[2024-01-24 11:59:10,758] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:10,760] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:10,760] [INFO] DQC Reference Directory: /var/lib/cwl/stgb150560d-c41a-46d8-9d77-1d42d94a8df8/dqc_reference
[2024-01-24 11:59:12,057] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:12,058] [INFO] Task started: Prodigal
[2024-01-24 11:59:12,059] [INFO] Running command: gunzip -c /var/lib/cwl/stg09e51f8f-90cd-4927-9ca0-44d7e6e747a0/GCF_017358165.1_ASM1735816v1_genomic.fna.gz | prodigal -d GCF_017358165.1_ASM1735816v1_genomic.fna/cds.fna -a GCF_017358165.1_ASM1735816v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:16,060] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:16,061] [INFO] Task started: HMMsearch
[2024-01-24 11:59:16,061] [INFO] Running command: hmmsearch --tblout GCF_017358165.1_ASM1735816v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb150560d-c41a-46d8-9d77-1d42d94a8df8/dqc_reference/reference_markers.hmm GCF_017358165.1_ASM1735816v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:16,366] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:16,367] [INFO] Found 6/6 markers.
[2024-01-24 11:59:16,396] [INFO] Query marker FASTA was written to GCF_017358165.1_ASM1735816v1_genomic.fna/markers.fasta
[2024-01-24 11:59:16,398] [INFO] Task started: Blastn
[2024-01-24 11:59:16,398] [INFO] Running command: blastn -query GCF_017358165.1_ASM1735816v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb150560d-c41a-46d8-9d77-1d42d94a8df8/dqc_reference/reference_markers.fasta -out GCF_017358165.1_ASM1735816v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:17,008] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:17,011] [INFO] Selected 9 target genomes.
[2024-01-24 11:59:17,012] [INFO] Target genome list was writen to GCF_017358165.1_ASM1735816v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:17,039] [INFO] Task started: fastANI
[2024-01-24 11:59:17,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg09e51f8f-90cd-4927-9ca0-44d7e6e747a0/GCF_017358165.1_ASM1735816v1_genomic.fna.gz --refList GCF_017358165.1_ASM1735816v1_genomic.fna/target_genomes.txt --output GCF_017358165.1_ASM1735816v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:21,150] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:21,151] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb150560d-c41a-46d8-9d77-1d42d94a8df8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:21,151] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb150560d-c41a-46d8-9d77-1d42d94a8df8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:21,160] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:21,161] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:21,161] [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
Thermosipho ferrireducens	strain=JL129W03	GCA_017358165.1	2571116	2571116	type	True	100.0	659	660	95	conclusive
Thermosipho atlanticus	strain=DSM 15807	GCA_900129985.1	238991	238991	type	True	77.5002	113	660	95	below_threshold
Thermosipho affectus	strain=ik275mar	GCA_001990485.1	660294	660294	type	True	77.3774	81	660	95	below_threshold
Thermosipho africanus	strain=Ob7	GCA_003351105.1	2421	2421	type	True	77.0555	89	660	95	below_threshold
Thermosipho japonicus	strain=DSM 13481	GCA_014201655.1	90323	90323	type	True	77.0027	89	660	95	below_threshold
Thermosipho globiformans	strain=JCM 15059	GCA_003990895.1	380685	380685	type	True	76.7635	97	660	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:21,166] [INFO] DFAST Taxonomy check result was written to GCF_017358165.1_ASM1735816v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:21,167] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:21,167] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:21,167] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb150560d-c41a-46d8-9d77-1d42d94a8df8/dqc_reference/checkm_data
[2024-01-24 11:59:21,169] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:21,196] [INFO] Task started: CheckM
[2024-01-24 11:59:21,197] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017358165.1_ASM1735816v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017358165.1_ASM1735816v1_genomic.fna/checkm_input GCF_017358165.1_ASM1735816v1_genomic.fna/checkm_result
[2024-01-24 11:59:40,949] [INFO] Task succeeded: CheckM
[2024-01-24 11:59:40,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:59:40,988] [INFO] ===== Completeness check finished =====
[2024-01-24 11:59:40,989] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:59:40,989] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017358165.1_ASM1735816v1_genomic.fna/markers.fasta)
[2024-01-24 11:59:40,989] [INFO] Task started: Blastn
[2024-01-24 11:59:40,989] [INFO] Running command: blastn -query GCF_017358165.1_ASM1735816v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb150560d-c41a-46d8-9d77-1d42d94a8df8/dqc_reference/reference_markers_gtdb.fasta -out GCF_017358165.1_ASM1735816v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:41,787] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:41,791] [INFO] Selected 13 target genomes.
[2024-01-24 11:59:41,791] [INFO] Target genome list was writen to GCF_017358165.1_ASM1735816v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:59:41,805] [INFO] Task started: fastANI
[2024-01-24 11:59:41,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg09e51f8f-90cd-4927-9ca0-44d7e6e747a0/GCF_017358165.1_ASM1735816v1_genomic.fna.gz --refList GCF_017358165.1_ASM1735816v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017358165.1_ASM1735816v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:59:47,521] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:47,528] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:59:47,528] [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_017358165.1	s__JL129W03 sp017358165	100.0	659	660	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__Fervidobacteriaceae;g__JL129W03	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900129985.1	s__Thermosipho_A atlanticus	77.4764	114	660	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__Fervidobacteriaceae;g__Thermosipho_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001990485.1	s__Thermosipho affectus	77.3406	83	660	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__Fervidobacteriaceae;g__Thermosipho	95.0	98.44	97.33	0.96	0.94	6	-
GCF_003351105.1	s__Thermosipho africanus	77.0555	89	660	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__Fervidobacteriaceae;g__Thermosipho	95.0	98.56	98.53	0.93	0.90	3	-
GCF_014201655.1	s__Thermosipho japonicus	77.0027	89	660	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__Fervidobacteriaceae;g__Thermosipho	95.0	95.40	95.40	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:59:47,530] [INFO] GTDB search result was written to GCF_017358165.1_ASM1735816v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:59:47,531] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:59:47,533] [INFO] DFAST_QC result json was written to GCF_017358165.1_ASM1735816v1_genomic.fna/dqc_result.json
[2024-01-24 11:59:47,534] [INFO] DFAST_QC completed!
[2024-01-24 11:59:47,534] [INFO] Total running time: 0h0m37s