[2024-01-24 13:57:43,907] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:43,908] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:43,909] [INFO] DQC Reference Directory: /var/lib/cwl/stg7fa3aa92-9490-4a34-ba6d-f2a12d9642b9/dqc_reference
[2024-01-24 13:57:45,150] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:45,151] [INFO] Task started: Prodigal
[2024-01-24 13:57:45,151] [INFO] Running command: gunzip -c /var/lib/cwl/stgb481b302-15a8-4e36-b5d1-253b2e87fe0c/GCF_014647535.1_ASM1464753v1_genomic.fna.gz | prodigal -d GCF_014647535.1_ASM1464753v1_genomic.fna/cds.fna -a GCF_014647535.1_ASM1464753v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:56,331] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:56,331] [INFO] Task started: HMMsearch
[2024-01-24 13:57:56,331] [INFO] Running command: hmmsearch --tblout GCF_014647535.1_ASM1464753v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7fa3aa92-9490-4a34-ba6d-f2a12d9642b9/dqc_reference/reference_markers.hmm GCF_014647535.1_ASM1464753v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:56,558] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:56,560] [INFO] Found 6/6 markers.
[2024-01-24 13:57:56,585] [INFO] Query marker FASTA was written to GCF_014647535.1_ASM1464753v1_genomic.fna/markers.fasta
[2024-01-24 13:57:56,585] [INFO] Task started: Blastn
[2024-01-24 13:57:56,585] [INFO] Running command: blastn -query GCF_014647535.1_ASM1464753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7fa3aa92-9490-4a34-ba6d-f2a12d9642b9/dqc_reference/reference_markers.fasta -out GCF_014647535.1_ASM1464753v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:57,221] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:57,224] [INFO] Selected 11 target genomes.
[2024-01-24 13:57:57,225] [INFO] Target genome list was writen to GCF_014647535.1_ASM1464753v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:57,234] [INFO] Task started: fastANI
[2024-01-24 13:57:57,234] [INFO] Running command: fastANI --query /var/lib/cwl/stgb481b302-15a8-4e36-b5d1-253b2e87fe0c/GCF_014647535.1_ASM1464753v1_genomic.fna.gz --refList GCF_014647535.1_ASM1464753v1_genomic.fna/target_genomes.txt --output GCF_014647535.1_ASM1464753v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:04,019] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:04,019] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7fa3aa92-9490-4a34-ba6d-f2a12d9642b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:04,020] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7fa3aa92-9490-4a34-ba6d-f2a12d9642b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:04,030] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:58:04,030] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:58:04,031] [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 thermophilus	strain=JCM10941	GCA_019973715.1	274	274	type	True	88.7662	527	661	95	below_threshold
Thermus thermophilus	strain=HB8	GCA_000091545.1	274	274	type	True	88.7458	538	661	95	below_threshold
Thermus parvatiensis	strain=RL	GCA_000252835.2	456163	456163	type	True	88.7394	516	661	95	below_threshold
Thermus parvatiensis	strain=RL	GCA_001535545.1	456163	456163	type	True	88.6891	541	661	95	below_threshold
Thermus arciformis	strain=CGMCC 1.6992	GCA_900102145.1	482827	482827	type	True	88.5617	549	661	95	below_threshold
Thermus arciformis	strain=JCM 15153	GCA_022556335.1	482827	482827	type	True	88.5024	549	661	95	below_threshold
Thermus aquaticus	strain=YT-1	GCA_001280255.1	271	271	type	True	85.9539	548	661	95	below_threshold
Thermus igniterrae	strain=ATCC 700962	GCA_000376265.1	88189	88189	type	True	85.8656	529	661	95	below_threshold
Thermus islandicus	strain=DSM 21543	GCA_000421625.1	540988	540988	type	True	85.6333	517	661	95	below_threshold
Thermus thermamylovorans	strain=CFH 72773T	GCA_004307015.1	2509362	2509362	type	True	85.5861	541	661	95	below_threshold
Thermus sediminis	strain=L198	GCA_003426945.1	1761908	1761908	type	True	85.419	520	661	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:04,032] [INFO] DFAST Taxonomy check result was written to GCF_014647535.1_ASM1464753v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:04,032] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:04,033] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:04,033] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7fa3aa92-9490-4a34-ba6d-f2a12d9642b9/dqc_reference/checkm_data
[2024-01-24 13:58:04,034] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:04,058] [INFO] Task started: CheckM
[2024-01-24 13:58:04,059] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014647535.1_ASM1464753v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014647535.1_ASM1464753v1_genomic.fna/checkm_input GCF_014647535.1_ASM1464753v1_genomic.fna/checkm_result
[2024-01-24 13:58:38,870] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:38,871] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:38,896] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:38,896] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:38,897] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014647535.1_ASM1464753v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:38,897] [INFO] Task started: Blastn
[2024-01-24 13:58:38,897] [INFO] Running command: blastn -query GCF_014647535.1_ASM1464753v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7fa3aa92-9490-4a34-ba6d-f2a12d9642b9/dqc_reference/reference_markers_gtdb.fasta -out GCF_014647535.1_ASM1464753v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:39,774] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:39,781] [INFO] Selected 12 target genomes.
[2024-01-24 13:58:39,781] [INFO] Target genome list was writen to GCF_014647535.1_ASM1464753v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:39,879] [INFO] Task started: fastANI
[2024-01-24 13:58:39,880] [INFO] Running command: fastANI --query /var/lib/cwl/stgb481b302-15a8-4e36-b5d1-253b2e87fe0c/GCF_014647535.1_ASM1464753v1_genomic.fna.gz --refList GCF_014647535.1_ASM1464753v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014647535.1_ASM1464753v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:47,749] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:47,765] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:47,765] [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_014647535.1	s__Thermus composti	100.0	658	661	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001535545.1	s__Thermus parvatiensis	88.7282	539	661	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.7334	98.79	98.79	0.97	0.97	2	-
GCF_000091545.1	s__Thermus thermophilus	88.7139	540	661	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.7334	98.46	96.78	0.92	0.87	18	-
GCF_900102145.1	s__Thermus arciformis	88.5873	548	661	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002355995.1	s__Thermus thermophilus_C	88.3576	523	661	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.6833	N/A	N/A	N/A	N/A	1	-
GCA_001311585.1	s__Thermus sp001311585	87.1976	358	661	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	86.9799	536	661	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001880325.1	s__Thermus brockianus	86.4296	537	661	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280255.1	s__Thermus aquaticus	85.9817	546	661	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	98.02	97.96	0.92	0.92	3	-
GCF_000376265.1	s__Thermus igniterrae	85.9694	523	661	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	85.6303	517	661	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004307015.1	s__Thermus thermamylovorans	85.5716	542	661	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 13:58:47,770] [INFO] GTDB search result was written to GCF_014647535.1_ASM1464753v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:47,771] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:47,777] [INFO] DFAST_QC result json was written to GCF_014647535.1_ASM1464753v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:47,777] [INFO] DFAST_QC completed!
[2024-01-24 13:58:47,777] [INFO] Total running time: 0h1m4s