[2024-01-24 15:19:49,588] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:19:49,611] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:19:49,612] [INFO] DQC Reference Directory: /var/lib/cwl/stg18262748-c831-4084-8a5a-9e628afb530e/dqc_reference
[2024-01-24 15:19:50,925] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:19:50,927] [INFO] Task started: Prodigal
[2024-01-24 15:19:50,927] [INFO] Running command: gunzip -c /var/lib/cwl/stg0bf9c571-ae6c-4eb6-a64d-fbf094ee7e7b/GCF_001021025.1_ASM102102v1_genomic.fna.gz | prodigal -d GCF_001021025.1_ASM102102v1_genomic.fna/cds.fna -a GCF_001021025.1_ASM102102v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:59,859] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:59,860] [INFO] Task started: HMMsearch
[2024-01-24 15:19:59,860] [INFO] Running command: hmmsearch --tblout GCF_001021025.1_ASM102102v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18262748-c831-4084-8a5a-9e628afb530e/dqc_reference/reference_markers.hmm GCF_001021025.1_ASM102102v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:20:00,096] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:20:00,098] [INFO] Found 6/6 markers.
[2024-01-24 15:20:00,125] [INFO] Query marker FASTA was written to GCF_001021025.1_ASM102102v1_genomic.fna/markers.fasta
[2024-01-24 15:20:00,126] [INFO] Task started: Blastn
[2024-01-24 15:20:00,126] [INFO] Running command: blastn -query GCF_001021025.1_ASM102102v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18262748-c831-4084-8a5a-9e628afb530e/dqc_reference/reference_markers.fasta -out GCF_001021025.1_ASM102102v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:00,997] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:01,001] [INFO] Selected 16 target genomes.
[2024-01-24 15:20:01,002] [INFO] Target genome list was writen to GCF_001021025.1_ASM102102v1_genomic.fna/target_genomes.txt
[2024-01-24 15:20:01,015] [INFO] Task started: fastANI
[2024-01-24 15:20:01,015] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bf9c571-ae6c-4eb6-a64d-fbf094ee7e7b/GCF_001021025.1_ASM102102v1_genomic.fna.gz --refList GCF_001021025.1_ASM102102v1_genomic.fna/target_genomes.txt --output GCF_001021025.1_ASM102102v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:20:09,856] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:09,856] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18262748-c831-4084-8a5a-9e628afb530e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:20:09,857] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18262748-c831-4084-8a5a-9e628afb530e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:20:09,878] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:20:09,878] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:20:09,878] [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 epidermidicanis	strain=DSM 45586	GCA_001021025.1	1050174	1050174	type	True	100.0	896	897	95	conclusive
Corynebacterium kalinowskii	strain=1959	GCA_009734385.1	2675216	2675216	type	True	79.6525	261	897	95	below_threshold
Corynebacterium hindlerae	strain=NML 93-0612	GCA_014117265.1	699041	699041	type	True	79.6355	258	897	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032	GCA_000011325.1	1718	1718	type	True	79.1092	124	897	95	below_threshold
Corynebacterium camporealensis	strain=DSM 44610	GCA_000980815.1	161896	161896	type	True	79.0853	140	897	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032	GCA_002847405.1	1718	1718	type	True	78.9795	120	897	95	below_threshold
Corynebacterium aquilae	strain=S-613	GCA_001941445.1	203263	203263	type	True	78.8663	134	897	95	below_threshold
Corynebacterium sanguinis	strain=CCUG 58655	GCA_007641235.1	2594913	2594913	type	True	78.4153	116	897	95	below_threshold
Corynebacterium mycetoides	strain=DSM 20632	GCA_900103625.1	38302	38302	type	True	78.246	124	897	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	78.1689	187	897	95	below_threshold
Corynebacterium humireducens	strain=DSM 45392	GCA_000819445.1	1223514	1223514	type	True	77.8149	166	897	95	below_threshold
Corynebacterium lipophiloflavum	strain=DSM 44291	GCA_000159635.1	161889	161889	type	True	77.6882	114	897	95	below_threshold
Corynebacterium pollutisoli	strain=VDS11	GCA_900177745.1	1610489	1610489	type	True	77.4593	147	897	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	77.2748	159	897	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:20:09,880] [INFO] DFAST Taxonomy check result was written to GCF_001021025.1_ASM102102v1_genomic.fna/tc_result.tsv
[2024-01-24 15:20:09,881] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:20:09,881] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:20:09,881] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18262748-c831-4084-8a5a-9e628afb530e/dqc_reference/checkm_data
[2024-01-24 15:20:09,882] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:20:09,917] [INFO] Task started: CheckM
[2024-01-24 15:20:09,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001021025.1_ASM102102v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001021025.1_ASM102102v1_genomic.fna/checkm_input GCF_001021025.1_ASM102102v1_genomic.fna/checkm_result
[2024-01-24 15:20:40,703] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:40,704] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:40,725] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:40,725] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:40,726] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001021025.1_ASM102102v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:40,726] [INFO] Task started: Blastn
[2024-01-24 15:20:40,726] [INFO] Running command: blastn -query GCF_001021025.1_ASM102102v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg18262748-c831-4084-8a5a-9e628afb530e/dqc_reference/reference_markers_gtdb.fasta -out GCF_001021025.1_ASM102102v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:41,915] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:41,919] [INFO] Selected 15 target genomes.
[2024-01-24 15:20:41,920] [INFO] Target genome list was writen to GCF_001021025.1_ASM102102v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:41,932] [INFO] Task started: fastANI
[2024-01-24 15:20:41,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg0bf9c571-ae6c-4eb6-a64d-fbf094ee7e7b/GCF_001021025.1_ASM102102v1_genomic.fna.gz --refList GCF_001021025.1_ASM102102v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001021025.1_ASM102102v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:50,760] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:50,775] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:50,775] [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_001021025.1	s__Corynebacterium epidermidicanis	100.0	897	897	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_014117265.1	s__Corynebacterium sp014117265	79.7325	257	897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.31	97.31	0.93	0.93	2	-
GCF_009734385.1	s__Corynebacterium sp009734385	79.6152	259	897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011325.1	s__Corynebacterium glutamicum	79.0799	123	897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.67	97.34	0.92	0.85	76	-
GCF_001941445.1	s__Corynebacterium aquilae	78.8693	134	897	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	78.4295	147	897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.90	99.90	0.99	0.99	2	-
GCF_007641235.1	s__Corynebacterium sanguinis	78.3628	117	897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.27	97.90	0.92	0.90	7	-
GCF_900103625.1	s__Corynebacterium mycetoides	78.2623	123	897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000550805.1	s__Corynebacterium vitaeruminis	78.1689	187	897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.60	0.94	0.94	3	-
GCF_002994655.1	s__Corynebacterium sp002994655	77.9475	142	897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000819445.1	s__Corynebacterium humireducens	77.8384	166	897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.80	97.60	0.97	0.93	3	-
GCF_000159635.1	s__Corynebacterium lipophiloflavum	77.6616	115	897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177745.1	s__Corynebacterium pollutisoli	77.4593	147	897	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.83	98.83	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:50,777] [INFO] GTDB search result was written to GCF_001021025.1_ASM102102v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:50,778] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:50,781] [INFO] DFAST_QC result json was written to GCF_001021025.1_ASM102102v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:50,782] [INFO] DFAST_QC completed!
[2024-01-24 15:20:50,782] [INFO] Total running time: 0h1m1s