[2024-01-25 17:51:05,569] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:51:05,570] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:51:05,570] [INFO] DQC Reference Directory: /var/lib/cwl/stg19c783b4-e7ba-4b82-ac94-e2f544d3c217/dqc_reference
[2024-01-25 17:51:06,731] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:51:06,732] [INFO] Task started: Prodigal
[2024-01-25 17:51:06,732] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb7db0c7-1cbf-4b48-8982-b5b9133c01ce/GCF_025822185.1_ASM2582218v1_genomic.fna.gz | prodigal -d GCF_025822185.1_ASM2582218v1_genomic.fna/cds.fna -a GCF_025822185.1_ASM2582218v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:51:26,361] [INFO] Task succeeded: Prodigal
[2024-01-25 17:51:26,361] [INFO] Task started: HMMsearch
[2024-01-25 17:51:26,361] [INFO] Running command: hmmsearch --tblout GCF_025822185.1_ASM2582218v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19c783b4-e7ba-4b82-ac94-e2f544d3c217/dqc_reference/reference_markers.hmm GCF_025822185.1_ASM2582218v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:51:26,682] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:51:26,683] [INFO] Found 6/6 markers.
[2024-01-25 17:51:26,735] [INFO] Query marker FASTA was written to GCF_025822185.1_ASM2582218v1_genomic.fna/markers.fasta
[2024-01-25 17:51:26,735] [INFO] Task started: Blastn
[2024-01-25 17:51:26,735] [INFO] Running command: blastn -query GCF_025822185.1_ASM2582218v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19c783b4-e7ba-4b82-ac94-e2f544d3c217/dqc_reference/reference_markers.fasta -out GCF_025822185.1_ASM2582218v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:27,828] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:27,831] [INFO] Selected 14 target genomes.
[2024-01-25 17:51:27,831] [INFO] Target genome list was writen to GCF_025822185.1_ASM2582218v1_genomic.fna/target_genomes.txt
[2024-01-25 17:51:27,854] [INFO] Task started: fastANI
[2024-01-25 17:51:27,854] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb7db0c7-1cbf-4b48-8982-b5b9133c01ce/GCF_025822185.1_ASM2582218v1_genomic.fna.gz --refList GCF_025822185.1_ASM2582218v1_genomic.fna/target_genomes.txt --output GCF_025822185.1_ASM2582218v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:51:46,200] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:46,201] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19c783b4-e7ba-4b82-ac94-e2f544d3c217/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:51:46,201] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19c783b4-e7ba-4b82-ac94-e2f544d3c217/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:51:46,210] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:51:46,210] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:51:46,210] [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 moriokaense	strain=JCM 6375	GCA_010726085.1	39691	39691	type	True	99.9965	2032	2032	95	conclusive
Mycolicibacterium moriokaense	strain=CIP105393	GCA_002086395.1	39691	39691	type	True	99.98	1998	2032	95	conclusive
Mycolicibacterium tusciae	strain=DSM 44338	GCA_002086795.1	75922	75922	type	True	83.6868	1366	2032	95	below_threshold
Mycolicibacterium gadium	strain=JCM 12688	GCA_010728925.1	1794	1794	type	True	83.4422	1401	2032	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	81.7747	1136	2032	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	81.5804	1107	2032	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	81.5727	1097	2032	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	81.5466	1105	2032	95	below_threshold
Mycolicibacterium malmesburyense	strain=WCM 7299	GCA_001050015.1	1566886	1566886	type	True	81.3591	1122	2032	95	below_threshold
Mycolicibacterium elephantis	strain=DSM 44368	GCA_004014805.1	81858	81858	type	True	81.3172	1111	2032	95	below_threshold
Mycolicibacterium komanii	strain=GPK 1020	GCA_001050035.1	1566885	1566885	type	True	81.1838	1166	2032	95	below_threshold
Mycobacterium lehmannii	strain=CECT 8763	GCA_002245535.1	2048550	2048550	type	True	80.9211	1071	2032	95	below_threshold
Mycolicibacterium chubuense	strain=DSM 44219	GCA_002086595.1	1800	1800	type	True	80.5115	965	2032	95	below_threshold
Mycolicibacterium llatzerense	strain=MG13	GCA_025331195.1	280871	280871	type	True	79.2724	784	2032	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:51:46,214] [INFO] DFAST Taxonomy check result was written to GCF_025822185.1_ASM2582218v1_genomic.fna/tc_result.tsv
[2024-01-25 17:51:46,214] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:51:46,214] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:51:46,215] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19c783b4-e7ba-4b82-ac94-e2f544d3c217/dqc_reference/checkm_data
[2024-01-25 17:51:46,215] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:51:46,276] [INFO] Task started: CheckM
[2024-01-25 17:51:46,276] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025822185.1_ASM2582218v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025822185.1_ASM2582218v1_genomic.fna/checkm_input GCF_025822185.1_ASM2582218v1_genomic.fna/checkm_result
[2024-01-25 17:52:46,787] [INFO] Task succeeded: CheckM
[2024-01-25 17:52:46,788] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:52:46,806] [INFO] ===== Completeness check finished =====
[2024-01-25 17:52:46,807] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:52:46,808] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025822185.1_ASM2582218v1_genomic.fna/markers.fasta)
[2024-01-25 17:52:46,808] [INFO] Task started: Blastn
[2024-01-25 17:52:46,808] [INFO] Running command: blastn -query GCF_025822185.1_ASM2582218v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19c783b4-e7ba-4b82-ac94-e2f544d3c217/dqc_reference/reference_markers_gtdb.fasta -out GCF_025822185.1_ASM2582218v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:48,418] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:48,421] [INFO] Selected 20 target genomes.
[2024-01-25 17:52:48,421] [INFO] Target genome list was writen to GCF_025822185.1_ASM2582218v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:52:48,444] [INFO] Task started: fastANI
[2024-01-25 17:52:48,444] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb7db0c7-1cbf-4b48-8982-b5b9133c01ce/GCF_025822185.1_ASM2582218v1_genomic.fna.gz --refList GCF_025822185.1_ASM2582218v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025822185.1_ASM2582218v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:53:16,474] [INFO] Task succeeded: fastANI
[2024-01-25 17:53:16,486] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:53:16,487] [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_010726085.1	s__Mycobacterium moriokaense	99.9965	2032	2032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000243415.2	s__Mycobacterium tusciae_A	83.7753	1410	2032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002591975.1	s__Mycobacterium neglectum	83.7523	1384	2032	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	83.6982	1482	2032	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	83.663	1371	2032	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	83.5678	1414	2032	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	83.4309	1403	2032	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	81.7722	1135	2032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001583415.1	s__Mycobacterium phlei	81.5951	1103	2032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_001722335.1	s__Mycobacterium flavescens_A	81.5559	1103	2032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050015.1	s__Mycobacterium malmesburyense	81.3587	1122	2032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050035.1	s__Mycobacterium komanii	81.1975	1163	2032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900240945.1	s__Mycobacterium sp900240945	81.0124	1181	2032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001500025.1	s__Mycobacterium sp001500025	80.9992	1133	2032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499905.1	s__Mycobacterium sp001499905	80.9347	1022	2032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002245535.1	s__Mycobacterium lehmannii	80.9123	1072	2032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.2034	97.95	97.72	0.91	0.88	6	-
GCF_001667505.1	s__Mycobacterium sp001667505	80.7572	1105	2032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873705.1	s__Mycobacterium sp014873705	80.6855	1130	2032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.28	98.28	0.92	0.92	2	-
GCF_000328565.1	s__Mycobacterium sp000328565	80.6194	1083	2032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570325.1	s__Mycobacterium sp004570325	80.5463	943	2032	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 17:53:16,488] [INFO] GTDB search result was written to GCF_025822185.1_ASM2582218v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:53:16,488] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:53:16,492] [INFO] DFAST_QC result json was written to GCF_025822185.1_ASM2582218v1_genomic.fna/dqc_result.json
[2024-01-25 17:53:16,492] [INFO] DFAST_QC completed!
[2024-01-25 17:53:16,492] [INFO] Total running time: 0h2m11s