[2024-01-24 13:21:40,976] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:40,979] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:40,979] [INFO] DQC Reference Directory: /var/lib/cwl/stg185c385b-4f9b-4036-b198-22cd11b2c143/dqc_reference
[2024-01-24 13:21:42,262] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:42,263] [INFO] Task started: Prodigal
[2024-01-24 13:21:42,263] [INFO] Running command: gunzip -c /var/lib/cwl/stgb46eca23-4b2e-4859-b218-592600e8f945/GCF_003813965.1_ASM381396v1_genomic.fna.gz | prodigal -d GCF_003813965.1_ASM381396v1_genomic.fna/cds.fna -a GCF_003813965.1_ASM381396v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:57,629] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:57,630] [INFO] Task started: HMMsearch
[2024-01-24 13:21:57,630] [INFO] Running command: hmmsearch --tblout GCF_003813965.1_ASM381396v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg185c385b-4f9b-4036-b198-22cd11b2c143/dqc_reference/reference_markers.hmm GCF_003813965.1_ASM381396v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:57,833] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:57,834] [INFO] Found 6/6 markers.
[2024-01-24 13:21:57,858] [INFO] Query marker FASTA was written to GCF_003813965.1_ASM381396v1_genomic.fna/markers.fasta
[2024-01-24 13:21:57,858] [INFO] Task started: Blastn
[2024-01-24 13:21:57,859] [INFO] Running command: blastn -query GCF_003813965.1_ASM381396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg185c385b-4f9b-4036-b198-22cd11b2c143/dqc_reference/reference_markers.fasta -out GCF_003813965.1_ASM381396v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:58,583] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:58,586] [INFO] Selected 22 target genomes.
[2024-01-24 13:21:58,587] [INFO] Target genome list was writen to GCF_003813965.1_ASM381396v1_genomic.fna/target_genomes.txt
[2024-01-24 13:21:58,599] [INFO] Task started: fastANI
[2024-01-24 13:21:58,599] [INFO] Running command: fastANI --query /var/lib/cwl/stgb46eca23-4b2e-4859-b218-592600e8f945/GCF_003813965.1_ASM381396v1_genomic.fna.gz --refList GCF_003813965.1_ASM381396v1_genomic.fna/target_genomes.txt --output GCF_003813965.1_ASM381396v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:11,117] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:11,118] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg185c385b-4f9b-4036-b198-22cd11b2c143/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:11,118] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg185c385b-4f9b-4036-b198-22cd11b2c143/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:11,139] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:11,139] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:11,139] [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 choanae	strain=200CH	GCA_003813965.1	1862358	1862358	type	True	100.0	995	995	95	conclusive
Corynebacterium diphtheriae		GCA_902809765.1	1717	1717	type	True	79.6386	52	995	95	below_threshold
Corynebacterium efficiens	strain=YS-314	GCA_000011305.1	152794	152794	type	True	79.0733	57	995	95	below_threshold
Corynebacterium aquilae	strain=S-613	GCA_001941445.1	203263	203263	type	True	78.8191	96	995	95	below_threshold
Corynebacterium pseudopelargi	strain=812CH	GCA_003814005.1	2080757	2080757	type	True	78.7502	76	995	95	below_threshold
Corynebacterium lujinxingii	strain=zg-917	GCA_014490555.1	2763010	2763010	type	True	78.7021	51	995	95	below_threshold
Corynebacterium humireducens	strain=DSM 45392	GCA_000819445.1	1223514	1223514	type	True	78.5564	62	995	95	below_threshold
Corynebacterium pelargi	strain=136/3	GCA_004114895.1	1471400	1471400	type	True	78.2603	80	995	95	below_threshold
Corynebacterium efficiens	strain=YS-314	GCA_000160795.1	152794	152794	type	True	77.7526	55	995	95	below_threshold
Corynebacterium pelargi	strain=CCM 8517	GCA_014635485.1	1471400	1471400	type	True	77.2659	74	995	95	below_threshold
Corynebacterium ciconiae	strain=DSM 44920	GCA_000372385.1	227319	227319	type	True	77.0776	80	995	95	below_threshold
Corynebacterium spheniscorum	strain=CCUG 45512	GCA_008693095.1	185761	185761	type	True	77.0333	64	995	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	76.9593	55	995	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:11,146] [INFO] DFAST Taxonomy check result was written to GCF_003813965.1_ASM381396v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:11,147] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:11,147] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:11,147] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg185c385b-4f9b-4036-b198-22cd11b2c143/dqc_reference/checkm_data
[2024-01-24 13:22:11,149] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:11,179] [INFO] Task started: CheckM
[2024-01-24 13:22:11,179] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003813965.1_ASM381396v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003813965.1_ASM381396v1_genomic.fna/checkm_input GCF_003813965.1_ASM381396v1_genomic.fna/checkm_result
[2024-01-24 13:22:59,238] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:59,239] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:59,256] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:59,256] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:59,257] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003813965.1_ASM381396v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:59,257] [INFO] Task started: Blastn
[2024-01-24 13:22:59,257] [INFO] Running command: blastn -query GCF_003813965.1_ASM381396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg185c385b-4f9b-4036-b198-22cd11b2c143/dqc_reference/reference_markers_gtdb.fasta -out GCF_003813965.1_ASM381396v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:00,378] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:00,381] [INFO] Selected 22 target genomes.
[2024-01-24 13:23:00,382] [INFO] Target genome list was writen to GCF_003813965.1_ASM381396v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:00,396] [INFO] Task started: fastANI
[2024-01-24 13:23:00,396] [INFO] Running command: fastANI --query /var/lib/cwl/stgb46eca23-4b2e-4859-b218-592600e8f945/GCF_003813965.1_ASM381396v1_genomic.fna.gz --refList GCF_003813965.1_ASM381396v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003813965.1_ASM381396v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:12,263] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:12,277] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:12,278] [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_003813965.1	s__Corynebacterium choanae	100.0	995	995	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_001457455.1	s__Corynebacterium diphtheriae	79.7578	53	995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.05	95.03	0.92	0.83	346	-
GCF_000011305.1	s__Corynebacterium efficiens	79.0923	58	995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.90	99.90	0.99	0.99	2	-
GCF_014490555.1	s__Corynebacterium sp014490555	78.8406	52	995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	0.99	3	-
GCF_001941445.1	s__Corynebacterium aquilae	78.445	93	995	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	78.3745	61	995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.80	97.60	0.97	0.93	3	-
GCF_001586215.1	s__Corynebacterium simulans	78.2786	53	995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.78	97.47	0.94	0.92	11	-
GCF_000738175.1	s__Corynebacterium jeikeium_C	78.2214	54	995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114895.1	s__Corynebacterium pelargi	78.0811	79	995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017307055.1	s__Corynebacterium sp017307055	77.7894	144	995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000988205.1	s__Corynebacterium minutissimum_A	77.6384	50	995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.53	96.09	0.91	0.89	16	-
GCF_002994655.1	s__Corynebacterium sp002994655	77.4092	87	995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016342265.1	s__Corynebacterium sp016342265	77.1463	75	995	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	77.0776	80	995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113445.1	s__Corynebacterium spheniscorum	76.9763	64	995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:12,280] [INFO] GTDB search result was written to GCF_003813965.1_ASM381396v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:12,281] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:12,297] [INFO] DFAST_QC result json was written to GCF_003813965.1_ASM381396v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:12,298] [INFO] DFAST_QC completed!
[2024-01-24 13:23:12,298] [INFO] Total running time: 0h1m31s