[2024-01-24 15:10:53,974] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:53,978] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:53,979] [INFO] DQC Reference Directory: /var/lib/cwl/stg98557075-8d17-49f9-a723-8cb74614d0be/dqc_reference
[2024-01-24 15:10:56,638] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:56,639] [INFO] Task started: Prodigal
[2024-01-24 15:10:56,639] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f34abd2-06cf-497c-8c80-496576853865/GCF_027946175.1_ASM2794617v1_genomic.fna.gz | prodigal -d GCF_027946175.1_ASM2794617v1_genomic.fna/cds.fna -a GCF_027946175.1_ASM2794617v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:01,204] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:01,204] [INFO] Task started: HMMsearch
[2024-01-24 15:11:01,204] [INFO] Running command: hmmsearch --tblout GCF_027946175.1_ASM2794617v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98557075-8d17-49f9-a723-8cb74614d0be/dqc_reference/reference_markers.hmm GCF_027946175.1_ASM2794617v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:01,464] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:01,465] [INFO] Found 6/6 markers.
[2024-01-24 15:11:01,490] [INFO] Query marker FASTA was written to GCF_027946175.1_ASM2794617v1_genomic.fna/markers.fasta
[2024-01-24 15:11:01,490] [INFO] Task started: Blastn
[2024-01-24 15:11:01,490] [INFO] Running command: blastn -query GCF_027946175.1_ASM2794617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98557075-8d17-49f9-a723-8cb74614d0be/dqc_reference/reference_markers.fasta -out GCF_027946175.1_ASM2794617v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:02,436] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:02,439] [INFO] Selected 21 target genomes.
[2024-01-24 15:11:02,440] [INFO] Target genome list was writen to GCF_027946175.1_ASM2794617v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:02,501] [INFO] Task started: fastANI
[2024-01-24 15:11:02,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f34abd2-06cf-497c-8c80-496576853865/GCF_027946175.1_ASM2794617v1_genomic.fna.gz --refList GCF_027946175.1_ASM2794617v1_genomic.fna/target_genomes.txt --output GCF_027946175.1_ASM2794617v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:09,605] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:09,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98557075-8d17-49f9-a723-8cb74614d0be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:09,606] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98557075-8d17-49f9-a723-8cb74614d0be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:09,610] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:09,610] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:09,610] [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
Nitratiruptor tergarcus	strain=DSM 16512	GCA_900176045.1	269259	269259	type	True	99.9679	635	646	95	conclusive
Nitrosophilus labii	strain=HRV44	GCA_014466985.1	2706014	2706014	type	True	77.8603	117	646	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:09,613] [INFO] DFAST Taxonomy check result was written to GCF_027946175.1_ASM2794617v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:09,618] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:09,618] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:09,618] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98557075-8d17-49f9-a723-8cb74614d0be/dqc_reference/checkm_data
[2024-01-24 15:11:09,620] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:09,646] [INFO] Task started: CheckM
[2024-01-24 15:11:09,646] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027946175.1_ASM2794617v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027946175.1_ASM2794617v1_genomic.fna/checkm_input GCF_027946175.1_ASM2794617v1_genomic.fna/checkm_result
[2024-01-24 15:11:30,931] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:30,932] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:30,949] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:30,950] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:30,950] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027946175.1_ASM2794617v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:30,951] [INFO] Task started: Blastn
[2024-01-24 15:11:30,951] [INFO] Running command: blastn -query GCF_027946175.1_ASM2794617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98557075-8d17-49f9-a723-8cb74614d0be/dqc_reference/reference_markers_gtdb.fasta -out GCF_027946175.1_ASM2794617v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:31,791] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:31,798] [INFO] Selected 18 target genomes.
[2024-01-24 15:11:31,798] [INFO] Target genome list was writen to GCF_027946175.1_ASM2794617v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:31,829] [INFO] Task started: fastANI
[2024-01-24 15:11:31,830] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f34abd2-06cf-497c-8c80-496576853865/GCF_027946175.1_ASM2794617v1_genomic.fna.gz --refList GCF_027946175.1_ASM2794617v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027946175.1_ASM2794617v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:38,871] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:38,886] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:38,886] [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_900176045.1	s__Nitratiruptor tergarcus	99.9679	635	646	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Nitratiruptoraceae;g__Nitratiruptor	95.0	95.63	95.63	0.89	0.89	3	conclusive
GCF_016593235.1	s__Nitratiruptor sp016593235	81.2427	290	646	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Nitratiruptoraceae;g__Nitratiruptor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016629565.1	s__YY08-10 sp016629565	80.6903	197	646	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Nitratiruptoraceae;g__YY08-10	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000010325.1	s__YY08-10 sp000010325	80.3856	199	646	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Nitratiruptoraceae;g__YY08-10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494535.1	s__Nitratiruptor sp015494535	77.8368	131	646	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Nitratiruptoraceae;g__Nitratiruptor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494595.1	s__Nitratiruptor sp015494595	77.7706	158	646	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Nitratiruptoraceae;g__Nitratiruptor	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:38,889] [INFO] GTDB search result was written to GCF_027946175.1_ASM2794617v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:38,890] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:38,893] [INFO] DFAST_QC result json was written to GCF_027946175.1_ASM2794617v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:38,893] [INFO] DFAST_QC completed!
[2024-01-24 15:11:38,893] [INFO] Total running time: 0h0m45s