[2024-01-25 20:01:20,806] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:01:20,807] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:01:20,807] [INFO] DQC Reference Directory: /var/lib/cwl/stg35c0e502-8949-40ee-853f-876f76072c3d/dqc_reference
[2024-01-25 20:01:21,919] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:01:21,920] [INFO] Task started: Prodigal
[2024-01-25 20:01:21,920] [INFO] Running command: gunzip -c /var/lib/cwl/stg17f12cd2-c368-4d1a-8a66-6ac4f16add51/GCF_030440555.1_ASM3044055v1_genomic.fna.gz | prodigal -d GCF_030440555.1_ASM3044055v1_genomic.fna/cds.fna -a GCF_030440555.1_ASM3044055v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:01:26,009] [INFO] Task succeeded: Prodigal
[2024-01-25 20:01:26,010] [INFO] Task started: HMMsearch
[2024-01-25 20:01:26,010] [INFO] Running command: hmmsearch --tblout GCF_030440555.1_ASM3044055v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35c0e502-8949-40ee-853f-876f76072c3d/dqc_reference/reference_markers.hmm GCF_030440555.1_ASM3044055v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:01:26,210] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:01:26,211] [INFO] Found 6/6 markers.
[2024-01-25 20:01:26,230] [INFO] Query marker FASTA was written to GCF_030440555.1_ASM3044055v1_genomic.fna/markers.fasta
[2024-01-25 20:01:26,230] [INFO] Task started: Blastn
[2024-01-25 20:01:26,230] [INFO] Running command: blastn -query GCF_030440555.1_ASM3044055v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35c0e502-8949-40ee-853f-876f76072c3d/dqc_reference/reference_markers.fasta -out GCF_030440555.1_ASM3044055v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:26,917] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:26,920] [INFO] Selected 22 target genomes.
[2024-01-25 20:01:26,920] [INFO] Target genome list was writen to GCF_030440555.1_ASM3044055v1_genomic.fna/target_genomes.txt
[2024-01-25 20:01:26,935] [INFO] Task started: fastANI
[2024-01-25 20:01:26,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg17f12cd2-c368-4d1a-8a66-6ac4f16add51/GCF_030440555.1_ASM3044055v1_genomic.fna.gz --refList GCF_030440555.1_ASM3044055v1_genomic.fna/target_genomes.txt --output GCF_030440555.1_ASM3044055v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:01:34,616] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:34,616] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35c0e502-8949-40ee-853f-876f76072c3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:01:34,617] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35c0e502-8949-40ee-853f-876f76072c3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:01:34,627] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:01:34,627] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:01:34,627] [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 caspium	strain=DSM 44850	GCA_000379705.1	234828	234828	type	True	99.9909	610	621	95	conclusive
Corynebacterium crudilactis	strain=JZ16	GCA_001643015.1	1652495	1652495	type	True	79.0141	55	621	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032	GCA_000011325.1	1718	1718	type	True	79.0097	53	621	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032 substr. K051	GCA_000382905.1	1718	1718	type	True	78.9682	54	621	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032	GCA_011761195.1	1718	1718	type	True	78.9488	51	621	95	below_threshold
Corynebacterium renale	strain=DSM 20688	GCA_002563965.1	1724	1724	type	True	78.8884	61	621	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032	GCA_002847405.1	1718	1718	type	True	78.7206	55	621	95	below_threshold
Corynebacterium rouxii	strain=FRC0190	GCA_902702935.1	2719119	2719119	type	True	78.6484	50	621	95	below_threshold
Corynebacterium callunae	strain=DSM 20147	GCA_000344785.1	1721	1721	type	True	78.608	58	621	95	below_threshold
Corynebacterium kutscheri	strain=DSM 20755	GCA_000980835.1	35755	35755	type	True	78.4019	51	621	95	below_threshold
Corynebacterium renale	strain=NCTC7448	GCA_900478035.1	1724	1724	type	True	78.3345	63	621	95	below_threshold
Corynebacterium kutscheri	strain=NCTC11138	GCA_900637605.1	35755	35755	type	True	78.2384	50	621	95	below_threshold
Corynebacterium callunae	strain=DSM 20147	GCA_000420585.1	1721	1721	type	True	77.1668	55	621	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:01:34,629] [INFO] DFAST Taxonomy check result was written to GCF_030440555.1_ASM3044055v1_genomic.fna/tc_result.tsv
[2024-01-25 20:01:34,629] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:01:34,629] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:01:34,629] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35c0e502-8949-40ee-853f-876f76072c3d/dqc_reference/checkm_data
[2024-01-25 20:01:34,630] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:01:34,653] [INFO] Task started: CheckM
[2024-01-25 20:01:34,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030440555.1_ASM3044055v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030440555.1_ASM3044055v1_genomic.fna/checkm_input GCF_030440555.1_ASM3044055v1_genomic.fna/checkm_result
[2024-01-25 20:01:52,134] [INFO] Task succeeded: CheckM
[2024-01-25 20:01:52,135] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:01:52,199] [INFO] ===== Completeness check finished =====
[2024-01-25 20:01:52,199] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:01:52,199] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030440555.1_ASM3044055v1_genomic.fna/markers.fasta)
[2024-01-25 20:01:52,199] [INFO] Task started: Blastn
[2024-01-25 20:01:52,200] [INFO] Running command: blastn -query GCF_030440555.1_ASM3044055v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35c0e502-8949-40ee-853f-876f76072c3d/dqc_reference/reference_markers_gtdb.fasta -out GCF_030440555.1_ASM3044055v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:53,180] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:53,183] [INFO] Selected 22 target genomes.
[2024-01-25 20:01:53,183] [INFO] Target genome list was writen to GCF_030440555.1_ASM3044055v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:01:53,199] [INFO] Task started: fastANI
[2024-01-25 20:01:53,199] [INFO] Running command: fastANI --query /var/lib/cwl/stg17f12cd2-c368-4d1a-8a66-6ac4f16add51/GCF_030440555.1_ASM3044055v1_genomic.fna.gz --refList GCF_030440555.1_ASM3044055v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030440555.1_ASM3044055v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:02:01,799] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:01,804] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:02:01,805] [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_000379705.1	s__Corynebacterium caspium	99.9909	610	621	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_000011325.1	s__Corynebacterium glutamicum	79.3291	54	621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.67	97.34	0.92	0.85	76	-
GCF_000980835.1	s__Corynebacterium kutscheri	78.9647	51	621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.70	99.55	0.99	0.98	4	-
GCF_001643015.1	s__Corynebacterium crudilactis	78.8014	53	621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355155.1	s__Corynebacterium suranareeae	78.6002	52	621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902702935.1	s__Corynebacterium rouxii	78.526	51	621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000344785.1	s__Corynebacterium callunae	78.5176	59	621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002563965.1	s__Corynebacterium renale	77.9725	59	621	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.02	98.07	0.97	0.94	5	-
--------------------------------------------------------------------------------
[2024-01-25 20:02:01,806] [INFO] GTDB search result was written to GCF_030440555.1_ASM3044055v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:02:01,806] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:02:01,809] [INFO] DFAST_QC result json was written to GCF_030440555.1_ASM3044055v1_genomic.fna/dqc_result.json
[2024-01-25 20:02:01,809] [INFO] DFAST_QC completed!
[2024-01-25 20:02:01,809] [INFO] Total running time: 0h0m41s