[2024-01-24 11:43:52,895] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:52,897] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:52,898] [INFO] DQC Reference Directory: /var/lib/cwl/stga9475976-b666-4cf9-8fa8-6349ee36a542/dqc_reference
[2024-01-24 11:43:54,133] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:54,134] [INFO] Task started: Prodigal
[2024-01-24 11:43:54,134] [INFO] Running command: gunzip -c /var/lib/cwl/stgb853c58f-9484-47be-9a8c-ba46671cc863/GCF_018598175.1_ASM1859817v1_genomic.fna.gz | prodigal -d GCF_018598175.1_ASM1859817v1_genomic.fna/cds.fna -a GCF_018598175.1_ASM1859817v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:34,586] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:34,586] [INFO] Task started: HMMsearch
[2024-01-24 11:44:34,586] [INFO] Running command: hmmsearch --tblout GCF_018598175.1_ASM1859817v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9475976-b666-4cf9-8fa8-6349ee36a542/dqc_reference/reference_markers.hmm GCF_018598175.1_ASM1859817v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:34,891] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:34,892] [INFO] Found 6/6 markers.
[2024-01-24 11:44:34,945] [INFO] Query marker FASTA was written to GCF_018598175.1_ASM1859817v1_genomic.fna/markers.fasta
[2024-01-24 11:44:34,946] [INFO] Task started: Blastn
[2024-01-24 11:44:34,946] [INFO] Running command: blastn -query GCF_018598175.1_ASM1859817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9475976-b666-4cf9-8fa8-6349ee36a542/dqc_reference/reference_markers.fasta -out GCF_018598175.1_ASM1859817v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:35,532] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:35,535] [INFO] Selected 19 target genomes.
[2024-01-24 11:44:35,536] [INFO] Target genome list was writen to GCF_018598175.1_ASM1859817v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:35,542] [INFO] Task started: fastANI
[2024-01-24 11:44:35,543] [INFO] Running command: fastANI --query /var/lib/cwl/stgb853c58f-9484-47be-9a8c-ba46671cc863/GCF_018598175.1_ASM1859817v1_genomic.fna.gz --refList GCF_018598175.1_ASM1859817v1_genomic.fna/target_genomes.txt --output GCF_018598175.1_ASM1859817v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:53,100] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:53,100] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9475976-b666-4cf9-8fa8-6349ee36a542/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:53,101] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9475976-b666-4cf9-8fa8-6349ee36a542/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:53,107] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:53,107] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:53,107] [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
Dawidia cretensis	strain=PWU5	GCA_018598175.1	2782350	2782350	type	True	100.0	2373	2377	95	conclusive
Dawidia soli	strain=PWU37	GCA_018598185.1	2782352	2782352	type	True	84.2001	1744	2377	95	below_threshold
Ohtaekwangia koreensis	strain=DSM 25262	GCA_900167975.1	688867	688867	type	True	77.1698	172	2377	95	below_threshold
Chryseolinea serpens	strain=DSM 24574	GCA_900129725.1	947013	947013	type	True	76.9181	285	2377	95	below_threshold
Chryseolinea soli	strain=KIS68-18	GCA_003589925.1	2321403	2321403	type	True	76.8738	294	2377	95	below_threshold
Chryseosolibacter histidini	strain=PWU4	GCA_018598225.1	2782349	2782349	type	True	76.7301	211	2377	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:53,109] [INFO] DFAST Taxonomy check result was written to GCF_018598175.1_ASM1859817v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:53,109] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:53,109] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:53,109] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9475976-b666-4cf9-8fa8-6349ee36a542/dqc_reference/checkm_data
[2024-01-24 11:44:53,110] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:53,173] [INFO] Task started: CheckM
[2024-01-24 11:44:53,173] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018598175.1_ASM1859817v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018598175.1_ASM1859817v1_genomic.fna/checkm_input GCF_018598175.1_ASM1859817v1_genomic.fna/checkm_result
[2024-01-24 11:46:37,958] [INFO] Task succeeded: CheckM
[2024-01-24 11:46:37,959] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:46:37,978] [INFO] ===== Completeness check finished =====
[2024-01-24 11:46:37,978] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:46:37,978] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018598175.1_ASM1859817v1_genomic.fna/markers.fasta)
[2024-01-24 11:46:37,979] [INFO] Task started: Blastn
[2024-01-24 11:46:37,979] [INFO] Running command: blastn -query GCF_018598175.1_ASM1859817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9475976-b666-4cf9-8fa8-6349ee36a542/dqc_reference/reference_markers_gtdb.fasta -out GCF_018598175.1_ASM1859817v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:46:38,767] [INFO] Task succeeded: Blastn
[2024-01-24 11:46:38,771] [INFO] Selected 17 target genomes.
[2024-01-24 11:46:38,771] [INFO] Target genome list was writen to GCF_018598175.1_ASM1859817v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:46:38,802] [INFO] Task started: fastANI
[2024-01-24 11:46:38,802] [INFO] Running command: fastANI --query /var/lib/cwl/stgb853c58f-9484-47be-9a8c-ba46671cc863/GCF_018598175.1_ASM1859817v1_genomic.fna.gz --refList GCF_018598175.1_ASM1859817v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018598175.1_ASM1859817v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:55,004] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:55,014] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:55,014] [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
GCA_018598175.1	s__Ohtaekwangia sp018598175	100.0	2373	2377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Ohtaekwangia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018598185.1	s__Ohtaekwangia sp018598185	84.202	1744	2377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Ohtaekwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167975.1	s__Ohtaekwangia koreensis	77.1698	172	2377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Ohtaekwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735595.1	s__Chryseolinea sp016735595	77.1574	286	2377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Chryseolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902168185.1	s__Ohtaekwangia sp902168185	76.9647	199	2377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Ohtaekwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129725.1	s__Chryseolinea serpens	76.935	283	2377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Chryseolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003589925.1	s__Chryseolinea soli	76.8738	294	2377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Chryseolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902168205.1	s__Ohtaekwangia sp902168205	76.8637	239	2377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Ohtaekwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018598225.1	s__PWU20 sp018598225	76.7404	210	2377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__PWU20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002432545.1	s__Ohtaekwangia sp002432545	76.5753	180	2377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Ohtaekwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242315.1	s__ZC4RG29 sp003242315	76.1719	50	2377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ZC4RG29	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012031955.1	s__ZC4RG29 sp012031955	76.0622	64	2377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ZC4RG29	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018267215.1	s__ELB16-189 sp018267215	75.4163	50	2377	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	99.99	99.99	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:55,016] [INFO] GTDB search result was written to GCF_018598175.1_ASM1859817v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:55,016] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:55,019] [INFO] DFAST_QC result json was written to GCF_018598175.1_ASM1859817v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:55,019] [INFO] DFAST_QC completed!
[2024-01-24 11:46:55,020] [INFO] Total running time: 0h3m2s