[2024-01-24 14:39:14,967] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:14,969] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:14,969] [INFO] DQC Reference Directory: /var/lib/cwl/stge24600d7-9ebc-4f36-b9ee-52e1fbfcc045/dqc_reference
[2024-01-24 14:39:16,438] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:16,439] [INFO] Task started: Prodigal
[2024-01-24 14:39:16,440] [INFO] Running command: gunzip -c /var/lib/cwl/stg826989ed-8328-4401-a166-da20226878d2/GCF_014117265.1_ASM1411726v1_genomic.fna.gz | prodigal -d GCF_014117265.1_ASM1411726v1_genomic.fna/cds.fna -a GCF_014117265.1_ASM1411726v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:25,320] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:25,321] [INFO] Task started: HMMsearch
[2024-01-24 14:39:25,321] [INFO] Running command: hmmsearch --tblout GCF_014117265.1_ASM1411726v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge24600d7-9ebc-4f36-b9ee-52e1fbfcc045/dqc_reference/reference_markers.hmm GCF_014117265.1_ASM1411726v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:25,584] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:25,585] [INFO] Found 6/6 markers.
[2024-01-24 14:39:25,614] [INFO] Query marker FASTA was written to GCF_014117265.1_ASM1411726v1_genomic.fna/markers.fasta
[2024-01-24 14:39:25,615] [INFO] Task started: Blastn
[2024-01-24 14:39:25,615] [INFO] Running command: blastn -query GCF_014117265.1_ASM1411726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge24600d7-9ebc-4f36-b9ee-52e1fbfcc045/dqc_reference/reference_markers.fasta -out GCF_014117265.1_ASM1411726v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:26,586] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:26,590] [INFO] Selected 16 target genomes.
[2024-01-24 14:39:26,591] [INFO] Target genome list was writen to GCF_014117265.1_ASM1411726v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:26,597] [INFO] Task started: fastANI
[2024-01-24 14:39:26,598] [INFO] Running command: fastANI --query /var/lib/cwl/stg826989ed-8328-4401-a166-da20226878d2/GCF_014117265.1_ASM1411726v1_genomic.fna.gz --refList GCF_014117265.1_ASM1411726v1_genomic.fna/target_genomes.txt --output GCF_014117265.1_ASM1411726v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:35,658] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:35,658] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge24600d7-9ebc-4f36-b9ee-52e1fbfcc045/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:35,658] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge24600d7-9ebc-4f36-b9ee-52e1fbfcc045/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:35,672] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:35,672] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:35,672] [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
Corynebacterium hindlerae	strain=NML 93-0612	GCA_014117265.1	699041	699041	type	True	100.0	891	893	95	conclusive
Corynebacterium kalinowskii	strain=1959	GCA_009734385.1	2675216	2675216	type	True	79.9994	377	893	95	below_threshold
Corynebacterium epidermidicanis	strain=DSM 45586	GCA_001021025.1	1050174	1050174	type	True	79.2637	275	893	95	below_threshold
Corynebacterium renale	strain=NCTC7448	GCA_900478035.1	1724	1724	type	True	78.7837	110	893	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	78.5419	215	893	95	below_threshold
Corynebacterium aquilae	strain=S-613	GCA_001941445.1	203263	203263	type	True	78.4488	176	893	95	below_threshold
Corynebacterium ureicelerivorans	strain=IMMIB RIV-2301	GCA_000747315.1	401472	401472	type	True	77.8448	117	893	95	below_threshold
Corynebacterium pollutisoli	strain=VDS11	GCA_900177745.1	1610489	1610489	type	True	77.8117	204	893	95	below_threshold
Corynebacterium efficiens	strain=YS-314	GCA_000160795.1	152794	152794	type	True	77.7246	188	893	95	below_threshold
Gordonia spumicola	strain=NBRC 107696	GCA_009932475.1	589161	589161	type	True	77.6729	72	893	95	below_threshold
Corynebacterium sanguinis	strain=CCUG 58655	GCA_007641235.1	2594913	2594913	type	True	77.57	136	893	95	below_threshold
Corynebacterium lipophiloflavum	strain=DSM 44291	GCA_000159635.1	161889	161889	type	True	77.3504	123	893	95	below_threshold
Corynebacterium appendicis	strain=DSM 44531	GCA_900156665.1	163202	163202	type	True	77.1621	127	893	95	below_threshold
Corynebacterium afermentans subsp. lipophilum	strain=CCUG 32105	GCA_015351335.1	144184	38286	type	True	77.1547	144	893	95	below_threshold
Corynebacterium mucifaciens	strain=ATCC 700355	GCA_012396315.1	57171	57171	type	True	77.1388	117	893	95	below_threshold
Rhodococcus oxybenzonivorans	strain=S2-17	GCA_003130705.1	1990687	1990687	type	True	76.5889	75	893	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:35,674] [INFO] DFAST Taxonomy check result was written to GCF_014117265.1_ASM1411726v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:35,675] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:35,675] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:35,675] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge24600d7-9ebc-4f36-b9ee-52e1fbfcc045/dqc_reference/checkm_data
[2024-01-24 14:39:35,676] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:35,708] [INFO] Task started: CheckM
[2024-01-24 14:39:35,708] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014117265.1_ASM1411726v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014117265.1_ASM1411726v1_genomic.fna/checkm_input GCF_014117265.1_ASM1411726v1_genomic.fna/checkm_result
[2024-01-24 14:40:07,831] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:07,832] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:07,851] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:07,852] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:07,852] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014117265.1_ASM1411726v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:07,853] [INFO] Task started: Blastn
[2024-01-24 14:40:07,853] [INFO] Running command: blastn -query GCF_014117265.1_ASM1411726v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge24600d7-9ebc-4f36-b9ee-52e1fbfcc045/dqc_reference/reference_markers_gtdb.fasta -out GCF_014117265.1_ASM1411726v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:09,266] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:09,270] [INFO] Selected 16 target genomes.
[2024-01-24 14:40:09,270] [INFO] Target genome list was writen to GCF_014117265.1_ASM1411726v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:09,303] [INFO] Task started: fastANI
[2024-01-24 14:40:09,303] [INFO] Running command: fastANI --query /var/lib/cwl/stg826989ed-8328-4401-a166-da20226878d2/GCF_014117265.1_ASM1411726v1_genomic.fna.gz --refList GCF_014117265.1_ASM1411726v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014117265.1_ASM1411726v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:19,002] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:19,015] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:19,016] [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_014117265.1	s__Corynebacterium sp014117265	100.0	891	893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.31	97.31	0.93	0.93	2	conclusive
GCF_009734385.1	s__Corynebacterium sp009734385	80.0289	375	893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001021025.1	s__Corynebacterium epidermidicanis	79.3034	276	893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002563965.1	s__Corynebacterium renale	78.7567	110	893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.02	98.07	0.97	0.94	5	-
GCF_000550805.1	s__Corynebacterium vitaeruminis	78.6201	216	893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.60	0.94	0.94	3	-
GCF_001941445.1	s__Corynebacterium aquilae	78.4262	176	893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011305.1	s__Corynebacterium efficiens	78.078	185	893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.90	99.90	0.99	0.99	2	-
GCF_900177745.1	s__Corynebacterium pollutisoli	77.8446	202	893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.83	98.83	0.98	0.98	2	-
GCF_007641235.1	s__Corynebacterium sanguinis	77.5906	137	893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.27	97.90	0.92	0.90	7	-
GCF_009932475.1	s__Gordonia spumicola	77.438	72	893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019209935.1	s__Corynebacterium sp019209935	77.3532	145	893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	95.84	95.84	0.96	0.96	2	-
GCA_012838985.1	s__Corynebacterium sp012838985	77.2179	160	893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156665.1	s__Corynebacterium appendicis	77.1621	127	893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012396315.1	s__Corynebacterium mucifaciens	77.1388	117	893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	95.74	95.74	0.89	0.89	2	-
GCF_001807265.1	s__Corynebacterium sp001807265	77.1191	136	893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.96	97.96	0.92	0.92	2	-
GCF_003130705.1	s__Rhodococcus sp003130705	76.4212	73	893	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Rhodococcus	95.0	96.82	95.95	0.80	0.77	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:19,017] [INFO] GTDB search result was written to GCF_014117265.1_ASM1411726v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:19,018] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:19,022] [INFO] DFAST_QC result json was written to GCF_014117265.1_ASM1411726v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:19,023] [INFO] DFAST_QC completed!
[2024-01-24 14:40:19,023] [INFO] Total running time: 0h1m4s