[2024-01-24 14:06:30,243] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:30,245] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:30,245] [INFO] DQC Reference Directory: /var/lib/cwl/stgf170cd01-c863-4702-8e1e-78f849ef9c8d/dqc_reference
[2024-01-24 14:06:31,546] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:31,547] [INFO] Task started: Prodigal
[2024-01-24 14:06:31,548] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b302f35-043e-41d4-8a79-d49dde39a3b7/GCF_000235405.2_ASM23540v3_genomic.fna.gz | prodigal -d GCF_000235405.2_ASM23540v3_genomic.fna/cds.fna -a GCF_000235405.2_ASM23540v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:36,852] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:36,853] [INFO] Task started: HMMsearch
[2024-01-24 14:06:36,853] [INFO] Running command: hmmsearch --tblout GCF_000235405.2_ASM23540v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf170cd01-c863-4702-8e1e-78f849ef9c8d/dqc_reference/reference_markers.hmm GCF_000235405.2_ASM23540v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:37,044] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:37,045] [INFO] Found 6/6 markers.
[2024-01-24 14:06:37,067] [INFO] Query marker FASTA was written to GCF_000235405.2_ASM23540v3_genomic.fna/markers.fasta
[2024-01-24 14:06:37,067] [INFO] Task started: Blastn
[2024-01-24 14:06:37,067] [INFO] Running command: blastn -query GCF_000235405.2_ASM23540v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgf170cd01-c863-4702-8e1e-78f849ef9c8d/dqc_reference/reference_markers.fasta -out GCF_000235405.2_ASM23540v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:37,605] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:37,608] [INFO] Selected 11 target genomes.
[2024-01-24 14:06:37,608] [INFO] Target genome list was writen to GCF_000235405.2_ASM23540v3_genomic.fna/target_genomes.txt
[2024-01-24 14:06:37,618] [INFO] Task started: fastANI
[2024-01-24 14:06:37,618] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b302f35-043e-41d4-8a79-d49dde39a3b7/GCF_000235405.2_ASM23540v3_genomic.fna.gz --refList GCF_000235405.2_ASM23540v3_genomic.fna/target_genomes.txt --output GCF_000235405.2_ASM23540v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:42,101] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:42,101] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf170cd01-c863-4702-8e1e-78f849ef9c8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:42,102] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf170cd01-c863-4702-8e1e-78f849ef9c8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:42,107] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:42,107] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:42,107] [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
Fervidobacterium pennivorans	strain=DSM 9078	GCA_000235405.3	93466	93466	type	True	100.0	721	722	95	conclusive
Fervidobacterium changbaicum	strain=CBS-1	GCA_004117075.1	310769	310769	type	True	80.522	317	722	95	below_threshold
Fervidobacterium changbaicum	strain=DSM 17883	GCA_900100515.1	310769	310769	type	True	80.1463	304	722	95	below_threshold
Fervidobacterium thailandense	strain=FC2004	GCA_001719065.1	1008305	1008305	type	True	77.697	58	722	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:42,109] [INFO] DFAST Taxonomy check result was written to GCF_000235405.2_ASM23540v3_genomic.fna/tc_result.tsv
[2024-01-24 14:06:42,109] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:42,109] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:42,110] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf170cd01-c863-4702-8e1e-78f849ef9c8d/dqc_reference/checkm_data
[2024-01-24 14:06:42,111] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:42,133] [INFO] Task started: CheckM
[2024-01-24 14:06:42,133] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000235405.2_ASM23540v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000235405.2_ASM23540v3_genomic.fna/checkm_input GCF_000235405.2_ASM23540v3_genomic.fna/checkm_result
[2024-01-24 14:07:03,888] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:03,889] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:03,912] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:03,913] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:03,913] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000235405.2_ASM23540v3_genomic.fna/markers.fasta)
[2024-01-24 14:07:03,913] [INFO] Task started: Blastn
[2024-01-24 14:07:03,913] [INFO] Running command: blastn -query GCF_000235405.2_ASM23540v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgf170cd01-c863-4702-8e1e-78f849ef9c8d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000235405.2_ASM23540v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:04,577] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:04,581] [INFO] Selected 14 target genomes.
[2024-01-24 14:07:04,581] [INFO] Target genome list was writen to GCF_000235405.2_ASM23540v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:04,593] [INFO] Task started: fastANI
[2024-01-24 14:07:04,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b302f35-043e-41d4-8a79-d49dde39a3b7/GCF_000235405.2_ASM23540v3_genomic.fna.gz --refList GCF_000235405.2_ASM23540v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000235405.2_ASM23540v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:10,613] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:10,619] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:10,619] [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_000235405.2	s__Fervidobacterium pennivorans	100.0	721	722	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__Fervidobacteriaceae;g__Fervidobacterium	95.0	98.05	97.86	0.95	0.93	3	conclusive
GCF_001644665.1	s__Fervidobacterium pennivorans_A	91.9027	591	722	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__Fervidobacteriaceae;g__Fervidobacterium	95.0	98.95	98.92	0.89	0.86	4	-
GCF_004117075.1	s__Fervidobacterium changbaicum	80.5199	316	722	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__Fervidobacteriaceae;g__Fervidobacterium	95.0	99.46	98.92	0.95	0.90	3	-
GCF_001719065.1	s__Fervidobacterium_A thailandense	77.7046	57	722	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__Fervidobacteriaceae;g__Fervidobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002432805.1	s__Fervidobacterium sp002432805	77.5835	51	722	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Thermotogales;f__Fervidobacteriaceae;g__Fervidobacterium	95.0	99.87	99.87	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:10,621] [INFO] GTDB search result was written to GCF_000235405.2_ASM23540v3_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:10,621] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:10,624] [INFO] DFAST_QC result json was written to GCF_000235405.2_ASM23540v3_genomic.fna/dqc_result.json
[2024-01-24 14:07:10,624] [INFO] DFAST_QC completed!
[2024-01-24 14:07:10,624] [INFO] Total running time: 0h0m40s