[2024-01-24 11:13:49,586] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:13:49,588] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:13:49,588] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8331d98-af08-4aff-b95b-a8ed8187e571/dqc_reference
[2024-01-24 11:13:50,810] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:13:50,811] [INFO] Task started: Prodigal
[2024-01-24 11:13:50,811] [INFO] Running command: gunzip -c /var/lib/cwl/stg5eb407b1-a1cd-441e-9df2-adb0380670a8/GCF_003259615.1_ASM325961v1_genomic.fna.gz | prodigal -d GCF_003259615.1_ASM325961v1_genomic.fna/cds.fna -a GCF_003259615.1_ASM325961v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:14:13,191] [INFO] Task succeeded: Prodigal
[2024-01-24 11:14:13,191] [INFO] Task started: HMMsearch
[2024-01-24 11:14:13,192] [INFO] Running command: hmmsearch --tblout GCF_003259615.1_ASM325961v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8331d98-af08-4aff-b95b-a8ed8187e571/dqc_reference/reference_markers.hmm GCF_003259615.1_ASM325961v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:14:13,522] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:14:13,524] [INFO] Found 6/6 markers.
[2024-01-24 11:14:13,574] [INFO] Query marker FASTA was written to GCF_003259615.1_ASM325961v1_genomic.fna/markers.fasta
[2024-01-24 11:14:13,575] [INFO] Task started: Blastn
[2024-01-24 11:14:13,575] [INFO] Running command: blastn -query GCF_003259615.1_ASM325961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8331d98-af08-4aff-b95b-a8ed8187e571/dqc_reference/reference_markers.fasta -out GCF_003259615.1_ASM325961v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:14,197] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:14,201] [INFO] Selected 13 target genomes.
[2024-01-24 11:14:14,202] [INFO] Target genome list was writen to GCF_003259615.1_ASM325961v1_genomic.fna/target_genomes.txt
[2024-01-24 11:14:14,207] [INFO] Task started: fastANI
[2024-01-24 11:14:14,207] [INFO] Running command: fastANI --query /var/lib/cwl/stg5eb407b1-a1cd-441e-9df2-adb0380670a8/GCF_003259615.1_ASM325961v1_genomic.fna.gz --refList GCF_003259615.1_ASM325961v1_genomic.fna/target_genomes.txt --output GCF_003259615.1_ASM325961v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:14:26,431] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:26,432] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8331d98-af08-4aff-b95b-a8ed8187e571/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:14:26,432] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8331d98-af08-4aff-b95b-a8ed8187e571/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:14:26,446] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:14:26,446] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:14:26,447] [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
Pedobacter cryoconitis	strain=DSM 14825	GCA_003259615.1	188932	188932	suspected-type	True	100.0	1976	1982	95	conclusive
Pedobacter lusitanus	strain=NL19	GCA_000832545.1	1503925	1503925	type	True	82.7621	1086	1982	95	below_threshold
Pedobacter hartonius	strain=DSM 19033	GCA_900107535.1	425514	425514	type	True	79.5766	475	1982	95	below_threshold
Pedobacter westerhofensis	strain=DSM 19036	GCA_900182595.1	425512	425512	type	True	79.5673	467	1982	95	below_threshold
Pedobacter antarcticus	strain=4BY	GCA_000722885.1	34086	34086	type	True	78.9784	364	1982	95	below_threshold
Pedobacter antarcticus	strain=ATCC 51969	GCA_900112985.1	34086	34086	type	True	78.97	378	1982	95	below_threshold
Pedobacter frigoris	strain=RP-3-15	GCA_005116445.1	2571272	2571272	type	True	77.9342	242	1982	95	below_threshold
Pedobacter mucosus	strain=Q8-18	GCA_022200785.1	2895286	2895286	type	True	77.4275	138	1982	95	below_threshold
Pedobacter ginsenosidimutans	strain=KACC 14530	GCA_001442625.1	687842	687842	type	True	77.2234	170	1982	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	76.1161	64	1982	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:14:26,448] [INFO] DFAST Taxonomy check result was written to GCF_003259615.1_ASM325961v1_genomic.fna/tc_result.tsv
[2024-01-24 11:14:26,449] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:14:26,449] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:14:26,449] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8331d98-af08-4aff-b95b-a8ed8187e571/dqc_reference/checkm_data
[2024-01-24 11:14:26,450] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:14:26,504] [INFO] Task started: CheckM
[2024-01-24 11:14:26,505] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003259615.1_ASM325961v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003259615.1_ASM325961v1_genomic.fna/checkm_input GCF_003259615.1_ASM325961v1_genomic.fna/checkm_result
[2024-01-24 11:15:30,514] [INFO] Task succeeded: CheckM
[2024-01-24 11:15:30,515] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:15:30,536] [INFO] ===== Completeness check finished =====
[2024-01-24 11:15:30,537] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:15:30,537] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003259615.1_ASM325961v1_genomic.fna/markers.fasta)
[2024-01-24 11:15:30,537] [INFO] Task started: Blastn
[2024-01-24 11:15:30,538] [INFO] Running command: blastn -query GCF_003259615.1_ASM325961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8331d98-af08-4aff-b95b-a8ed8187e571/dqc_reference/reference_markers_gtdb.fasta -out GCF_003259615.1_ASM325961v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:15:31,328] [INFO] Task succeeded: Blastn
[2024-01-24 11:15:31,332] [INFO] Selected 6 target genomes.
[2024-01-24 11:15:31,332] [INFO] Target genome list was writen to GCF_003259615.1_ASM325961v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:15:31,352] [INFO] Task started: fastANI
[2024-01-24 11:15:31,352] [INFO] Running command: fastANI --query /var/lib/cwl/stg5eb407b1-a1cd-441e-9df2-adb0380670a8/GCF_003259615.1_ASM325961v1_genomic.fna.gz --refList GCF_003259615.1_ASM325961v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003259615.1_ASM325961v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:15:40,640] [INFO] Task succeeded: fastANI
[2024-01-24 11:15:40,647] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:15:40,648] [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_003259615.1	s__Pedobacter cryoconitis	100.0	1976	1982	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014200595.1	s__Pedobacter cryoconitis_C	89.2974	1605	1982	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.76	98.76	0.93	0.93	2	-
GCF_001590605.1	s__Pedobacter cryoconitis_A	88.4354	1443	1982	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200605.1	s__Pedobacter cryoconitis_B	83.6101	1266	1982	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.88	98.88	0.94	0.94	2	-
GCA_014302835.1	s__Pedobacter sp014302835	82.9373	927	1982	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000832545.1	s__Pedobacter lusitanus	82.7623	1086	1982	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:15:40,649] [INFO] GTDB search result was written to GCF_003259615.1_ASM325961v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:15:40,650] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:15:40,652] [INFO] DFAST_QC result json was written to GCF_003259615.1_ASM325961v1_genomic.fna/dqc_result.json
[2024-01-24 11:15:40,652] [INFO] DFAST_QC completed!
[2024-01-24 11:15:40,652] [INFO] Total running time: 0h1m51s