88	6	-
GCA_000762985.1	s__Mycobacterium rufum_A	80.0298	928	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613185.1	s__Mycobacterium cosmeticum	79.1684	821	2014	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.89	98.33	0.93	0.89	4	-
--------------------------------------------------------------------------------
[2024-01-25 20:05:56,028] [INFO] GTDB search result was written to GCF_002591975.1_ASM259197v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:05:56,029] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:05:56,050] [INFO] DFAST_QC result json was written to GCF_002591975.1_ASM259197v1_genomic.fna/dqc_result.json
[2024-01-25 20:05:56,050] [INFO] DFAST_QC completed!
[2024-01-25 20:05:56,050] [INFO] Total running time: 0h1m51s