[2024-01-24 13:46:01,074] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:01,077] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:01,077] [INFO] DQC Reference Directory: /var/lib/cwl/stg18e68b96-17cb-4462-99da-cb6671993c9d/dqc_reference
[2024-01-24 13:46:02,420] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:02,421] [INFO] Task started: Prodigal
[2024-01-24 13:46:02,422] [INFO] Running command: gunzip -c /var/lib/cwl/stg44686600-f3fa-4115-827b-e888284f8305/GCF_031454255.1_ASM3145425v1_genomic.fna.gz | prodigal -d GCF_031454255.1_ASM3145425v1_genomic.fna/cds.fna -a GCF_031454255.1_ASM3145425v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:10,145] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:10,146] [INFO] Task started: HMMsearch
[2024-01-24 13:46:10,146] [INFO] Running command: hmmsearch --tblout GCF_031454255.1_ASM3145425v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18e68b96-17cb-4462-99da-cb6671993c9d/dqc_reference/reference_markers.hmm GCF_031454255.1_ASM3145425v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:10,373] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:10,375] [INFO] Found 6/6 markers.
[2024-01-24 13:46:10,397] [INFO] Query marker FASTA was written to GCF_031454255.1_ASM3145425v1_genomic.fna/markers.fasta
[2024-01-24 13:46:10,397] [INFO] Task started: Blastn
[2024-01-24 13:46:10,397] [INFO] Running command: blastn -query GCF_031454255.1_ASM3145425v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18e68b96-17cb-4462-99da-cb6671993c9d/dqc_reference/reference_markers.fasta -out GCF_031454255.1_ASM3145425v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:11,341] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:11,348] [INFO] Selected 18 target genomes.
[2024-01-24 13:46:11,349] [INFO] Target genome list was writen to GCF_031454255.1_ASM3145425v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:11,370] [INFO] Task started: fastANI
[2024-01-24 13:46:11,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg44686600-f3fa-4115-827b-e888284f8305/GCF_031454255.1_ASM3145425v1_genomic.fna.gz --refList GCF_031454255.1_ASM3145425v1_genomic.fna/target_genomes.txt --output GCF_031454255.1_ASM3145425v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:19,664] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:19,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18e68b96-17cb-4462-99da-cb6671993c9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:19,665] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18e68b96-17cb-4462-99da-cb6671993c9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:19,683] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:19,683] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:19,683] [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 suicordis	strain=DSM 45110	GCA_015351405.1	203264	203264	type	True	99.9951	739	749	95	conclusive
Corynebacterium dentalis	strain=Marseille-P4122	GCA_900232865.1	2014528	2014528	type	True	81.0126	470	749	95	below_threshold
Corynebacterium urogenitale	strain=LMM-1652	GCA_009026825.1	2487892	2487892	type	True	79.3517	249	749	95	below_threshold
Corynebacterium falsenii	strain=FDAARGOS_1494	GCA_020099275.1	108486	108486	type	True	78.9388	262	749	95	below_threshold
Corynebacterium jeikeium	strain=NCTC11913	GCA_900461185.1	38289	38289	suspected-type	True	78.6332	232	749	95	below_threshold
Corynebacterium aquilae	strain=S-613	GCA_001941445.1	203263	203263	type	True	78.6039	97	749	95	below_threshold
Corynebacterium zhongnanshanii	strain=zg-320	GCA_014490575.1	2768834	2768834	type	True	78.5382	209	749	95	below_threshold
Corynebacterium jeikeium	strain=ATCC 43734	GCA_000163435.1	38289	38289	suspected-type	True	78.469	231	749	95	below_threshold
Corynebacterium urealyticum	strain=NCTC12011	GCA_900187235.1	43771	43771	type	True	78.4521	200	749	95	below_threshold
Corynebacterium urealyticum	strain=FDAARGOS_994	GCA_016127975.1	43771	43771	type	True	78.3098	197	749	95	below_threshold
Corynebacterium resistens	strain=DSM 45100	GCA_000177535.2	258224	258224	type	True	78.2539	162	749	95	below_threshold
Corynebacterium heidelbergense	strain=DSM 104638	GCA_003285565.1	2055947	2055947	type	True	78.1715	152	749	95	below_threshold
Corynebacterium occultum	strain=2039	GCA_009734425.1	2675219	2675219	type	True	77.9985	135	749	95	below_threshold
Corynebacterium mycetoides	strain=DSM 20632	GCA_900103625.1	38302	38302	type	True	77.5157	125	749	95	below_threshold
Corynebacterium mastitidis	strain=DSM 44356	GCA_000375365.1	161890	161890	type	True	77.4837	122	749	95	below_threshold
Corynebacterium urinipleomorphum	strain=Marseille-P2799	GCA_900155535.1	1852380	1852380	type	True	77.4614	91	749	95	below_threshold
Dietzia kunjamensis subsp. schimae	strain=DSM 45139	GCA_900182685.1	498198	322509	type	True	76.3335	70	749	95	below_threshold
Dietzia kunjamensis	strain=DSM 44907	GCA_003610395.1	322509	322509	type	True	76.1459	79	749	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:19,684] [INFO] DFAST Taxonomy check result was written to GCF_031454255.1_ASM3145425v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:19,685] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:19,685] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:19,685] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18e68b96-17cb-4462-99da-cb6671993c9d/dqc_reference/checkm_data
[2024-01-24 13:46:19,686] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:19,710] [INFO] Task started: CheckM
[2024-01-24 13:46:19,711] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031454255.1_ASM3145425v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031454255.1_ASM3145425v1_genomic.fna/checkm_input GCF_031454255.1_ASM3145425v1_genomic.fna/checkm_result
[2024-01-24 13:46:48,717] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:48,718] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:48,735] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:48,735] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:48,735] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031454255.1_ASM3145425v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:48,736] [INFO] Task started: Blastn
[2024-01-24 13:46:48,736] [INFO] Running command: blastn -query GCF_031454255.1_ASM3145425v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18e68b96-17cb-4462-99da-cb6671993c9d/dqc_reference/reference_markers_gtdb.fasta -out GCF_031454255.1_ASM3145425v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:49,939] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:49,942] [INFO] Selected 20 target genomes.
[2024-01-24 13:46:49,942] [INFO] Target genome list was writen to GCF_031454255.1_ASM3145425v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:49,971] [INFO] Task started: fastANI
[2024-01-24 13:46:49,971] [INFO] Running command: fastANI --query /var/lib/cwl/stg44686600-f3fa-4115-827b-e888284f8305/GCF_031454255.1_ASM3145425v1_genomic.fna.gz --refList GCF_031454255.1_ASM3145425v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031454255.1_ASM3145425v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:46:59,463] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:59,485] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:46:59,485] [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_015351405.1	s__Corynebacterium sp015351405	99.9951	739	749	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900232865.1	s__Corynebacterium dentalis	81.0212	469	749	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.56	98.56	0.96	0.96	2	-
GCF_009026825.1	s__Corynebacterium sp009026825	79.3237	247	749	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000525655.1	s__Corynebacterium falsenii	78.7587	266	749	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.72	98.72	0.95	0.95	2	-
GCF_000738175.1	s__Corynebacterium jeikeium_C	78.6477	252	749	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014490575.1	s__Corynebacterium sp014490575	78.6296	210	749	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.40	97.50	0.99	0.97	7	-
GCF_001807485.1	s__Corynebacterium sp001807485	78.5194	248	749	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.83	97.75	0.93	0.93	3	-
GCF_001941445.1	s__Corynebacterium aquilae	78.4559	96	749	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000163435.1	s__Corynebacterium jeikeium	78.4523	232	749	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.68	96.00	0.93	0.90	9	-
GCF_000069945.1	s__Corynebacterium urealyticum	78.4387	199	749	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.66	97.50	0.94	0.89	9	-
GCF_000738265.1	s__Corynebacterium jeikeium_A	78.3672	240	749	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.92	97.52	0.95	0.93	11	-
GCF_000177535.2	s__Corynebacterium resistens	78.3183	163	749	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003285565.1	s__Corynebacterium heidelbergense	78.1715	152	749	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.29	96.29	0.86	0.86	2	-
GCF_009734425.1	s__Corynebacterium sp009734425	77.9727	136	749	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001815985.1	s__Corynebacterium sp001815985	77.8706	213	749	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.95	96.87	0.95	0.94	3	-
GCF_000375365.1	s__Corynebacterium mastitidis	77.4583	123	749	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.64	96.64	0.96	0.96	2	-
GCA_019120175.1	s__Corynebacterium faecigallinarum	77.3331	165	749	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103625.1	s__Corynebacterium mycetoides	77.2342	123	749	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003600225.1	s__QZFT01 sp003600225	75.9601	74	749	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__QZFT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119875.1	s__Dietzia intestinigallinarum	75.6354	54	749	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Dietzia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:46:59,487] [INFO] GTDB search result was written to GCF_031454255.1_ASM3145425v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:46:59,488] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:46:59,493] [INFO] DFAST_QC result json was written to GCF_031454255.1_ASM3145425v1_genomic.fna/dqc_result.json
[2024-01-24 13:46:59,494] [INFO] DFAST_QC completed!
[2024-01-24 13:46:59,494] [INFO] Total running time: 0h0m58s