[2024-01-24 13:48:59,813] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,815] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,815] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c53adca-1c2f-4f00-917b-bd2997a83e81/dqc_reference
[2024-01-24 13:49:01,195] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,196] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,197] [INFO] Running command: gunzip -c /var/lib/cwl/stgf809f027-8ea7-4aef-ace6-9b91ef1a676c/GCF_008930985.1_ASM893098v1_genomic.fna.gz | prodigal -d GCF_008930985.1_ASM893098v1_genomic.fna/cds.fna -a GCF_008930985.1_ASM893098v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:09,647] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:09,648] [INFO] Task started: HMMsearch
[2024-01-24 13:49:09,648] [INFO] Running command: hmmsearch --tblout GCF_008930985.1_ASM893098v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c53adca-1c2f-4f00-917b-bd2997a83e81/dqc_reference/reference_markers.hmm GCF_008930985.1_ASM893098v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:09,900] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:09,901] [INFO] Found 6/6 markers.
[2024-01-24 13:49:09,928] [INFO] Query marker FASTA was written to GCF_008930985.1_ASM893098v1_genomic.fna/markers.fasta
[2024-01-24 13:49:09,928] [INFO] Task started: Blastn
[2024-01-24 13:49:09,928] [INFO] Running command: blastn -query GCF_008930985.1_ASM893098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c53adca-1c2f-4f00-917b-bd2997a83e81/dqc_reference/reference_markers.fasta -out GCF_008930985.1_ASM893098v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:10,955] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:10,959] [INFO] Selected 21 target genomes.
[2024-01-24 13:49:10,960] [INFO] Target genome list was writen to GCF_008930985.1_ASM893098v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:10,969] [INFO] Task started: fastANI
[2024-01-24 13:49:10,970] [INFO] Running command: fastANI --query /var/lib/cwl/stgf809f027-8ea7-4aef-ace6-9b91ef1a676c/GCF_008930985.1_ASM893098v1_genomic.fna.gz --refList GCF_008930985.1_ASM893098v1_genomic.fna/target_genomes.txt --output GCF_008930985.1_ASM893098v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:20,478] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:20,479] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c53adca-1c2f-4f00-917b-bd2997a83e81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:20,479] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c53adca-1c2f-4f00-917b-bd2997a83e81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:20,496] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:49:20,496] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:49:20,496] [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 ciconiae	strain=DSM 44920	GCA_000372385.1	227319	227319	type	True	84.538	689	811	95	below_threshold
Corynebacterium mastitidis	strain=DSM 44356	GCA_000375365.1	161890	161890	type	True	78.2586	183	811	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	78.2019	214	811	95	below_threshold
Corynebacterium frankenforstense	strain=ST18	GCA_001941485.1	1230998	1230998	type	True	78.0715	198	811	95	below_threshold
Corynebacterium halotolerans	strain=DSM 44683	GCA_000688435.1	225326	225326	type	True	78.0596	213	811	95	below_threshold
Corynebacterium humireducens	strain=DSM 45392	GCA_000819445.1	1223514	1223514	type	True	78.0521	194	811	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	78.0085	226	811	95	below_threshold
Corynebacterium efficiens	strain=YS-314	GCA_000011305.1	152794	152794	type	True	77.9357	176	811	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	77.9077	194	811	95	below_threshold
Corynebacterium occultum	strain=2039	GCA_009734425.1	2675219	2675219	type	True	77.8731	183	811	95	below_threshold
Corynebacterium afermentans subsp. lipophilum	strain=CCUG 32105	GCA_015351335.1	144184	38286	type	True	77.82	153	811	95	below_threshold
Corynebacterium efficiens	strain=YS-314	GCA_000160795.1	152794	152794	type	True	77.8072	181	811	95	below_threshold
Corynebacterium ihumii	strain=GD7	GCA_000403725.2	1232427	1232427	type	True	77.7972	161	811	95	below_threshold
Corynebacterium lowii	strain=NML 130206	GCA_001412085.1	1544413	1544413	type	True	77.7124	157	811	95	below_threshold
Corynebacterium haemomassiliense	strain=Marseille-Q3615	GCA_013978595.1	2754726	2754726	type	True	77.6311	171	811	95	below_threshold
Corynebacterium fournieri	strain=Marseille-P2948	GCA_900176865.1	1852390	1852390	type	True	77.5037	160	811	95	below_threshold
Corynebacterium sphenisci	strain=DSM 44792	GCA_001941505.1	191493	191493	type	True	77.3423	182	811	95	below_threshold
Corynebacterium pilosum	strain=CIP103422	GCA_001044155.1	35756	35756	type	True	77.3318	128	811	95	below_threshold
Corynebacterium pilosum	strain=NCTC11862	GCA_900447205.1	35756	35756	type	True	77.304	129	811	95	below_threshold
Corynebacterium pilosum	strain=DSM 20521	GCA_000373805.1	35756	35756	type	True	77.2258	126	811	95	below_threshold
Rhodococcus ruber	strain=NBRC 15591	GCA_001894945.1	1830	1830	type	True	76.4654	96	811	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:20,498] [INFO] DFAST Taxonomy check result was written to GCF_008930985.1_ASM893098v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:20,499] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:20,499] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:20,499] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c53adca-1c2f-4f00-917b-bd2997a83e81/dqc_reference/checkm_data
[2024-01-24 13:49:20,500] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:20,528] [INFO] Task started: CheckM
[2024-01-24 13:49:20,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008930985.1_ASM893098v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008930985.1_ASM893098v1_genomic.fna/checkm_input GCF_008930985.1_ASM893098v1_genomic.fna/checkm_result
[2024-01-24 13:49:50,427] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:50,429] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:50,449] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:50,449] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:50,450] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008930985.1_ASM893098v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:50,450] [INFO] Task started: Blastn
[2024-01-24 13:49:50,450] [INFO] Running command: blastn -query GCF_008930985.1_ASM893098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c53adca-1c2f-4f00-917b-bd2997a83e81/dqc_reference/reference_markers_gtdb.fasta -out GCF_008930985.1_ASM893098v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:51,878] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:51,882] [INFO] Selected 19 target genomes.
[2024-01-24 13:49:51,882] [INFO] Target genome list was writen to GCF_008930985.1_ASM893098v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:51,913] [INFO] Task started: fastANI
[2024-01-24 13:49:51,913] [INFO] Running command: fastANI --query /var/lib/cwl/stgf809f027-8ea7-4aef-ace6-9b91ef1a676c/GCF_008930985.1_ASM893098v1_genomic.fna.gz --refList GCF_008930985.1_ASM893098v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008930985.1_ASM893098v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:00,750] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:00,766] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:00,766] [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_008930665.1	s__Corynebacterium sp008930665	99.9959	810	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.86	95.30	0.97	0.95	18	conclusive
GCF_000372385.1	s__Corynebacterium ciconiae	84.538	689	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000375365.1	s__Corynebacterium mastitidis	78.2374	184	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.64	96.64	0.96	0.96	2	-
GCF_000341345.1	s__Corynebacterium halotolerans	78.2019	214	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001941485.1	s__Corynebacterium frankenforstense	78.1078	196	811	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	78.0521	194	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.80	97.60	0.97	0.93	3	-
GCF_000550805.1	s__Corynebacterium vitaeruminis	78.0085	226	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.60	0.94	0.94	3	-
GCF_001807265.1	s__Corynebacterium sp001807265	77.9227	155	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.96	97.96	0.92	0.92	2	-
GCF_000011305.1	s__Corynebacterium efficiens	77.9166	177	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.90	99.90	0.99	0.99	2	-
GCF_009734425.1	s__Corynebacterium sp009734425	77.8731	183	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002861385.1	s__Corynebacterium aurimucosum_C	77.8501	163	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.04	96.50	0.91	0.89	28	-
GCF_015351335.1	s__Corynebacterium lipophilum	77.82	153	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001412085.1	s__Corynebacterium lowii	77.7127	157	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000835165.1	s__Corynebacterium marinum	77.6663	184	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.21	98.42	0.97	0.94	3	-
GCF_013978595.1	s__Corynebacterium haemomassiliense	77.6502	170	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176865.1	s__Corynebacterium fournieri	77.5233	159	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012838985.1	s__Corynebacterium sp012838985	77.3389	149	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001941505.1	s__Corynebacterium sphenisci	77.3262	183	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373805.1	s__Corynebacterium pilosum	77.2258	126	811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.98	99.96	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:00,768] [INFO] GTDB search result was written to GCF_008930985.1_ASM893098v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:00,769] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:00,777] [INFO] DFAST_QC result json was written to GCF_008930985.1_ASM893098v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:00,777] [INFO] DFAST_QC completed!
[2024-01-24 13:50:00,777] [INFO] Total running time: 0h1m1s