[2024-01-25 17:37:50,878] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:37:50,894] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:37:50,894] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfac70ac-ddbd-49ec-ac77-be3b39b0681b/dqc_reference
[2024-01-25 17:37:52,061] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:37:52,062] [INFO] Task started: Prodigal
[2024-01-25 17:37:52,063] [INFO] Running command: gunzip -c /var/lib/cwl/stgcadd78c4-0406-4853-902d-9b693ed9f68d/GCF_003334855.1_ASM333485v1_genomic.fna.gz | prodigal -d GCF_003334855.1_ASM333485v1_genomic.fna/cds.fna -a GCF_003334855.1_ASM333485v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:38:27,489] [INFO] Task succeeded: Prodigal
[2024-01-25 17:38:27,490] [INFO] Task started: HMMsearch
[2024-01-25 17:38:27,490] [INFO] Running command: hmmsearch --tblout GCF_003334855.1_ASM333485v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfac70ac-ddbd-49ec-ac77-be3b39b0681b/dqc_reference/reference_markers.hmm GCF_003334855.1_ASM333485v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:38:27,804] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:38:27,805] [INFO] Found 6/6 markers.
[2024-01-25 17:38:27,867] [INFO] Query marker FASTA was written to GCF_003334855.1_ASM333485v1_genomic.fna/markers.fasta
[2024-01-25 17:38:27,867] [INFO] Task started: Blastn
[2024-01-25 17:38:27,867] [INFO] Running command: blastn -query GCF_003334855.1_ASM333485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfac70ac-ddbd-49ec-ac77-be3b39b0681b/dqc_reference/reference_markers.fasta -out GCF_003334855.1_ASM333485v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:28,437] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:28,441] [INFO] Selected 9 target genomes.
[2024-01-25 17:38:28,441] [INFO] Target genome list was writen to GCF_003334855.1_ASM333485v1_genomic.fna/target_genomes.txt
[2024-01-25 17:38:28,444] [INFO] Task started: fastANI
[2024-01-25 17:38:28,445] [INFO] Running command: fastANI --query /var/lib/cwl/stgcadd78c4-0406-4853-902d-9b693ed9f68d/GCF_003334855.1_ASM333485v1_genomic.fna.gz --refList GCF_003334855.1_ASM333485v1_genomic.fna/target_genomes.txt --output GCF_003334855.1_ASM333485v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:38:42,969] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:42,970] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfac70ac-ddbd-49ec-ac77-be3b39b0681b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:38:42,970] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfac70ac-ddbd-49ec-ac77-be3b39b0681b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:38:42,976] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:38:42,976] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:38:42,976] [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
Larkinella punicea	strain=ZZJ9	GCA_003334855.1	2315727	2315727	type	True	100.0	2635	2636	95	conclusive
Larkinella humicola	strain=MA1	GCA_008727875.1	2607654	2607654	type	True	92.5629	2217	2636	95	below_threshold
Larkinella knui	strain=KCTC42998	GCA_003858645.1	2025310	2025310	type	True	83.4984	1769	2636	95	below_threshold
Larkinella rosea	strain=KCTC52004	GCA_003858635.1	2025312	2025312	type	True	81.8273	1682	2636	95	below_threshold
Larkinella terrae	strain=KCTC 52001	GCA_009668025.1	2025311	2025311	type	True	81.7718	1641	2636	95	below_threshold
Hymenobacter metallicola	strain=9PBR-1	GCA_004745645.1	2563114	2563114	type	True	75.642	64	2636	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:38:42,978] [INFO] DFAST Taxonomy check result was written to GCF_003334855.1_ASM333485v1_genomic.fna/tc_result.tsv
[2024-01-25 17:38:42,978] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:38:42,978] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:38:42,978] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfac70ac-ddbd-49ec-ac77-be3b39b0681b/dqc_reference/checkm_data
[2024-01-25 17:38:42,979] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:38:43,053] [INFO] Task started: CheckM
[2024-01-25 17:38:43,053] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003334855.1_ASM333485v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003334855.1_ASM333485v1_genomic.fna/checkm_input GCF_003334855.1_ASM333485v1_genomic.fna/checkm_result
[2024-01-25 17:40:15,557] [INFO] Task succeeded: CheckM
[2024-01-25 17:40:15,558] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:40:15,587] [INFO] ===== Completeness check finished =====
[2024-01-25 17:40:15,587] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:40:15,588] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003334855.1_ASM333485v1_genomic.fna/markers.fasta)
[2024-01-25 17:40:15,588] [INFO] Task started: Blastn
[2024-01-25 17:40:15,588] [INFO] Running command: blastn -query GCF_003334855.1_ASM333485v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfac70ac-ddbd-49ec-ac77-be3b39b0681b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003334855.1_ASM333485v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:16,426] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:16,430] [INFO] Selected 6 target genomes.
[2024-01-25 17:40:16,431] [INFO] Target genome list was writen to GCF_003334855.1_ASM333485v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:40:16,443] [INFO] Task started: fastANI
[2024-01-25 17:40:16,443] [INFO] Running command: fastANI --query /var/lib/cwl/stgcadd78c4-0406-4853-902d-9b693ed9f68d/GCF_003334855.1_ASM333485v1_genomic.fna.gz --refList GCF_003334855.1_ASM333485v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003334855.1_ASM333485v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:40:29,738] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:29,743] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:40:29,744] [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_003334855.1	s__Larkinella punicea	100.0	2635	2636	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006149005.1	s__Larkinella sp006149005	93.0636	2252	2636	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008727875.1	s__Larkinella sp008727875	92.5727	2215	2636	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003858645.1	s__Larkinella knui	83.5047	1767	2636	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003858635.1	s__Larkinella rosea	81.8353	1679	2636	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009668025.1	s__Larkinella terrae	81.7561	1643	2636	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:40:29,745] [INFO] GTDB search result was written to GCF_003334855.1_ASM333485v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:40:29,746] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:40:29,748] [INFO] DFAST_QC result json was written to GCF_003334855.1_ASM333485v1_genomic.fna/dqc_result.json
[2024-01-25 17:40:29,748] [INFO] DFAST_QC completed!
[2024-01-25 17:40:29,748] [INFO] Total running time: 0h2m39s