[2024-01-24 12:21:54,087] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:54,093] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:54,093] [INFO] DQC Reference Directory: /var/lib/cwl/stg17b456cc-6460-466d-82c8-79066895991b/dqc_reference
[2024-01-24 12:21:55,271] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:55,272] [INFO] Task started: Prodigal
[2024-01-24 12:21:55,272] [INFO] Running command: gunzip -c /var/lib/cwl/stgc9fc6852-08d8-4573-94e7-04c1eaa0f829/GCF_002924615.1_ASM292461v1_genomic.fna.gz | prodigal -d GCF_002924615.1_ASM292461v1_genomic.fna/cds.fna -a GCF_002924615.1_ASM292461v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:00,054] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:00,055] [INFO] Task started: HMMsearch
[2024-01-24 12:22:00,055] [INFO] Running command: hmmsearch --tblout GCF_002924615.1_ASM292461v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17b456cc-6460-466d-82c8-79066895991b/dqc_reference/reference_markers.hmm GCF_002924615.1_ASM292461v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:00,440] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:00,441] [INFO] Found 6/6 markers.
[2024-01-24 12:22:00,490] [INFO] Query marker FASTA was written to GCF_002924615.1_ASM292461v1_genomic.fna/markers.fasta
[2024-01-24 12:22:00,491] [INFO] Task started: Blastn
[2024-01-24 12:22:00,491] [INFO] Running command: blastn -query GCF_002924615.1_ASM292461v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17b456cc-6460-466d-82c8-79066895991b/dqc_reference/reference_markers.fasta -out GCF_002924615.1_ASM292461v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:01,187] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:01,190] [INFO] Selected 8 target genomes.
[2024-01-24 12:22:01,190] [INFO] Target genome list was writen to GCF_002924615.1_ASM292461v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:01,249] [INFO] Task started: fastANI
[2024-01-24 12:22:01,250] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9fc6852-08d8-4573-94e7-04c1eaa0f829/GCF_002924615.1_ASM292461v1_genomic.fna.gz --refList GCF_002924615.1_ASM292461v1_genomic.fna/target_genomes.txt --output GCF_002924615.1_ASM292461v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:05,739] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:05,739] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17b456cc-6460-466d-82c8-79066895991b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:05,740] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17b456cc-6460-466d-82c8-79066895991b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:05,747] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:22:05,747] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:22:05,747] [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
Petrotoga halophila	strain=DSM 16923	GCA_002924615.1	301141	301141	type	True	100.0	738	754	95	inconclusive
Petrotoga miotherma	strain=DSM 10691	GCA_002895605.1	28237	28237	type	True	97.34	559	754	95	inconclusive
Petrotoga mexicana	strain=DSM 14811	GCA_002895565.1	204046	204046	type	True	94.8154	566	754	95	below_threshold
Petrotoga mobilis	strain=SJ95	GCA_000018605.1	69499	69499	type	True	91.807	545	754	95	below_threshold
Petrotoga sibirica	strain=DSM 13575	GCA_002924625.1	156202	156202	type	True	90.5664	519	754	95	below_threshold
Petrotoga sibirica	strain=DSM 13575	GCA_004366085.1	156202	156202	type	True	90.4955	521	754	95	below_threshold
Petrotoga olearia	strain=DSM 13574	GCA_002895525.1	156203	156203	type	True	90.1076	531	754	95	below_threshold
Petrotoga olearia	strain=DSM 13574	GCA_003688505.1	156203	156203	type	True	90.05	542	754	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:05,749] [INFO] DFAST Taxonomy check result was written to GCF_002924615.1_ASM292461v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:05,750] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:05,750] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:05,750] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17b456cc-6460-466d-82c8-79066895991b/dqc_reference/checkm_data
[2024-01-24 12:22:05,751] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:05,783] [INFO] Task started: CheckM
[2024-01-24 12:22:05,783] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002924615.1_ASM292461v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002924615.1_ASM292461v1_genomic.fna/checkm_input GCF_002924615.1_ASM292461v1_genomic.fna/checkm_result
[2024-01-24 12:22:28,519] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:28,520] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 28.70%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:28,554] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:28,554] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:28,555] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002924615.1_ASM292461v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:28,555] [INFO] Task started: Blastn
[2024-01-24 12:22:28,555] [INFO] Running command: blastn -query GCF_002924615.1_ASM292461v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg17b456cc-6460-466d-82c8-79066895991b/dqc_reference/reference_markers_gtdb.fasta -out GCF_002924615.1_ASM292461v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:29,326] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:29,331] [INFO] Selected 5 target genomes.
[2024-01-24 12:22:29,331] [INFO] Target genome list was writen to GCF_002924615.1_ASM292461v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:29,334] [INFO] Task started: fastANI
[2024-01-24 12:22:29,335] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9fc6852-08d8-4573-94e7-04c1eaa0f829/GCF_002924615.1_ASM292461v1_genomic.fna.gz --refList GCF_002924615.1_ASM292461v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002924615.1_ASM292461v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:32,370] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:32,376] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:22:32,376] [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_002895605.1	s__Petrotoga miotherma	97.2734	561	754	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Petrotogaceae;g__Petrotoga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002895565.1	s__Petrotoga mexicana	94.8154	566	754	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Petrotogaceae;g__Petrotoga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000018605.1	s__Petrotoga mobilis	91.7615	545	754	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Petrotogaceae;g__Petrotoga	95.0	96.50	96.03	0.88	0.86	7	-
GCF_002924625.1	s__Petrotoga sibirica	90.5664	519	754	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Petrotogaceae;g__Petrotoga	95.0	99.07	98.25	0.96	0.94	4	-
GCF_002895525.1	s__Petrotoga olearia	90.0754	533	754	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Petrotogaceae;g__Petrotoga	95.0	98.66	97.35	0.95	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:22:32,378] [INFO] GTDB search result was written to GCF_002924615.1_ASM292461v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:32,379] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:32,381] [INFO] DFAST_QC result json was written to GCF_002924615.1_ASM292461v1_genomic.fna/dqc_result.json
[2024-01-24 12:22:32,381] [INFO] DFAST_QC completed!
[2024-01-24 12:22:32,381] [INFO] Total running time: 0h0m38s