[2024-01-24 14:31:00,263] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:00,290] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:00,291] [INFO] DQC Reference Directory: /var/lib/cwl/stgba4b4e82-7d91-4aa4-ae0f-0251088fdc34/dqc_reference
[2024-01-24 14:31:02,105] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:02,106] [INFO] Task started: Prodigal
[2024-01-24 14:31:02,106] [INFO] Running command: gunzip -c /var/lib/cwl/stg97dae575-0d81-4975-951f-e4f948eecf33/GCF_014201835.1_ASM1420183v1_genomic.fna.gz | prodigal -d GCF_014201835.1_ASM1420183v1_genomic.fna/cds.fna -a GCF_014201835.1_ASM1420183v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:07,098] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:07,098] [INFO] Task started: HMMsearch
[2024-01-24 14:31:07,098] [INFO] Running command: hmmsearch --tblout GCF_014201835.1_ASM1420183v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba4b4e82-7d91-4aa4-ae0f-0251088fdc34/dqc_reference/reference_markers.hmm GCF_014201835.1_ASM1420183v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:07,415] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:07,416] [INFO] Found 6/6 markers.
[2024-01-24 14:31:07,441] [INFO] Query marker FASTA was written to GCF_014201835.1_ASM1420183v1_genomic.fna/markers.fasta
[2024-01-24 14:31:07,442] [INFO] Task started: Blastn
[2024-01-24 14:31:07,442] [INFO] Running command: blastn -query GCF_014201835.1_ASM1420183v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba4b4e82-7d91-4aa4-ae0f-0251088fdc34/dqc_reference/reference_markers.fasta -out GCF_014201835.1_ASM1420183v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:08,046] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:08,049] [INFO] Selected 15 target genomes.
[2024-01-24 14:31:08,049] [INFO] Target genome list was writen to GCF_014201835.1_ASM1420183v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:08,071] [INFO] Task started: fastANI
[2024-01-24 14:31:08,071] [INFO] Running command: fastANI --query /var/lib/cwl/stg97dae575-0d81-4975-951f-e4f948eecf33/GCF_014201835.1_ASM1420183v1_genomic.fna.gz --refList GCF_014201835.1_ASM1420183v1_genomic.fna/target_genomes.txt --output GCF_014201835.1_ASM1420183v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:16,174] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:16,174] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba4b4e82-7d91-4aa4-ae0f-0251088fdc34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:16,175] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba4b4e82-7d91-4aa4-ae0f-0251088fdc34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:16,181] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:31:16,181] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:16,181] [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
Pectinatus brassicae	strain=DSM 24661	GCA_014201835.1	862415	862415	type	True	100.0	903	908	95	conclusive
Pectinatus brassicae	strain=MB591	GCA_015732205.1	862415	862415	type	True	99.9918	904	908	95	conclusive
Pectinatus sottacetonis	strain=MB620	GCA_015732155.1	1002795	1002795	type	True	79.0135	278	908	95	below_threshold
Megamonas funiformis	strain=JCM 14723	GCA_010669225.1	437897	437897	type	True	77.0203	83	908	95	below_threshold
Megamonas funiformis	strain=YIT 11815	GCA_000245775.1	437897	437897	type	True	76.9982	82	908	95	below_threshold
Propionispira arboris	strain=DSM 2179	GCA_900109225.1	84035	84035	type	True	76.7827	63	908	95	below_threshold
Propionispira raffinosivorans	strain=DSM 20765	GCA_000381065.1	86959	86959	type	True	76.4847	66	908	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:16,183] [INFO] DFAST Taxonomy check result was written to GCF_014201835.1_ASM1420183v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:16,183] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:16,183] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:16,183] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba4b4e82-7d91-4aa4-ae0f-0251088fdc34/dqc_reference/checkm_data
[2024-01-24 14:31:16,184] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:16,215] [INFO] Task started: CheckM
[2024-01-24 14:31:16,215] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014201835.1_ASM1420183v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014201835.1_ASM1420183v1_genomic.fna/checkm_input GCF_014201835.1_ASM1420183v1_genomic.fna/checkm_result
[2024-01-24 14:31:35,924] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:35,925] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:35,940] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:35,940] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:35,940] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014201835.1_ASM1420183v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:35,940] [INFO] Task started: Blastn
[2024-01-24 14:31:35,941] [INFO] Running command: blastn -query GCF_014201835.1_ASM1420183v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba4b4e82-7d91-4aa4-ae0f-0251088fdc34/dqc_reference/reference_markers_gtdb.fasta -out GCF_014201835.1_ASM1420183v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:36,727] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:36,730] [INFO] Selected 21 target genomes.
[2024-01-24 14:31:36,730] [INFO] Target genome list was writen to GCF_014201835.1_ASM1420183v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:36,744] [INFO] Task started: fastANI
[2024-01-24 14:31:36,744] [INFO] Running command: fastANI --query /var/lib/cwl/stg97dae575-0d81-4975-951f-e4f948eecf33/GCF_014201835.1_ASM1420183v1_genomic.fna.gz --refList GCF_014201835.1_ASM1420183v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014201835.1_ASM1420183v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:45,337] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:45,343] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:45,343] [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_014201835.1	s__Pectinatus brassicae	100.0	903	908	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Pectinatus	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_015732155.1	s__Pectinatus sottacetonis	79.0323	277	908	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Pectinatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015732185.1	s__Pectinatus haikarae	77.9781	165	908	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Pectinatus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002314325.1	s__Megamonas hypermegale_A	77.0887	50	908	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Megamonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010669225.1	s__Megamonas funiformis	77.0203	83	908	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Megamonas	95.0	97.89	97.23	0.89	0.80	26	-
GCF_900109225.1	s__Propionispira arboris	76.7472	64	908	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Propionispira	96.4486	N/A	N/A	N/A	N/A	1	-
GCF_000381065.1	s__Propionispira raffinosivorans	76.5162	65	908	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Propionispira	96.4486	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:45,344] [INFO] GTDB search result was written to GCF_014201835.1_ASM1420183v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:45,345] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:45,347] [INFO] DFAST_QC result json was written to GCF_014201835.1_ASM1420183v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:45,347] [INFO] DFAST_QC completed!
[2024-01-24 14:31:45,347] [INFO] Total running time: 0h0m45s