[2024-01-24 11:51:06,096] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:06,200] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:06,200] [INFO] DQC Reference Directory: /var/lib/cwl/stg2bca7717-543b-4382-81f4-5efbb8997f37/dqc_reference
[2024-01-24 11:51:07,479] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:07,481] [INFO] Task started: Prodigal
[2024-01-24 11:51:07,481] [INFO] Running command: gunzip -c /var/lib/cwl/stg28196c24-97af-4359-8755-42b1b79046e0/GCF_001535545.1_ASM153554v1_genomic.fna.gz | prodigal -d GCF_001535545.1_ASM153554v1_genomic.fna/cds.fna -a GCF_001535545.1_ASM153554v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:18,458] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:18,459] [INFO] Task started: HMMsearch
[2024-01-24 11:51:18,459] [INFO] Running command: hmmsearch --tblout GCF_001535545.1_ASM153554v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2bca7717-543b-4382-81f4-5efbb8997f37/dqc_reference/reference_markers.hmm GCF_001535545.1_ASM153554v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:18,722] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:18,724] [INFO] Found 6/6 markers.
[2024-01-24 11:51:18,748] [INFO] Query marker FASTA was written to GCF_001535545.1_ASM153554v1_genomic.fna/markers.fasta
[2024-01-24 11:51:18,749] [INFO] Task started: Blastn
[2024-01-24 11:51:18,749] [INFO] Running command: blastn -query GCF_001535545.1_ASM153554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bca7717-543b-4382-81f4-5efbb8997f37/dqc_reference/reference_markers.fasta -out GCF_001535545.1_ASM153554v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:19,357] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:19,361] [INFO] Selected 7 target genomes.
[2024-01-24 11:51:19,362] [INFO] Target genome list was writen to GCF_001535545.1_ASM153554v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:19,381] [INFO] Task started: fastANI
[2024-01-24 11:51:19,381] [INFO] Running command: fastANI --query /var/lib/cwl/stg28196c24-97af-4359-8755-42b1b79046e0/GCF_001535545.1_ASM153554v1_genomic.fna.gz --refList GCF_001535545.1_ASM153554v1_genomic.fna/target_genomes.txt --output GCF_001535545.1_ASM153554v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:23,898] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:23,898] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2bca7717-543b-4382-81f4-5efbb8997f37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:23,899] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2bca7717-543b-4382-81f4-5efbb8997f37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:23,912] [INFO] Found 7 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:51:23,912] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:51:23,912] [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
Thermus parvatiensis	strain=RL	GCA_001535545.1	456163	456163	type	True	100.0	671	671	95	inconclusive
Thermus parvatiensis	strain=RL	GCA_000252835.2	456163	456163	type	True	98.7735	646	671	95	inconclusive
Thermus thermophilus	strain=HB8	GCA_000091545.1	274	274	type	True	95.6989	590	671	95	inconclusive
Thermus thermophilus	strain=JCM10941	GCA_019973715.1	274	274	type	True	95.6385	591	671	95	inconclusive
Thermus arciformis	strain=CGMCC 1.6992	GCA_900102145.1	482827	482827	type	True	90.1923	528	671	95	below_threshold
Thermus arciformis	strain=JCM 15153	GCA_022556335.1	482827	482827	type	True	90.1407	531	671	95	below_threshold
Thermus islandicus	strain=DSM 21543	GCA_000421625.1	540988	540988	type	True	85.4824	499	671	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:23,914] [INFO] DFAST Taxonomy check result was written to GCF_001535545.1_ASM153554v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:23,915] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:23,915] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:23,915] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2bca7717-543b-4382-81f4-5efbb8997f37/dqc_reference/checkm_data
[2024-01-24 11:51:23,916] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:23,943] [INFO] Task started: CheckM
[2024-01-24 11:51:23,943] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001535545.1_ASM153554v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001535545.1_ASM153554v1_genomic.fna/checkm_input GCF_001535545.1_ASM153554v1_genomic.fna/checkm_result
[2024-01-24 11:51:57,125] [INFO] Task succeeded: CheckM
[2024-01-24 11:51:57,126] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:51:57,151] [INFO] ===== Completeness check finished =====
[2024-01-24 11:51:57,151] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:51:57,152] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001535545.1_ASM153554v1_genomic.fna/markers.fasta)
[2024-01-24 11:51:57,152] [INFO] Task started: Blastn
[2024-01-24 11:51:57,153] [INFO] Running command: blastn -query GCF_001535545.1_ASM153554v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bca7717-543b-4382-81f4-5efbb8997f37/dqc_reference/reference_markers_gtdb.fasta -out GCF_001535545.1_ASM153554v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:58,096] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:58,100] [INFO] Selected 9 target genomes.
[2024-01-24 11:51:58,100] [INFO] Target genome list was writen to GCF_001535545.1_ASM153554v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:51:58,108] [INFO] Task started: fastANI
[2024-01-24 11:51:58,109] [INFO] Running command: fastANI --query /var/lib/cwl/stg28196c24-97af-4359-8755-42b1b79046e0/GCF_001535545.1_ASM153554v1_genomic.fna.gz --refList GCF_001535545.1_ASM153554v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001535545.1_ASM153554v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:03,785] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:03,795] [INFO] Found 9 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 11:52:03,796] [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_001535545.1	s__Thermus parvatiensis	100.0	671	671	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.7334	98.79	98.79	0.97	0.97	2	inconclusive
GCF_000091545.1	s__Thermus thermophilus	95.7374	588	671	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.7334	98.46	96.78	0.92	0.87	18	inconclusive
GCA_002355995.1	s__Thermus thermophilus_C	94.1366	585	671	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.6833	N/A	N/A	N/A	N/A	1	-
GCF_900102145.1	s__Thermus arciformis	90.1663	529	671	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647535.1	s__Thermus composti	88.7931	527	671	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001311585.1	s__Thermus sp001311585	87.6182	363	671	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000794385.1	s__Thermus sp000794385	86.2124	519	671	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421625.1	s__Thermus islandicus	85.5105	500	671	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003426945.1	s__Thermus sediminis	84.9829	514	671	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:03,798] [INFO] GTDB search result was written to GCF_001535545.1_ASM153554v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:03,798] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:03,801] [INFO] DFAST_QC result json was written to GCF_001535545.1_ASM153554v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:03,801] [INFO] DFAST_QC completed!
[2024-01-24 11:52:03,801] [INFO] Total running time: 0h0m58s