[2024-01-24 12:21:59,326] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:59,330] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:59,331] [INFO] DQC Reference Directory: /var/lib/cwl/stgaeb6f35a-ec13-455b-948c-273af514b286/dqc_reference
[2024-01-24 12:22:00,835] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:00,836] [INFO] Task started: Prodigal
[2024-01-24 12:22:00,836] [INFO] Running command: gunzip -c /var/lib/cwl/stg907eecb2-7e61-4e4a-aef9-aacabeabd923/GCF_000020985.1_ASM2098v1_genomic.fna.gz | prodigal -d GCF_000020985.1_ASM2098v1_genomic.fna/cds.fna -a GCF_000020985.1_ASM2098v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:04,703] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:04,703] [INFO] Task started: HMMsearch
[2024-01-24 12:22:04,703] [INFO] Running command: hmmsearch --tblout GCF_000020985.1_ASM2098v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaeb6f35a-ec13-455b-948c-273af514b286/dqc_reference/reference_markers.hmm GCF_000020985.1_ASM2098v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:05,055] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:05,056] [INFO] Found 6/6 markers.
[2024-01-24 12:22:05,098] [INFO] Query marker FASTA was written to GCF_000020985.1_ASM2098v1_genomic.fna/markers.fasta
[2024-01-24 12:22:05,099] [INFO] Task started: Blastn
[2024-01-24 12:22:05,099] [INFO] Running command: blastn -query GCF_000020985.1_ASM2098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaeb6f35a-ec13-455b-948c-273af514b286/dqc_reference/reference_markers.fasta -out GCF_000020985.1_ASM2098v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:05,738] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:05,741] [INFO] Selected 19 target genomes.
[2024-01-24 12:22:05,742] [INFO] Target genome list was writen to GCF_000020985.1_ASM2098v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:05,749] [INFO] Task started: fastANI
[2024-01-24 12:22:05,749] [INFO] Running command: fastANI --query /var/lib/cwl/stg907eecb2-7e61-4e4a-aef9-aacabeabd923/GCF_000020985.1_ASM2098v1_genomic.fna.gz --refList GCF_000020985.1_ASM2098v1_genomic.fna/target_genomes.txt --output GCF_000020985.1_ASM2098v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:13,710] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:13,711] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaeb6f35a-ec13-455b-948c-273af514b286/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:13,711] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaeb6f35a-ec13-455b-948c-273af514b286/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:13,716] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:22:13,716] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:22:13,716] [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 aggregans	strain=TGE-P1	GCA_001514535.1	86166	86166	type	True	79.7337	400	667	95	below_threshold
Thermodesulfovibrio thiophilus	strain=DSM 17215	GCA_000423865.1	340095	340095	type	True	78.8043	321	667	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:13,718] [INFO] DFAST Taxonomy check result was written to GCF_000020985.1_ASM2098v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:13,718] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:13,718] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:13,719] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaeb6f35a-ec13-455b-948c-273af514b286/dqc_reference/checkm_data
[2024-01-24 12:22:13,720] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:13,744] [INFO] Task started: CheckM
[2024-01-24 12:22:13,744] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000020985.1_ASM2098v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000020985.1_ASM2098v1_genomic.fna/checkm_input GCF_000020985.1_ASM2098v1_genomic.fna/checkm_result
[2024-01-24 12:22:33,980] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:33,982] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:34,017] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:34,018] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:34,018] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000020985.1_ASM2098v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:34,019] [INFO] Task started: Blastn
[2024-01-24 12:22:34,019] [INFO] Running command: blastn -query GCF_000020985.1_ASM2098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaeb6f35a-ec13-455b-948c-273af514b286/dqc_reference/reference_markers_gtdb.fasta -out GCF_000020985.1_ASM2098v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:34,903] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:34,908] [INFO] Selected 12 target genomes.
[2024-01-24 12:22:34,909] [INFO] Target genome list was writen to GCF_000020985.1_ASM2098v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:34,920] [INFO] Task started: fastANI
[2024-01-24 12:22:34,921] [INFO] Running command: fastANI --query /var/lib/cwl/stg907eecb2-7e61-4e4a-aef9-aacabeabd923/GCF_000020985.1_ASM2098v1_genomic.fna.gz --refList GCF_000020985.1_ASM2098v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000020985.1_ASM2098v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:39,635] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:39,642] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:22:39,642] [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_000020985.1	s__Thermodesulfovibrio yellowstonii	100.0	660	667	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__Thermodesulfovibrionaceae;g__Thermodesulfovibrio	95.0	99.02	98.99	0.93	0.91	3	conclusive
GCA_002339325.1	s__Thermodesulfovibrio sp002339325	80.6029	236	667	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__Thermodesulfovibrionaceae;g__Thermodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002878055.1	s__Thermodesulfovibrio aggregans_A	80.2685	301	667	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	79.7321	400	667	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__Thermodesulfovibrionaceae;g__Thermodesulfovibrio	95.0	99.76	99.76	1.00	1.00	2	-
GCF_000423865.1	s__Thermodesulfovibrio thiophilus	78.792	323	667	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__Thermodesulfovibrionaceae;g__Thermodesulfovibrio	95.0	98.51	98.51	0.93	0.93	2	-
GCA_011338125.1	s__Thermodesulfovibrio aggregans_B	78.4626	225	667	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__Thermodesulfovibrionaceae;g__Thermodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001707915.1	s__Thermodesulfovibrio sp001707915	78.3663	277	667	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__Thermodesulfovibrionaceae;g__Thermodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:22:39,644] [INFO] GTDB search result was written to GCF_000020985.1_ASM2098v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:39,645] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:39,647] [INFO] DFAST_QC result json was written to GCF_000020985.1_ASM2098v1_genomic.fna/dqc_result.json
[2024-01-24 12:22:39,647] [INFO] DFAST_QC completed!
[2024-01-24 12:22:39,647] [INFO] Total running time: 0h0m40s