[2024-01-25 18:39:35,655] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:39:35,656] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:39:35,657] [INFO] DQC Reference Directory: /var/lib/cwl/stg49f973ec-c0fe-4341-aa6f-65d7852e3938/dqc_reference
[2024-01-25 18:39:36,780] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:39:36,780] [INFO] Task started: Prodigal
[2024-01-25 18:39:36,780] [INFO] Running command: gunzip -c /var/lib/cwl/stg2daad7b2-ed47-4ba2-bb53-9bef5e6d8c17/GCF_003990895.1_ASM399089v1_genomic.fna.gz | prodigal -d GCF_003990895.1_ASM399089v1_genomic.fna/cds.fna -a GCF_003990895.1_ASM399089v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:39:39,801] [INFO] Task succeeded: Prodigal
[2024-01-25 18:39:39,802] [INFO] Task started: HMMsearch
[2024-01-25 18:39:39,802] [INFO] Running command: hmmsearch --tblout GCF_003990895.1_ASM399089v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49f973ec-c0fe-4341-aa6f-65d7852e3938/dqc_reference/reference_markers.hmm GCF_003990895.1_ASM399089v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:39:39,998] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:39:39,999] [INFO] Found 6/6 markers.
[2024-01-25 18:39:40,022] [INFO] Query marker FASTA was written to GCF_003990895.1_ASM399089v1_genomic.fna/markers.fasta
[2024-01-25 18:39:40,022] [INFO] Task started: Blastn
[2024-01-25 18:39:40,022] [INFO] Running command: blastn -query GCF_003990895.1_ASM399089v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49f973ec-c0fe-4341-aa6f-65d7852e3938/dqc_reference/reference_markers.fasta -out GCF_003990895.1_ASM399089v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:39:40,543] [INFO] Task succeeded: Blastn
[2024-01-25 18:39:40,545] [INFO] Selected 11 target genomes.
[2024-01-25 18:39:40,546] [INFO] Target genome list was writen to GCF_003990895.1_ASM399089v1_genomic.fna/target_genomes.txt
[2024-01-25 18:39:40,555] [INFO] Task started: fastANI
[2024-01-25 18:39:40,555] [INFO] Running command: fastANI --query /var/lib/cwl/stg2daad7b2-ed47-4ba2-bb53-9bef5e6d8c17/GCF_003990895.1_ASM399089v1_genomic.fna.gz --refList GCF_003990895.1_ASM399089v1_genomic.fna/target_genomes.txt --output GCF_003990895.1_ASM399089v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:39:45,299] [INFO] Task succeeded: fastANI
[2024-01-25 18:39:45,299] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49f973ec-c0fe-4341-aa6f-65d7852e3938/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:39:45,300] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49f973ec-c0fe-4341-aa6f-65d7852e3938/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:39:45,306] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:39:45,306] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 18:39:45,306] [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 globiformans	strain=JCM 15059	GCA_003990895.1	380685	380685	type	True	100.0	619	621	95	inconclusive
Thermosipho japonicus	strain=DSM 13481	GCA_014201655.1	90323	90323	type	True	95.3224	582	621	95	inconclusive
Thermosipho africanus	strain=Ob7	GCA_003351105.1	2421	2421	type	True	94.3259	551	621	95	below_threshold
Thermosipho melanesiensis	strain=BI429	GCA_000016905.1	46541	46541	type	True	77.9075	225	621	95	below_threshold
Thermosipho affectus	strain=ik275mar	GCA_001990485.1	660294	660294	type	True	77.754	190	621	95	below_threshold
Thermosipho atlanticus	strain=DSM 15807	GCA_900129985.1	238991	238991	type	True	77.6207	123	621	95	below_threshold
Thermosipho ferrireducens	strain=JL129W03	GCA_017358165.1	2571116	2571116	type	True	76.8355	88	621	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:39:45,309] [INFO] DFAST Taxonomy check result was written to GCF_003990895.1_ASM399089v1_genomic.fna/tc_result.tsv
[2024-01-25 18:39:45,309] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:39:45,309] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:39:45,310] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49f973ec-c0fe-4341-aa6f-65d7852e3938/dqc_reference/checkm_data
[2024-01-25 18:39:45,310] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:39:45,332] [INFO] Task started: CheckM
[2024-01-25 18:39:45,333] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003990895.1_ASM399089v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003990895.1_ASM399089v1_genomic.fna/checkm_input GCF_003990895.1_ASM399089v1_genomic.fna/checkm_result
[2024-01-25 18:40:00,918] [INFO] Task succeeded: CheckM
[2024-01-25 18:40:00,919] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:40:00,935] [INFO] ===== Completeness check finished =====
[2024-01-25 18:40:00,936] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:40:00,936] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003990895.1_ASM399089v1_genomic.fna/markers.fasta)
[2024-01-25 18:40:00,936] [INFO] Task started: Blastn
[2024-01-25 18:40:00,936] [INFO] Running command: blastn -query GCF_003990895.1_ASM399089v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49f973ec-c0fe-4341-aa6f-65d7852e3938/dqc_reference/reference_markers_gtdb.fasta -out GCF_003990895.1_ASM399089v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:01,649] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:01,652] [INFO] Selected 16 target genomes.
[2024-01-25 18:40:01,652] [INFO] Target genome list was writen to GCF_003990895.1_ASM399089v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:40:01,668] [INFO] Task started: fastANI
[2024-01-25 18:40:01,668] [INFO] Running command: fastANI --query /var/lib/cwl/stg2daad7b2-ed47-4ba2-bb53-9bef5e6d8c17/GCF_003990895.1_ASM399089v1_genomic.fna.gz --refList GCF_003990895.1_ASM399089v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003990895.1_ASM399089v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:40:06,619] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:06,625] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:40:06,625] [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_014201655.1	s__Thermosipho japonicus	95.3581	581	621	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__Fervidobacteriaceae;g__Thermosipho	95.0	95.40	95.40	0.94	0.94	2	conclusive
GCF_003351105.1	s__Thermosipho africanus	94.29	552	621	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__Fervidobacteriaceae;g__Thermosipho	95.0	98.56	98.53	0.93	0.90	3	-
GCF_000016905.1	s__Thermosipho melanesiensis	77.8923	226	621	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__Fervidobacteriaceae;g__Thermosipho	95.0	100.00	100.00	1.00	1.00	7	-
GCF_001990485.1	s__Thermosipho affectus	77.7371	191	621	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__Fervidobacteriaceae;g__Thermosipho	95.0	98.44	97.33	0.96	0.94	6	-
GCF_900129985.1	s__Thermosipho_A atlanticus	77.6207	123	621	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__Fervidobacteriaceae;g__Thermosipho_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017656335.1	s__Thermosipho_A sp017656335	77.5705	172	621	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__Fervidobacteriaceae;g__Thermosipho_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017656345.1	s__Thermosipho_A sp017656345	77.3192	135	621	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__Fervidobacteriaceae;g__Thermosipho_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:40:06,627] [INFO] GTDB search result was written to GCF_003990895.1_ASM399089v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:40:06,628] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:40:06,632] [INFO] DFAST_QC result json was written to GCF_003990895.1_ASM399089v1_genomic.fna/dqc_result.json
[2024-01-25 18:40:06,632] [INFO] DFAST_QC completed!
[2024-01-25 18:40:06,632] [INFO] Total running time: 0h0m31s