[2024-01-24 11:35:11,720] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:11,727] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:11,728] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e0c4fee-44d4-4977-bc4a-7767e65d1f29/dqc_reference
[2024-01-24 11:35:13,038] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:13,039] [INFO] Task started: Prodigal
[2024-01-24 11:35:13,040] [INFO] Running command: gunzip -c /var/lib/cwl/stg7902355c-4bde-428c-81da-5fdc89d45de5/GCF_016728665.1_ASM1672866v1_genomic.fna.gz | prodigal -d GCF_016728665.1_ASM1672866v1_genomic.fna/cds.fna -a GCF_016728665.1_ASM1672866v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:21,181] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:21,181] [INFO] Task started: HMMsearch
[2024-01-24 11:35:21,181] [INFO] Running command: hmmsearch --tblout GCF_016728665.1_ASM1672866v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e0c4fee-44d4-4977-bc4a-7767e65d1f29/dqc_reference/reference_markers.hmm GCF_016728665.1_ASM1672866v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:21,403] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:21,405] [INFO] Found 6/6 markers.
[2024-01-24 11:35:21,431] [INFO] Query marker FASTA was written to GCF_016728665.1_ASM1672866v1_genomic.fna/markers.fasta
[2024-01-24 11:35:21,432] [INFO] Task started: Blastn
[2024-01-24 11:35:21,432] [INFO] Running command: blastn -query GCF_016728665.1_ASM1672866v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e0c4fee-44d4-4977-bc4a-7767e65d1f29/dqc_reference/reference_markers.fasta -out GCF_016728665.1_ASM1672866v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:22,309] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:22,312] [INFO] Selected 11 target genomes.
[2024-01-24 11:35:22,312] [INFO] Target genome list was writen to GCF_016728665.1_ASM1672866v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:22,333] [INFO] Task started: fastANI
[2024-01-24 11:35:22,333] [INFO] Running command: fastANI --query /var/lib/cwl/stg7902355c-4bde-428c-81da-5fdc89d45de5/GCF_016728665.1_ASM1672866v1_genomic.fna.gz --refList GCF_016728665.1_ASM1672866v1_genomic.fna/target_genomes.txt --output GCF_016728665.1_ASM1672866v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:28,098] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:28,099] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e0c4fee-44d4-4977-bc4a-7767e65d1f29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:28,099] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e0c4fee-44d4-4977-bc4a-7767e65d1f29/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:28,109] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:28,109] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:28,109] [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 propinquum	strain=FDAARGOS_1112	GCA_016728665.1	43769	43769	type	True	100.0	825	826	95	conclusive
Corynebacterium propinquum	strain=DSM 44285	GCA_000375525.1	43769	43769	type	True	99.9821	803	826	95	conclusive
Corynebacterium pseudodiphtheriticum	strain=DSM 44287	GCA_000688415.1	37637	37637	type	True	86.062	576	826	95	below_threshold
Corynebacterium striatum	strain=FDAARGOS_1054	GCA_016403285.1	43770	43770	type	True	78.5374	120	826	95	below_threshold
Corynebacterium lizhenjunii	strain=ZJ-599	GCA_011038655.2	2709394	2709394	type	True	78.4928	85	826	95	below_threshold
Corynebacterium striatum	strain=NBRC 15291	GCA_006538485.1	43770	43770	type	True	78.4909	116	826	95	below_threshold
Corynebacterium camporealensis	strain=DSM 44610	GCA_000980815.1	161896	161896	type	True	78.3429	120	826	95	below_threshold
Corynebacterium camporealensis	strain=CIP 105508	GCA_000766885.2	161896	161896	type	True	78.1913	123	826	95	below_threshold
Corynebacterium yudongzhengii	strain=2183	GCA_003065405.1	2080740	2080740	type	True	77.7936	102	826	95	below_threshold
Corynebacterium aurimucosum	strain=FDAARGOS_1109	GCA_016728705.1	169292	169292	suspected-type	True	77.7284	115	826	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:28,111] [INFO] DFAST Taxonomy check result was written to GCF_016728665.1_ASM1672866v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:28,111] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:28,112] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:28,112] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e0c4fee-44d4-4977-bc4a-7767e65d1f29/dqc_reference/checkm_data
[2024-01-24 11:35:28,113] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:28,140] [INFO] Task started: CheckM
[2024-01-24 11:35:28,140] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016728665.1_ASM1672866v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016728665.1_ASM1672866v1_genomic.fna/checkm_input GCF_016728665.1_ASM1672866v1_genomic.fna/checkm_result
[2024-01-24 11:35:57,118] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:57,119] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:57,138] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:57,139] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:57,139] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016728665.1_ASM1672866v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:57,140] [INFO] Task started: Blastn
[2024-01-24 11:35:57,140] [INFO] Running command: blastn -query GCF_016728665.1_ASM1672866v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e0c4fee-44d4-4977-bc4a-7767e65d1f29/dqc_reference/reference_markers_gtdb.fasta -out GCF_016728665.1_ASM1672866v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:58,300] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:58,304] [INFO] Selected 17 target genomes.
[2024-01-24 11:35:58,305] [INFO] Target genome list was writen to GCF_016728665.1_ASM1672866v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:58,319] [INFO] Task started: fastANI
[2024-01-24 11:35:58,320] [INFO] Running command: fastANI --query /var/lib/cwl/stg7902355c-4bde-428c-81da-5fdc89d45de5/GCF_016728665.1_ASM1672866v1_genomic.fna.gz --refList GCF_016728665.1_ASM1672866v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016728665.1_ASM1672866v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:06,993] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:07,005] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:07,006] [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_000375525.1	s__Corynebacterium propinquum	99.9821	803	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.98	97.48	0.95	0.92	13	conclusive
GCF_000688415.1	s__Corynebacterium pseudodiphtheriticum	86.0468	577	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.46	98.41	0.95	0.91	10	-
GCF_000478175.1	s__Corynebacterium sp000478175	79.1658	128	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.95	99.95	0.99	0.98	3	-
GCF_001586215.1	s__Corynebacterium simulans	78.5776	114	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.78	97.47	0.94	0.92	11	-
GCF_011038655.2	s__Corynebacterium lizhenjunii	78.5446	85	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.69	98.69	0.97	0.97	2	-
GCF_000069945.1	s__Corynebacterium urealyticum	78.4589	66	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.66	97.50	0.94	0.89	9	-
GCF_000022905.1	s__Corynebacterium aurimucosum	78.2235	119	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCF_000980815.1	s__Corynebacterium camporealensis	78.2175	119	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.96	99.96	1.00	1.00	2	-
GCF_000159135.1	s__Corynebacterium striatum	77.8538	102	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.44	95.19	0.92	0.85	41	-
GCF_016728705.1	s__Corynebacterium sp001807205	77.7993	116	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.15	96.83	0.93	0.90	8	-
GCF_003065405.1	s__Corynebacterium yudongzhengii	77.7936	102	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001836165.1	s__Corynebacterium sp001836165	77.6487	112	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.96	97.92	0.93	0.93	3	-
GCF_000420605.1	s__Corynebacterium massiliense	77.4961	93	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017942225.1	s__Corynebacterium sp017942225	77.2069	79	826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:07,007] [INFO] GTDB search result was written to GCF_016728665.1_ASM1672866v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:07,008] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:07,011] [INFO] DFAST_QC result json was written to GCF_016728665.1_ASM1672866v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:07,011] [INFO] DFAST_QC completed!
[2024-01-24 11:36:07,011] [INFO] Total running time: 0h0m55s