[2024-01-24 12:40:20,595] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:20,597] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:20,598] [INFO] DQC Reference Directory: /var/lib/cwl/stgb64b6327-3609-4051-aa47-707935d93a2a/dqc_reference
[2024-01-24 12:40:21,834] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:21,835] [INFO] Task started: Prodigal
[2024-01-24 12:40:21,835] [INFO] Running command: gunzip -c /var/lib/cwl/stg382e98fa-64ed-4f60-9373-fa3361c02764/GCF_003426945.1_ASM342694v1_genomic.fna.gz | prodigal -d GCF_003426945.1_ASM342694v1_genomic.fna/cds.fna -a GCF_003426945.1_ASM342694v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:33,393] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:33,394] [INFO] Task started: HMMsearch
[2024-01-24 12:40:33,394] [INFO] Running command: hmmsearch --tblout GCF_003426945.1_ASM342694v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb64b6327-3609-4051-aa47-707935d93a2a/dqc_reference/reference_markers.hmm GCF_003426945.1_ASM342694v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:33,610] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:33,612] [INFO] Found 6/6 markers.
[2024-01-24 12:40:33,638] [INFO] Query marker FASTA was written to GCF_003426945.1_ASM342694v1_genomic.fna/markers.fasta
[2024-01-24 12:40:33,638] [INFO] Task started: Blastn
[2024-01-24 12:40:33,639] [INFO] Running command: blastn -query GCF_003426945.1_ASM342694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb64b6327-3609-4051-aa47-707935d93a2a/dqc_reference/reference_markers.fasta -out GCF_003426945.1_ASM342694v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:34,225] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:34,229] [INFO] Selected 12 target genomes.
[2024-01-24 12:40:34,230] [INFO] Target genome list was writen to GCF_003426945.1_ASM342694v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:34,235] [INFO] Task started: fastANI
[2024-01-24 12:40:34,235] [INFO] Running command: fastANI --query /var/lib/cwl/stg382e98fa-64ed-4f60-9373-fa3361c02764/GCF_003426945.1_ASM342694v1_genomic.fna.gz --refList GCF_003426945.1_ASM342694v1_genomic.fna/target_genomes.txt --output GCF_003426945.1_ASM342694v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:41,484] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:41,485] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb64b6327-3609-4051-aa47-707935d93a2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:41,485] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb64b6327-3609-4051-aa47-707935d93a2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:41,497] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:41,497] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:41,497] [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 sediminis	strain=L198	GCA_003426945.1	1761908	1761908	type	True	100.0	715	718	95	conclusive
Thermus aquaticus	strain=YT-1	GCA_001280255.1	271	271	type	True	88.5901	580	718	95	below_threshold
Thermus arciformis	strain=CGMCC 1.6992	GCA_900102145.1	482827	482827	type	True	86.4274	567	718	95	below_threshold
Thermus arciformis	strain=JCM 15153	GCA_022556335.1	482827	482827	type	True	86.2888	559	718	95	below_threshold
Thermus igniterrae	strain=ATCC 700962	GCA_000376265.1	88189	88189	type	True	85.733	546	718	95	below_threshold
Thermus islandicus	strain=DSM 21543	GCA_000421625.1	540988	540988	type	True	85.4428	533	718	95	below_threshold
Thermus thermamylovorans	strain=CFH 72773T	GCA_004307015.1	2509362	2509362	type	True	85.379	558	718	95	below_threshold
Thermus thermophilus	strain=JCM10941	GCA_019973715.1	274	274	type	True	85.2247	564	718	95	below_threshold
Thermus thermophilus	strain=HB8	GCA_000091545.1	274	274	type	True	85.2024	541	718	95	below_threshold
Thermus parvatiensis	strain=RL	GCA_000252835.2	456163	456163	type	True	84.751	517	718	95	below_threshold
Thermus caliditerrae	strain=YIM 77925	GCA_021462525.1	1330700	1330700	type	True	84.6658	552	718	95	below_threshold
Thermus scotoductus	strain=DSM 8553	GCA_000381045.1	37636	37636	suspected-type	True	83.5906	503	718	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:41,499] [INFO] DFAST Taxonomy check result was written to GCF_003426945.1_ASM342694v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:41,499] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:41,499] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:41,499] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb64b6327-3609-4051-aa47-707935d93a2a/dqc_reference/checkm_data
[2024-01-24 12:40:41,500] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:41,522] [INFO] Task started: CheckM
[2024-01-24 12:40:41,523] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003426945.1_ASM342694v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003426945.1_ASM342694v1_genomic.fna/checkm_input GCF_003426945.1_ASM342694v1_genomic.fna/checkm_result
[2024-01-24 12:41:15,721] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:15,722] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:15,741] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:15,741] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:15,742] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003426945.1_ASM342694v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:15,742] [INFO] Task started: Blastn
[2024-01-24 12:41:15,742] [INFO] Running command: blastn -query GCF_003426945.1_ASM342694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb64b6327-3609-4051-aa47-707935d93a2a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003426945.1_ASM342694v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:16,588] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:16,591] [INFO] Selected 13 target genomes.
[2024-01-24 12:41:16,591] [INFO] Target genome list was writen to GCF_003426945.1_ASM342694v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:16,600] [INFO] Task started: fastANI
[2024-01-24 12:41:16,600] [INFO] Running command: fastANI --query /var/lib/cwl/stg382e98fa-64ed-4f60-9373-fa3361c02764/GCF_003426945.1_ASM342694v1_genomic.fna.gz --refList GCF_003426945.1_ASM342694v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003426945.1_ASM342694v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:24,070] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:24,085] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:24,086] [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_003426945.1	s__Thermus sediminis	100.0	716	718	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_001280255.1	s__Thermus aquaticus	88.597	579	718	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	98.02	97.96	0.92	0.92	3	-
GCF_900102145.1	s__Thermus arciformis	86.3982	571	718	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	85.9224	353	718	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000376265.1	s__Thermus igniterrae	85.7498	546	718	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001311545.1	s__Thermus kawarayensis	85.737	330	718	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	85.4447	535	718	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	85.3924	558	718	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011053565.1	s__Thermus islandicus_A	85.3234	304	718	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000236585.1	s__Thermus sp000236585	85.3019	559	718	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	85.2582	543	718	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.6833	N/A	N/A	N/A	N/A	1	-
GCF_000091545.1	s__Thermus thermophilus	85.1848	541	718	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.7334	98.46	96.78	0.92	0.87	18	-
GCF_000794385.1	s__Thermus sp000794385	84.6799	546	718	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 12:41:24,087] [INFO] GTDB search result was written to GCF_003426945.1_ASM342694v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:24,088] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:24,091] [INFO] DFAST_QC result json was written to GCF_003426945.1_ASM342694v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:24,091] [INFO] DFAST_QC completed!
[2024-01-24 12:41:24,091] [INFO] Total running time: 0h1m3s