[2024-01-24 12:53:55,279] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:55,282] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:55,282] [INFO] DQC Reference Directory: /var/lib/cwl/stg944dc25e-603f-42da-8dd0-8fe75feb50cf/dqc_reference
[2024-01-24 12:53:56,558] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:56,570] [INFO] Task started: Prodigal
[2024-01-24 12:53:56,571] [INFO] Running command: gunzip -c /var/lib/cwl/stg9346e5a2-7440-4303-9381-ccec36d9f747/GCF_019633635.1_ASM1963363v1_genomic.fna.gz | prodigal -d GCF_019633635.1_ASM1963363v1_genomic.fna/cds.fna -a GCF_019633635.1_ASM1963363v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:05,559] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:05,559] [INFO] Task started: HMMsearch
[2024-01-24 12:54:05,560] [INFO] Running command: hmmsearch --tblout GCF_019633635.1_ASM1963363v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg944dc25e-603f-42da-8dd0-8fe75feb50cf/dqc_reference/reference_markers.hmm GCF_019633635.1_ASM1963363v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:05,763] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:05,764] [INFO] Found 6/6 markers.
[2024-01-24 12:54:05,789] [INFO] Query marker FASTA was written to GCF_019633635.1_ASM1963363v1_genomic.fna/markers.fasta
[2024-01-24 12:54:05,789] [INFO] Task started: Blastn
[2024-01-24 12:54:05,790] [INFO] Running command: blastn -query GCF_019633635.1_ASM1963363v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg944dc25e-603f-42da-8dd0-8fe75feb50cf/dqc_reference/reference_markers.fasta -out GCF_019633635.1_ASM1963363v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:06,624] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:06,630] [INFO] Selected 10 target genomes.
[2024-01-24 12:54:06,631] [INFO] Target genome list was writen to GCF_019633635.1_ASM1963363v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:06,641] [INFO] Task started: fastANI
[2024-01-24 12:54:06,641] [INFO] Running command: fastANI --query /var/lib/cwl/stg9346e5a2-7440-4303-9381-ccec36d9f747/GCF_019633635.1_ASM1963363v1_genomic.fna.gz --refList GCF_019633635.1_ASM1963363v1_genomic.fna/target_genomes.txt --output GCF_019633635.1_ASM1963363v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:11,860] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:11,860] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg944dc25e-603f-42da-8dd0-8fe75feb50cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:11,861] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg944dc25e-603f-42da-8dd0-8fe75feb50cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:11,870] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:54:11,870] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:11,870] [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 glucuronolyticum	strain=DSM 44120	GCA_900176155.1	39791	39791	type	True	100.0	921	922	95	conclusive
Corynebacterium glucuronolyticum	strain=DSM 44120	GCA_019633635.1	39791	39791	type	True	100.0	921	922	95	conclusive
Corynebacterium glucuronolyticum	strain=FDAARGOS_1053	GCA_016127395.1	39791	39791	type	True	99.9929	922	922	95	conclusive
Corynebacterium pyruviciproducens	strain=ATCC BAA-1742	GCA_000411375.1	598660	598660	type	True	82.6535	526	922	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	78.2453	164	922	95	below_threshold
Corynebacterium jeddahense	strain=JCB	GCA_000577555.1	1414719	1414719	type	True	77.9635	128	922	95	below_threshold
Corynebacterium gottingense	strain=DSM 103494	GCA_003693265.1	2041036	2041036	type	True	77.9192	115	922	95	below_threshold
Corynebacterium bouchesdurhonense	strain=SN14	GCA_900078305.2	1720192	1720192	type	True	77.6364	124	922	95	below_threshold
Corynebacterium frankenforstense	strain=ST18	GCA_001941485.1	1230998	1230998	type	True	77.6147	177	922	95	below_threshold
Gordonia humi	strain=DSM 45298	GCA_014197435.1	686429	686429	type	True	76.1037	55	922	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:11,872] [INFO] DFAST Taxonomy check result was written to GCF_019633635.1_ASM1963363v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:11,873] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:11,873] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:11,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg944dc25e-603f-42da-8dd0-8fe75feb50cf/dqc_reference/checkm_data
[2024-01-24 12:54:11,874] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:11,903] [INFO] Task started: CheckM
[2024-01-24 12:54:11,904] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019633635.1_ASM1963363v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019633635.1_ASM1963363v1_genomic.fna/checkm_input GCF_019633635.1_ASM1963363v1_genomic.fna/checkm_result
[2024-01-24 12:54:41,298] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:41,299] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:41,316] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:41,316] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:41,316] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019633635.1_ASM1963363v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:41,317] [INFO] Task started: Blastn
[2024-01-24 12:54:41,317] [INFO] Running command: blastn -query GCF_019633635.1_ASM1963363v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg944dc25e-603f-42da-8dd0-8fe75feb50cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_019633635.1_ASM1963363v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:42,519] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:42,523] [INFO] Selected 21 target genomes.
[2024-01-24 12:54:42,523] [INFO] Target genome list was writen to GCF_019633635.1_ASM1963363v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:42,542] [INFO] Task started: fastANI
[2024-01-24 12:54:42,543] [INFO] Running command: fastANI --query /var/lib/cwl/stg9346e5a2-7440-4303-9381-ccec36d9f747/GCF_019633635.1_ASM1963363v1_genomic.fna.gz --refList GCF_019633635.1_ASM1963363v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019633635.1_ASM1963363v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:51,712] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:51,727] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:51,727] [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_900176155.1	s__Corynebacterium glucuronolyticum	100.0	921	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.97	98.66	0.94	0.91	8	conclusive
GCF_000411375.1	s__Corynebacterium pyruviciproducens	82.6379	527	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.67	97.67	0.91	0.91	2	-
GCF_000550805.1	s__Corynebacterium vitaeruminis	78.2453	164	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.60	0.94	0.94	3	-
GCF_000819445.1	s__Corynebacterium humireducens	77.9612	145	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.80	97.60	0.97	0.93	3	-
GCF_000577555.1	s__Corynebacterium jeddahense	77.9378	129	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003693265.1	s__Corynebacterium gottingense	77.9192	115	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.52	97.05	0.92	0.90	11	-
GCF_015351335.1	s__Corynebacterium lipophilum	77.8602	121	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001807265.1	s__Corynebacterium sp001807265	77.8205	124	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.96	97.96	0.92	0.92	2	-
GCF_000980815.1	s__Corynebacterium camporealensis	77.7984	96	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.96	99.96	1.00	1.00	2	-
GCA_900156035.1	s__Corynebacterium afermentans	77.7306	127	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.27	97.60	0.93	0.89	5	-
GCF_900177745.1	s__Corynebacterium pollutisoli	77.6479	161	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.83	98.83	0.98	0.98	2	-
GCF_900156665.1	s__Corynebacterium appendicis	77.6421	121	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001941485.1	s__Corynebacterium frankenforstense	77.6308	176	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078305.2	s__Corynebacterium bouchesdurhonense	77.6111	125	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCA_002339505.1	s__Corynebacterium sp002339505	77.5938	107	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000372385.1	s__Corynebacterium ciconiae	77.5653	93	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002994655.1	s__Corynebacterium sp002994655	77.4147	129	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539825.1	s__Corynebacterium variabile	77.2683	101	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.53	98.15	0.92	0.86	8	-
GCF_000375365.1	s__Corynebacterium mastitidis	77.0378	136	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.64	96.64	0.96	0.96	2	-
GCF_014197435.1	s__Gordonia humi	76.1037	55	922	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:51,729] [INFO] GTDB search result was written to GCF_019633635.1_ASM1963363v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:51,730] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:51,734] [INFO] DFAST_QC result json was written to GCF_019633635.1_ASM1963363v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:51,734] [INFO] DFAST_QC completed!
[2024-01-24 12:54:51,734] [INFO] Total running time: 0h0m56s