[2024-01-24 11:21:07,406] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:21:07,407] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:21:07,407] [INFO] DQC Reference Directory: /var/lib/cwl/stg540bbc09-05fb-46ff-925c-89c18d0b9770/dqc_reference
[2024-01-24 11:21:11,961] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:21:11,962] [INFO] Task started: Prodigal
[2024-01-24 11:21:11,962] [INFO] Running command: gunzip -c /var/lib/cwl/stg477ab639-a8b3-4020-9f80-b96d70917cc1/GCF_019973715.1_ASM1997371v1_genomic.fna.gz | prodigal -d GCF_019973715.1_ASM1997371v1_genomic.fna/cds.fna -a GCF_019973715.1_ASM1997371v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:21:23,297] [INFO] Task succeeded: Prodigal
[2024-01-24 11:21:23,297] [INFO] Task started: HMMsearch
[2024-01-24 11:21:23,297] [INFO] Running command: hmmsearch --tblout GCF_019973715.1_ASM1997371v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg540bbc09-05fb-46ff-925c-89c18d0b9770/dqc_reference/reference_markers.hmm GCF_019973715.1_ASM1997371v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:21:23,533] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:21:23,534] [INFO] Found 6/6 markers.
[2024-01-24 11:21:23,558] [INFO] Query marker FASTA was written to GCF_019973715.1_ASM1997371v1_genomic.fna/markers.fasta
[2024-01-24 11:21:23,558] [INFO] Task started: Blastn
[2024-01-24 11:21:23,558] [INFO] Running command: blastn -query GCF_019973715.1_ASM1997371v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg540bbc09-05fb-46ff-925c-89c18d0b9770/dqc_reference/reference_markers.fasta -out GCF_019973715.1_ASM1997371v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:24,144] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:24,148] [INFO] Selected 7 target genomes.
[2024-01-24 11:21:24,148] [INFO] Target genome list was writen to GCF_019973715.1_ASM1997371v1_genomic.fna/target_genomes.txt
[2024-01-24 11:21:24,152] [INFO] Task started: fastANI
[2024-01-24 11:21:24,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg477ab639-a8b3-4020-9f80-b96d70917cc1/GCF_019973715.1_ASM1997371v1_genomic.fna.gz --refList GCF_019973715.1_ASM1997371v1_genomic.fna/target_genomes.txt --output GCF_019973715.1_ASM1997371v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:28,839] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:28,839] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg540bbc09-05fb-46ff-925c-89c18d0b9770/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:28,840] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg540bbc09-05fb-46ff-925c-89c18d0b9770/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:28,851] [INFO] Found 7 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:21:28,851] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:21:28,851] [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	100.0	704	704	95	inconclusive
Thermus thermophilus	strain=HB8	GCA_000091545.1	274	274	type	True	99.9921	703	704	95	inconclusive
Thermus parvatiensis	strain=RL	GCA_000252835.2	456163	456163	type	True	95.7777	571	704	95	inconclusive
Thermus parvatiensis	strain=RL	GCA_001535545.1	456163	456163	type	True	95.6629	591	704	95	inconclusive
Thermus arciformis	strain=CGMCC 1.6992	GCA_900102145.1	482827	482827	type	True	91.2259	571	704	95	below_threshold
Thermus arciformis	strain=JCM 15153	GCA_022556335.1	482827	482827	type	True	91.206	565	704	95	below_threshold
Thermus thermamylovorans	strain=CFH 72773T	GCA_004307015.1	2509362	2509362	type	True	85.025	532	704	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:28,852] [INFO] DFAST Taxonomy check result was written to GCF_019973715.1_ASM1997371v1_genomic.fna/tc_result.tsv
[2024-01-24 11:21:28,853] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:28,853] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:28,853] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg540bbc09-05fb-46ff-925c-89c18d0b9770/dqc_reference/checkm_data
[2024-01-24 11:21:28,854] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:28,884] [INFO] Task started: CheckM
[2024-01-24 11:21:28,884] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019973715.1_ASM1997371v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019973715.1_ASM1997371v1_genomic.fna/checkm_input GCF_019973715.1_ASM1997371v1_genomic.fna/checkm_result
[2024-01-24 11:22:02,292] [INFO] Task succeeded: CheckM
[2024-01-24 11:22:02,293] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:22:02,313] [INFO] ===== Completeness check finished =====
[2024-01-24 11:22:02,313] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:22:02,314] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019973715.1_ASM1997371v1_genomic.fna/markers.fasta)
[2024-01-24 11:22:02,314] [INFO] Task started: Blastn
[2024-01-24 11:22:02,315] [INFO] Running command: blastn -query GCF_019973715.1_ASM1997371v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg540bbc09-05fb-46ff-925c-89c18d0b9770/dqc_reference/reference_markers_gtdb.fasta -out GCF_019973715.1_ASM1997371v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:22:03,177] [INFO] Task succeeded: Blastn
[2024-01-24 11:22:03,182] [INFO] Selected 10 target genomes.
[2024-01-24 11:22:03,182] [INFO] Target genome list was writen to GCF_019973715.1_ASM1997371v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:22:03,193] [INFO] Task started: fastANI
[2024-01-24 11:22:03,193] [INFO] Running command: fastANI --query /var/lib/cwl/stg477ab639-a8b3-4020-9f80-b96d70917cc1/GCF_019973715.1_ASM1997371v1_genomic.fna.gz --refList GCF_019973715.1_ASM1997371v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019973715.1_ASM1997371v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:22:09,701] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:09,716] [INFO] Found 10 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 11:22:09,717] [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_000091545.1	s__Thermus thermophilus	99.9921	703	704	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	95.7038	622	704	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.6833	N/A	N/A	N/A	N/A	1	inconclusive
GCF_001535545.1	s__Thermus parvatiensis	95.6629	591	704	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.7334	98.79	98.79	0.97	0.97	2	-
GCF_900102145.1	s__Thermus arciformis	91.2149	571	704	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	88.8822	370	704	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	88.7874	531	704	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	87.9793	357	704	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	86.3069	521	704	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	85.9118	558	704	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373145.1	s__Thermus oshimai	85.428	562	704	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	98.40	98.40	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:22:09,719] [INFO] GTDB search result was written to GCF_019973715.1_ASM1997371v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:22:09,719] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:22:09,722] [INFO] DFAST_QC result json was written to GCF_019973715.1_ASM1997371v1_genomic.fna/dqc_result.json
[2024-01-24 11:22:09,722] [INFO] DFAST_QC completed!
[2024-01-24 11:22:09,722] [INFO] Total running time: 0h1m2s