[2024-01-25 20:23:20,753] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:23:20,754] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:23:20,754] [INFO] DQC Reference Directory: /var/lib/cwl/stg5de15788-1b65-4104-8102-deb08c83cac8/dqc_reference
[2024-01-25 20:23:21,894] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:23:21,895] [INFO] Task started: Prodigal
[2024-01-25 20:23:21,895] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d65dbe7-a9c2-4707-915d-cfd3923b47cf/GCF_003716585.1_ASM371658v1_genomic.fna.gz | prodigal -d GCF_003716585.1_ASM371658v1_genomic.fna/cds.fna -a GCF_003716585.1_ASM371658v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:23:27,986] [INFO] Task succeeded: Prodigal
[2024-01-25 20:23:27,986] [INFO] Task started: HMMsearch
[2024-01-25 20:23:27,986] [INFO] Running command: hmmsearch --tblout GCF_003716585.1_ASM371658v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5de15788-1b65-4104-8102-deb08c83cac8/dqc_reference/reference_markers.hmm GCF_003716585.1_ASM371658v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:23:28,164] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:23:28,165] [INFO] Found 6/6 markers.
[2024-01-25 20:23:28,185] [INFO] Query marker FASTA was written to GCF_003716585.1_ASM371658v1_genomic.fna/markers.fasta
[2024-01-25 20:23:28,186] [INFO] Task started: Blastn
[2024-01-25 20:23:28,186] [INFO] Running command: blastn -query GCF_003716585.1_ASM371658v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5de15788-1b65-4104-8102-deb08c83cac8/dqc_reference/reference_markers.fasta -out GCF_003716585.1_ASM371658v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:23:28,955] [INFO] Task succeeded: Blastn
[2024-01-25 20:23:28,959] [INFO] Selected 20 target genomes.
[2024-01-25 20:23:28,959] [INFO] Target genome list was writen to GCF_003716585.1_ASM371658v1_genomic.fna/target_genomes.txt
[2024-01-25 20:23:28,979] [INFO] Task started: fastANI
[2024-01-25 20:23:28,979] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d65dbe7-a9c2-4707-915d-cfd3923b47cf/GCF_003716585.1_ASM371658v1_genomic.fna.gz --refList GCF_003716585.1_ASM371658v1_genomic.fna/target_genomes.txt --output GCF_003716585.1_ASM371658v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:23:42,719] [INFO] Task succeeded: fastANI
[2024-01-25 20:23:42,719] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5de15788-1b65-4104-8102-deb08c83cac8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:23:42,720] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5de15788-1b65-4104-8102-deb08c83cac8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:23:42,729] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:23:42,729] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:23:42,729] [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 alimapuense	strain=VA37-3	GCA_003716585.1	1576874	1576874	type	True	100.0	752	754	95	conclusive
Corynebacterium comes	strain=2019	GCA_009734405.1	2675218	2675218	type	True	78.6212	212	754	95	below_threshold
Corynebacterium testudinoris	strain=DSM 44614	GCA_001021045.1	136857	136857	type	True	78.5669	228	754	95	below_threshold
Corynebacterium marinum	strain=CGMCC 1.6998	GCA_014645275.1	349751	349751	type	True	78.5473	224	754	95	below_threshold
Corynebacterium pollutisoli	strain=VDS11	GCA_900177745.1	1610489	1610489	type	True	78.5324	228	754	95	below_threshold
Corynebacterium marinum	strain=DSM 44953	GCA_000835165.1	349751	349751	type	True	78.5218	224	754	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	78.0516	223	754	95	below_threshold
Corynebacterium occultum	strain=2039	GCA_009734425.1	2675219	2675219	type	True	77.996	165	754	95	below_threshold
Corynebacterium halotolerans	strain=DSM 44683	GCA_000688435.1	225326	225326	type	True	77.9549	221	754	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	77.9343	142	754	95	below_threshold
Corynebacterium efficiens	strain=YS-314	GCA_000011305.1	152794	152794	type	True	77.9175	142	754	95	below_threshold
Corynebacterium efficiens	strain=YS-314	GCA_000160795.1	152794	152794	type	True	77.7722	147	754	95	below_threshold
Corynebacterium aurimucosum	strain=FDAARGOS_1109	GCA_016728705.1	169292	169292	suspected-type	True	77.7379	100	754	95	below_threshold
Corynebacterium spheniscorum	strain=CCUG 45512	GCA_008693095.1	185761	185761	type	True	77.6119	102	754	95	below_threshold
Corynebacterium kalinowskii	strain=1959	GCA_009734385.1	2675216	2675216	type	True	77.5448	93	754	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:23:42,731] [INFO] DFAST Taxonomy check result was written to GCF_003716585.1_ASM371658v1_genomic.fna/tc_result.tsv
[2024-01-25 20:23:42,731] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:23:42,731] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:23:42,731] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5de15788-1b65-4104-8102-deb08c83cac8/dqc_reference/checkm_data
[2024-01-25 20:23:42,732] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:23:42,756] [INFO] Task started: CheckM
[2024-01-25 20:23:42,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003716585.1_ASM371658v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003716585.1_ASM371658v1_genomic.fna/checkm_input GCF_003716585.1_ASM371658v1_genomic.fna/checkm_result
[2024-01-25 20:24:05,078] [INFO] Task succeeded: CheckM
[2024-01-25 20:24:05,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:24:05,100] [INFO] ===== Completeness check finished =====
[2024-01-25 20:24:05,100] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:24:05,101] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003716585.1_ASM371658v1_genomic.fna/markers.fasta)
[2024-01-25 20:24:05,101] [INFO] Task started: Blastn
[2024-01-25 20:24:05,101] [INFO] Running command: blastn -query GCF_003716585.1_ASM371658v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5de15788-1b65-4104-8102-deb08c83cac8/dqc_reference/reference_markers_gtdb.fasta -out GCF_003716585.1_ASM371658v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:24:06,190] [INFO] Task succeeded: Blastn
[2024-01-25 20:24:06,193] [INFO] Selected 18 target genomes.
[2024-01-25 20:24:06,193] [INFO] Target genome list was writen to GCF_003716585.1_ASM371658v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:24:06,209] [INFO] Task started: fastANI
[2024-01-25 20:24:06,209] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d65dbe7-a9c2-4707-915d-cfd3923b47cf/GCF_003716585.1_ASM371658v1_genomic.fna.gz --refList GCF_003716585.1_ASM371658v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003716585.1_ASM371658v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:24:17,669] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:17,678] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:24:17,678] [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_003716585.1	s__Corynebacterium alimapuense	100.0	752	754	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_009734405.1	s__Corynebacterium sp009734405	78.6212	212	754	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001021045.1	s__Corynebacterium testudinoris	78.5836	227	754	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	78.5324	228	754	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.83	98.83	0.98	0.98	2	-
GCF_000835165.1	s__Corynebacterium marinum	78.5043	225	754	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.21	98.42	0.97	0.94	3	-
GCF_003955685.1	s__Corynebacterium sp003955685	78.3079	220	754	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341345.1	s__Corynebacterium halotolerans	78.0516	223	754	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009734425.1	s__Corynebacterium sp009734425	77.996	165	754	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	77.9343	142	754	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.60	0.94	0.94	3	-
GCF_000011305.1	s__Corynebacterium efficiens	77.8939	143	754	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.90	99.90	0.99	0.99	2	-
GCF_014837045.1	s__Corynebacterium sp014837045	77.8469	148	754	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016728705.1	s__Corynebacterium sp001807205	77.7379	100	754	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.15	96.83	0.93	0.90	8	-
GCF_900113445.1	s__Corynebacterium spheniscorum	77.5994	99	754	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_009734385.1	s__Corynebacterium sp009734385	77.5115	94	754	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:24:17,679] [INFO] GTDB search result was written to GCF_003716585.1_ASM371658v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:24:17,682] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:24:17,685] [INFO] DFAST_QC result json was written to GCF_003716585.1_ASM371658v1_genomic.fna/dqc_result.json
[2024-01-25 20:24:17,685] [INFO] DFAST_QC completed!
[2024-01-25 20:24:17,685] [INFO] Total running time: 0h0m57s