[2024-01-25 18:51:05,759] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:51:05,761] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:51:05,761] [INFO] DQC Reference Directory: /var/lib/cwl/stge5e75425-7dcc-4124-9876-d230465dac70/dqc_reference
[2024-01-25 18:51:06,903] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:51:06,904] [INFO] Task started: Prodigal
[2024-01-25 18:51:06,904] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b212743-6cce-451d-937b-76235f70dc72/GCF_000423865.1_ASM42386v1_genomic.fna.gz | prodigal -d GCF_000423865.1_ASM42386v1_genomic.fna/cds.fna -a GCF_000423865.1_ASM42386v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:51:10,064] [INFO] Task succeeded: Prodigal
[2024-01-25 18:51:10,064] [INFO] Task started: HMMsearch
[2024-01-25 18:51:10,064] [INFO] Running command: hmmsearch --tblout GCF_000423865.1_ASM42386v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5e75425-7dcc-4124-9876-d230465dac70/dqc_reference/reference_markers.hmm GCF_000423865.1_ASM42386v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:51:10,297] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:51:10,298] [INFO] Found 6/6 markers.
[2024-01-25 18:51:10,318] [INFO] Query marker FASTA was written to GCF_000423865.1_ASM42386v1_genomic.fna/markers.fasta
[2024-01-25 18:51:10,319] [INFO] Task started: Blastn
[2024-01-25 18:51:10,319] [INFO] Running command: blastn -query GCF_000423865.1_ASM42386v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5e75425-7dcc-4124-9876-d230465dac70/dqc_reference/reference_markers.fasta -out GCF_000423865.1_ASM42386v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:10,852] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:10,855] [INFO] Selected 17 target genomes.
[2024-01-25 18:51:10,856] [INFO] Target genome list was writen to GCF_000423865.1_ASM42386v1_genomic.fna/target_genomes.txt
[2024-01-25 18:51:10,879] [INFO] Task started: fastANI
[2024-01-25 18:51:10,879] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b212743-6cce-451d-937b-76235f70dc72/GCF_000423865.1_ASM42386v1_genomic.fna.gz --refList GCF_000423865.1_ASM42386v1_genomic.fna/target_genomes.txt --output GCF_000423865.1_ASM42386v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:51:18,368] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:18,369] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5e75425-7dcc-4124-9876-d230465dac70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:51:18,369] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5e75425-7dcc-4124-9876-d230465dac70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:51:18,374] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:51:18,374] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:51:18,374] [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
Thermodesulfovibrio thiophilus	strain=DSM 17215	GCA_000423865.1	340095	340095	type	True	100.0	616	616	95	conclusive
Thermodesulfovibrio aggregans	strain=TGE-P1	GCA_001514535.1	86166	86166	type	True	78.2283	281	616	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:51:18,375] [INFO] DFAST Taxonomy check result was written to GCF_000423865.1_ASM42386v1_genomic.fna/tc_result.tsv
[2024-01-25 18:51:18,376] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:51:18,376] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:51:18,376] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5e75425-7dcc-4124-9876-d230465dac70/dqc_reference/checkm_data
[2024-01-25 18:51:18,377] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:51:18,398] [INFO] Task started: CheckM
[2024-01-25 18:51:18,398] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000423865.1_ASM42386v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000423865.1_ASM42386v1_genomic.fna/checkm_input GCF_000423865.1_ASM42386v1_genomic.fna/checkm_result
[2024-01-25 18:51:34,440] [INFO] Task succeeded: CheckM
[2024-01-25 18:51:34,440] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:51:34,480] [INFO] ===== Completeness check finished =====
[2024-01-25 18:51:34,480] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:51:34,480] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000423865.1_ASM42386v1_genomic.fna/markers.fasta)
[2024-01-25 18:51:34,480] [INFO] Task started: Blastn
[2024-01-25 18:51:34,480] [INFO] Running command: blastn -query GCF_000423865.1_ASM42386v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge5e75425-7dcc-4124-9876-d230465dac70/dqc_reference/reference_markers_gtdb.fasta -out GCF_000423865.1_ASM42386v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:35,272] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:35,277] [INFO] Selected 12 target genomes.
[2024-01-25 18:51:35,277] [INFO] Target genome list was writen to GCF_000423865.1_ASM42386v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:51:35,295] [INFO] Task started: fastANI
[2024-01-25 18:51:35,295] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b212743-6cce-451d-937b-76235f70dc72/GCF_000423865.1_ASM42386v1_genomic.fna.gz --refList GCF_000423865.1_ASM42386v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000423865.1_ASM42386v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:51:39,983] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:39,988] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:51:39,989] [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_000423865.1	s__Thermodesulfovibrio thiophilus	100.0	616	616	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__Thermodesulfovibrionaceae;g__Thermodesulfovibrio	95.0	98.51	98.51	0.93	0.93	2	conclusive
GCF_000020985.1	s__Thermodesulfovibrio yellowstonii	78.7235	323	616	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__Thermodesulfovibrionaceae;g__Thermodesulfovibrio	95.0	99.02	98.99	0.93	0.91	3	-
GCA_002878055.1	s__Thermodesulfovibrio aggregans_A	78.5062	218	616	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__Thermodesulfovibrionaceae;g__Thermodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001514535.1	s__Thermodesulfovibrio aggregans	78.2283	281	616	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__Thermodesulfovibrionaceae;g__Thermodesulfovibrio	95.0	99.76	99.76	1.00	1.00	2	-
GCF_001707915.1	s__Thermodesulfovibrio sp001707915	77.8131	226	616	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__Thermodesulfovibrionaceae;g__Thermodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011338125.1	s__Thermodesulfovibrio aggregans_B	77.742	192	616	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__Thermodesulfovibrionaceae;g__Thermodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:51:39,990] [INFO] GTDB search result was written to GCF_000423865.1_ASM42386v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:51:39,991] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:51:39,993] [INFO] DFAST_QC result json was written to GCF_000423865.1_ASM42386v1_genomic.fna/dqc_result.json
[2024-01-25 18:51:39,993] [INFO] DFAST_QC completed!
[2024-01-25 18:51:39,993] [INFO] Total running time: 0h0m34s