[2024-01-25 19:53:05,545] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:53:05,547] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:53:05,547] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b52d006-3345-47be-b8c3-e7e446df2a51/dqc_reference
[2024-01-25 19:53:06,668] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:53:06,668] [INFO] Task started: Prodigal
[2024-01-25 19:53:06,669] [INFO] Running command: gunzip -c /var/lib/cwl/stga77f4180-e0fa-434c-acdd-5b2f075bf057/GCF_014635485.1_ASM1463548v1_genomic.fna.gz | prodigal -d GCF_014635485.1_ASM1463548v1_genomic.fna/cds.fna -a GCF_014635485.1_ASM1463548v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:53:13,874] [INFO] Task succeeded: Prodigal
[2024-01-25 19:53:13,875] [INFO] Task started: HMMsearch
[2024-01-25 19:53:13,875] [INFO] Running command: hmmsearch --tblout GCF_014635485.1_ASM1463548v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b52d006-3345-47be-b8c3-e7e446df2a51/dqc_reference/reference_markers.hmm GCF_014635485.1_ASM1463548v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:53:14,056] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:53:14,057] [INFO] Found 6/6 markers.
[2024-01-25 19:53:14,077] [INFO] Query marker FASTA was written to GCF_014635485.1_ASM1463548v1_genomic.fna/markers.fasta
[2024-01-25 19:53:14,077] [INFO] Task started: Blastn
[2024-01-25 19:53:14,077] [INFO] Running command: blastn -query GCF_014635485.1_ASM1463548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b52d006-3345-47be-b8c3-e7e446df2a51/dqc_reference/reference_markers.fasta -out GCF_014635485.1_ASM1463548v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:14,799] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:14,801] [INFO] Selected 14 target genomes.
[2024-01-25 19:53:14,802] [INFO] Target genome list was writen to GCF_014635485.1_ASM1463548v1_genomic.fna/target_genomes.txt
[2024-01-25 19:53:14,807] [INFO] Task started: fastANI
[2024-01-25 19:53:14,807] [INFO] Running command: fastANI --query /var/lib/cwl/stga77f4180-e0fa-434c-acdd-5b2f075bf057/GCF_014635485.1_ASM1463548v1_genomic.fna.gz --refList GCF_014635485.1_ASM1463548v1_genomic.fna/target_genomes.txt --output GCF_014635485.1_ASM1463548v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:53:22,323] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:22,324] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b52d006-3345-47be-b8c3-e7e446df2a51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:53:22,324] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b52d006-3345-47be-b8c3-e7e446df2a51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:53:22,332] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:53:22,333] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:53:22,333] [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 pelargi	strain=CCM 8517	GCA_014635485.1	1471400	1471400	type	True	100.0	778	778	95	conclusive
Corynebacterium pelargi	strain=136/3	GCA_004114895.1	1471400	1471400	type	True	99.9955	778	778	95	conclusive
Corynebacterium pseudopelargi	strain=812CH	GCA_003814005.1	2080757	2080757	type	True	89.6674	704	778	95	below_threshold
Corynebacterium gerontici	strain=W8	GCA_003813985.1	2079234	2079234	type	True	81.8919	435	778	95	below_threshold
Corynebacterium vitaeruminis	strain=DSM 20294	GCA_000550805.1	38305	38305	type	True	78.6164	197	778	95	below_threshold
Corynebacterium diphtheriae	strain=DSM 44123	GCA_001913265.1	1717	1717	type	True	77.9669	117	778	95	below_threshold
Corynebacterium efficiens	strain=YS-314	GCA_000011305.1	152794	152794	type	True	77.8519	155	778	95	below_threshold
Corynebacterium efficiens	strain=YS-314	GCA_000160795.1	152794	152794	type	True	77.7678	158	778	95	below_threshold
Corynebacterium pollutisoli	strain=VDS11	GCA_900177745.1	1610489	1610489	type	True	77.7177	144	778	95	below_threshold
Corynebacterium ureicelerivorans	strain=IMMIB RIV-2301	GCA_000747315.1	401472	401472	type	True	77.3298	108	778	95	below_threshold
Corynebacterium mucifaciens	strain=ATCC 700355	GCA_012396315.1	57171	57171	type	True	77.2991	105	778	95	below_threshold
Corynebacterium resistens	strain=DSM 45100	GCA_000177535.2	258224	258224	type	True	76.7529	82	778	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:53:22,334] [INFO] DFAST Taxonomy check result was written to GCF_014635485.1_ASM1463548v1_genomic.fna/tc_result.tsv
[2024-01-25 19:53:22,334] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:53:22,335] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:53:22,335] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b52d006-3345-47be-b8c3-e7e446df2a51/dqc_reference/checkm_data
[2024-01-25 19:53:22,336] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:53:22,360] [INFO] Task started: CheckM
[2024-01-25 19:53:22,361] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014635485.1_ASM1463548v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014635485.1_ASM1463548v1_genomic.fna/checkm_input GCF_014635485.1_ASM1463548v1_genomic.fna/checkm_result
[2024-01-25 19:53:47,156] [INFO] Task succeeded: CheckM
[2024-01-25 19:53:47,157] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:53:47,182] [INFO] ===== Completeness check finished =====
[2024-01-25 19:53:47,182] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:53:47,182] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014635485.1_ASM1463548v1_genomic.fna/markers.fasta)
[2024-01-25 19:53:47,182] [INFO] Task started: Blastn
[2024-01-25 19:53:47,183] [INFO] Running command: blastn -query GCF_014635485.1_ASM1463548v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b52d006-3345-47be-b8c3-e7e446df2a51/dqc_reference/reference_markers_gtdb.fasta -out GCF_014635485.1_ASM1463548v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:48,231] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:48,234] [INFO] Selected 18 target genomes.
[2024-01-25 19:53:48,234] [INFO] Target genome list was writen to GCF_014635485.1_ASM1463548v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:53:48,252] [INFO] Task started: fastANI
[2024-01-25 19:53:48,252] [INFO] Running command: fastANI --query /var/lib/cwl/stga77f4180-e0fa-434c-acdd-5b2f075bf057/GCF_014635485.1_ASM1463548v1_genomic.fna.gz --refList GCF_014635485.1_ASM1463548v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014635485.1_ASM1463548v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:53:57,891] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:57,901] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:53:57,901] [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_004114895.1	s__Corynebacterium pelargi	99.9955	778	778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003814005.1	s__Corynebacterium pseudopelargi	89.6674	704	778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003813985.1	s__Corynebacterium geronticis	81.8919	435	778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000550805.1	s__Corynebacterium vitaeruminis	78.6256	196	778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.86	98.60	0.94	0.94	3	-
GCF_902702935.1	s__Corynebacterium rouxii	78.3538	119	778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001457455.1	s__Corynebacterium diphtheriae	78.0818	117	778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.05	95.03	0.92	0.83	346	-
GCA_019209905.1	s__Corynebacterium sp019209905	77.9484	87	778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011305.1	s__Corynebacterium efficiens	77.8519	155	778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.90	99.90	0.99	0.99	2	-
GCF_900177745.1	s__Corynebacterium pollutisoli	77.7177	144	778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.83	98.83	0.98	0.98	2	-
GCF_900155535.1	s__Corynebacterium urinipleomorphum	77.5874	97	778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001021025.1	s__Corynebacterium epidermidicanis	77.5553	117	778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014490555.1	s__Corynebacterium sp014490555	77.4372	113	778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	0.99	3	-
GCF_001831515.1	s__Corynebacterium sp001831515	77.4042	120	778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	96.57	96.57	0.93	0.93	2	-
GCF_012396315.1	s__Corynebacterium mucifaciens	77.2991	105	778	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	95.74	95.74	0.89	0.89	2	-
GCF_000177535.2	s__Corynebacterium resistens	76.7529	82	778	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 19:53:57,902] [INFO] GTDB search result was written to GCF_014635485.1_ASM1463548v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:53:57,903] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:53:57,906] [INFO] DFAST_QC result json was written to GCF_014635485.1_ASM1463548v1_genomic.fna/dqc_result.json
[2024-01-25 19:53:57,906] [INFO] DFAST_QC completed!
[2024-01-25 19:53:57,906] [INFO] Total running time: 0h0m52s