[2024-01-25 18:51:50,585] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:51:50,588] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:51:50,589] [INFO] DQC Reference Directory: /var/lib/cwl/stg25c01839-6916-4081-bed9-a48e0603840b/dqc_reference
[2024-01-25 18:51:51,737] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:51:51,738] [INFO] Task started: Prodigal
[2024-01-25 18:51:51,738] [INFO] Running command: gunzip -c /var/lib/cwl/stg04f3896a-0f08-4792-85d0-685818fb9422/GCF_016127975.1_ASM1612797v1_genomic.fna.gz | prodigal -d GCF_016127975.1_ASM1612797v1_genomic.fna/cds.fna -a GCF_016127975.1_ASM1612797v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:51:58,159] [INFO] Task succeeded: Prodigal
[2024-01-25 18:51:58,159] [INFO] Task started: HMMsearch
[2024-01-25 18:51:58,159] [INFO] Running command: hmmsearch --tblout GCF_016127975.1_ASM1612797v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25c01839-6916-4081-bed9-a48e0603840b/dqc_reference/reference_markers.hmm GCF_016127975.1_ASM1612797v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:51:58,354] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:51:58,355] [INFO] Found 6/6 markers.
[2024-01-25 18:51:58,374] [INFO] Query marker FASTA was written to GCF_016127975.1_ASM1612797v1_genomic.fna/markers.fasta
[2024-01-25 18:51:58,375] [INFO] Task started: Blastn
[2024-01-25 18:51:58,375] [INFO] Running command: blastn -query GCF_016127975.1_ASM1612797v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25c01839-6916-4081-bed9-a48e0603840b/dqc_reference/reference_markers.fasta -out GCF_016127975.1_ASM1612797v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:59,281] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:59,284] [INFO] Selected 11 target genomes.
[2024-01-25 18:51:59,284] [INFO] Target genome list was writen to GCF_016127975.1_ASM1612797v1_genomic.fna/target_genomes.txt
[2024-01-25 18:51:59,293] [INFO] Task started: fastANI
[2024-01-25 18:51:59,293] [INFO] Running command: fastANI --query /var/lib/cwl/stg04f3896a-0f08-4792-85d0-685818fb9422/GCF_016127975.1_ASM1612797v1_genomic.fna.gz --refList GCF_016127975.1_ASM1612797v1_genomic.fna/target_genomes.txt --output GCF_016127975.1_ASM1612797v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:52:04,897] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:04,897] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25c01839-6916-4081-bed9-a48e0603840b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:52:04,897] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25c01839-6916-4081-bed9-a48e0603840b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:52:04,905] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:52:04,905] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:52:04,905] [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 urealyticum	strain=FDAARGOS_994	GCA_016127975.1	43771	43771	type	True	100.0	794	794	95	conclusive
Corynebacterium urealyticum	strain=NCTC12011	GCA_900187235.1	43771	43771	type	True	99.9997	791	794	95	conclusive
Corynebacterium urealyticum	strain=DSM 7109	GCA_000069945.1	43771	43771	type	True	99.9869	788	794	95	conclusive
Corynebacterium jeikeium	strain=NCTC11913	GCA_900461185.1	38289	38289	suspected-type	True	81.2335	324	794	95	below_threshold
Corynebacterium jeikeium	strain=ATCC 43734	GCA_000163435.1	38289	38289	suspected-type	True	80.5182	304	794	95	below_threshold
Corynebacterium falsenii	strain=FDAARGOS_1494	GCA_020099275.1	108486	108486	type	True	78.9937	287	794	95	below_threshold
Corynebacterium bovis	strain=DSM 20582	GCA_014191555.1	36808	36808	type	True	78.6575	252	794	95	below_threshold
Corynebacterium bovis	strain=FDAARGOS_1052	GCA_016128075.1	36808	36808	type	True	78.6255	251	794	95	below_threshold
Corynebacterium halotolerans	strain=YIM 70093 = DSM 44683	GCA_000341345.1	225326	225326	type	True	78.4794	250	794	95	below_threshold
Corynebacterium halotolerans	strain=DSM 44683	GCA_000688435.1	225326	225326	type	True	78.3084	234	794	95	below_threshold
Corynebacterium suicordis	strain=DSM 45110	GCA_015351405.1	203264	203264	type	True	78.0499	208	794	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:52:04,907] [INFO] DFAST Taxonomy check result was written to GCF_016127975.1_ASM1612797v1_genomic.fna/tc_result.tsv
[2024-01-25 18:52:04,907] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:52:04,907] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:52:04,907] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25c01839-6916-4081-bed9-a48e0603840b/dqc_reference/checkm_data
[2024-01-25 18:52:04,908] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:52:04,934] [INFO] Task started: CheckM
[2024-01-25 18:52:04,935] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016127975.1_ASM1612797v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016127975.1_ASM1612797v1_genomic.fna/checkm_input GCF_016127975.1_ASM1612797v1_genomic.fna/checkm_result
[2024-01-25 18:52:27,290] [INFO] Task succeeded: CheckM
[2024-01-25 18:52:27,291] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:52:27,305] [INFO] ===== Completeness check finished =====
[2024-01-25 18:52:27,305] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:52:27,306] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016127975.1_ASM1612797v1_genomic.fna/markers.fasta)
[2024-01-25 18:52:27,306] [INFO] Task started: Blastn
[2024-01-25 18:52:27,306] [INFO] Running command: blastn -query GCF_016127975.1_ASM1612797v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25c01839-6916-4081-bed9-a48e0603840b/dqc_reference/reference_markers_gtdb.fasta -out GCF_016127975.1_ASM1612797v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:28,672] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:28,675] [INFO] Selected 12 target genomes.
[2024-01-25 18:52:28,675] [INFO] Target genome list was writen to GCF_016127975.1_ASM1612797v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:52:28,689] [INFO] Task started: fastANI
[2024-01-25 18:52:28,689] [INFO] Running command: fastANI --query /var/lib/cwl/stg04f3896a-0f08-4792-85d0-685818fb9422/GCF_016127975.1_ASM1612797v1_genomic.fna.gz --refList GCF_016127975.1_ASM1612797v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016127975.1_ASM1612797v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:52:34,430] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:34,439] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:52:34,439] [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_000069945.1	s__Corynebacterium urealyticum	99.9869	788	794	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.66	97.50	0.94	0.89	9	conclusive
GCF_001815985.1	s__Corynebacterium sp001815985	93.9996	676	794	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.95	96.87	0.95	0.94	3	-
GCA_019120635.1	s__Corynebacterium intestinavium	92.3565	547	794	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000738175.1	s__Corynebacterium jeikeium_C	80.6545	318	794	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001807485.1	s__Corynebacterium sp001807485	79.7797	306	794	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.83	97.75	0.93	0.93	3	-
GCF_000738265.1	s__Corynebacterium jeikeium_A	79.5892	292	794	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.92	97.52	0.95	0.93	11	-
GCA_019114135.1	s__Corynebacterium avicola	78.6116	269	794	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000183325.1	s__Corynebacterium bovis	78.6102	212	794	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.01	98.42	0.92	0.83	23	-
GCF_000341345.1	s__Corynebacterium halotolerans	78.495	249	794	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	78.2255	180	794	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	78.2007	182	794	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.29	96.29	0.86	0.86	2	-
GCF_015351405.1	s__Corynebacterium sp015351405	78.0499	208	794	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 18:52:34,442] [INFO] GTDB search result was written to GCF_016127975.1_ASM1612797v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:52:34,443] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:52:34,446] [INFO] DFAST_QC result json was written to GCF_016127975.1_ASM1612797v1_genomic.fna/dqc_result.json
[2024-01-25 18:52:34,446] [INFO] DFAST_QC completed!
[2024-01-25 18:52:34,446] [INFO] Total running time: 0h0m44s