[2024-01-24 12:37:37,922] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:37,925] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:37,925] [INFO] DQC Reference Directory: /var/lib/cwl/stge114bf30-cbca-4aaf-8b55-2932f112cb53/dqc_reference
[2024-01-24 12:37:41,019] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:41,020] [INFO] Task started: Prodigal
[2024-01-24 12:37:41,021] [INFO] Running command: gunzip -c /var/lib/cwl/stg0abe767c-a310-4029-b94d-50c464ad513d/GCF_015732155.1_ASM1573215v1_genomic.fna.gz | prodigal -d GCF_015732155.1_ASM1573215v1_genomic.fna/cds.fna -a GCF_015732155.1_ASM1573215v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:46,517] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:46,518] [INFO] Task started: HMMsearch
[2024-01-24 12:37:46,518] [INFO] Running command: hmmsearch --tblout GCF_015732155.1_ASM1573215v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge114bf30-cbca-4aaf-8b55-2932f112cb53/dqc_reference/reference_markers.hmm GCF_015732155.1_ASM1573215v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:46,762] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:46,764] [INFO] Found 6/6 markers.
[2024-01-24 12:37:46,790] [INFO] Query marker FASTA was written to GCF_015732155.1_ASM1573215v1_genomic.fna/markers.fasta
[2024-01-24 12:37:46,790] [INFO] Task started: Blastn
[2024-01-24 12:37:46,790] [INFO] Running command: blastn -query GCF_015732155.1_ASM1573215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge114bf30-cbca-4aaf-8b55-2932f112cb53/dqc_reference/reference_markers.fasta -out GCF_015732155.1_ASM1573215v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:48,497] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:48,501] [INFO] Selected 12 target genomes.
[2024-01-24 12:37:48,501] [INFO] Target genome list was writen to GCF_015732155.1_ASM1573215v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:48,595] [INFO] Task started: fastANI
[2024-01-24 12:37:48,596] [INFO] Running command: fastANI --query /var/lib/cwl/stg0abe767c-a310-4029-b94d-50c464ad513d/GCF_015732155.1_ASM1573215v1_genomic.fna.gz --refList GCF_015732155.1_ASM1573215v1_genomic.fna/target_genomes.txt --output GCF_015732155.1_ASM1573215v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:54,081] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:54,082] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge114bf30-cbca-4aaf-8b55-2932f112cb53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:54,083] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge114bf30-cbca-4aaf-8b55-2932f112cb53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:54,098] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:54,098] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:54,098] [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 sottacetonis	strain=MB620	GCA_015732155.1	1002795	1002795	type	True	100.0	896	897	95	conclusive
Pectinatus brassicae	strain=MB591	GCA_015732205.1	862415	862415	type	True	79.4839	295	897	95	below_threshold
Pectinatus brassicae	strain=DSM 24661	GCA_014201835.1	862415	862415	type	True	79.007	274	897	95	below_threshold
Pectinatus cerevisiiphilus	strain=MB134	GCA_015732175.1	86956	86956	type	True	78.811	207	897	95	below_threshold
Pectinatus cerevisiiphilus	strain=DSM 20467	GCA_004341685.1	86956	86956	type	True	78.1348	206	897	95	below_threshold
Pectinatus frisingensis	strain=MB174	GCA_015732285.1	865	865	type	True	78.0123	214	897	95	below_threshold
Megamonas funiformis	strain=JCM 14723	GCA_010669225.1	437897	437897	type	True	77.6084	78	897	95	below_threshold
Megamonas funiformis	strain=YIT 11815	GCA_000245775.1	437897	437897	type	True	76.9958	71	897	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:54,100] [INFO] DFAST Taxonomy check result was written to GCF_015732155.1_ASM1573215v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:54,101] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:54,102] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:54,102] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge114bf30-cbca-4aaf-8b55-2932f112cb53/dqc_reference/checkm_data
[2024-01-24 12:37:54,103] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:54,147] [INFO] Task started: CheckM
[2024-01-24 12:37:54,149] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015732155.1_ASM1573215v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015732155.1_ASM1573215v1_genomic.fna/checkm_input GCF_015732155.1_ASM1573215v1_genomic.fna/checkm_result
[2024-01-24 12:38:16,990] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:16,991] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:17,010] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:17,011] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:17,011] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015732155.1_ASM1573215v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:17,012] [INFO] Task started: Blastn
[2024-01-24 12:38:17,012] [INFO] Running command: blastn -query GCF_015732155.1_ASM1573215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge114bf30-cbca-4aaf-8b55-2932f112cb53/dqc_reference/reference_markers_gtdb.fasta -out GCF_015732155.1_ASM1573215v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:17,987] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:17,990] [INFO] Selected 18 target genomes.
[2024-01-24 12:38:17,991] [INFO] Target genome list was writen to GCF_015732155.1_ASM1573215v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:18,032] [INFO] Task started: fastANI
[2024-01-24 12:38:18,032] [INFO] Running command: fastANI --query /var/lib/cwl/stg0abe767c-a310-4029-b94d-50c464ad513d/GCF_015732155.1_ASM1573215v1_genomic.fna.gz --refList GCF_015732155.1_ASM1573215v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015732155.1_ASM1573215v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:27,542] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:27,551] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:27,551] [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_015732155.1	s__Pectinatus sottacetonis	100.0	895	897	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Pectinatus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014201835.1	s__Pectinatus brassicae	78.9919	273	897	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Pectinatus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_015732185.1	s__Pectinatus haikarae	78.2756	210	897	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_004341685.1	s__Pectinatus cerevisiiphilus	78.1348	206	897	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Pectinatus	95.0	99.98	99.98	0.99	0.99	2	-
GCF_015732285.1	s__Pectinatus frisingensis	78.0464	212	897	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Pectinatus	95.0	98.00	97.22	0.85	0.81	9	-
GCF_010669225.1	s__Megamonas funiformis	77.2322	75	897	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Megamonas	95.0	97.89	97.23	0.89	0.80	26	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:27,553] [INFO] GTDB search result was written to GCF_015732155.1_ASM1573215v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:27,554] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:27,557] [INFO] DFAST_QC result json was written to GCF_015732155.1_ASM1573215v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:27,557] [INFO] DFAST_QC completed!
[2024-01-24 12:38:27,557] [INFO] Total running time: 0h0m50s