[2024-01-25 18:50:50,585] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:50:50,587] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:50:50,587] [INFO] DQC Reference Directory: /var/lib/cwl/stg373316ce-2a10-4d7e-bbcf-a1978d327b65/dqc_reference
[2024-01-25 18:50:51,717] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:50:51,718] [INFO] Task started: Prodigal
[2024-01-25 18:50:51,718] [INFO] Running command: gunzip -c /var/lib/cwl/stgc7a291a6-f6c4-4cb5-9d6d-9376e801c449/GCF_000091545.1_ASM9154v1_genomic.fna.gz | prodigal -d GCF_000091545.1_ASM9154v1_genomic.fna/cds.fna -a GCF_000091545.1_ASM9154v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:51:01,312] [INFO] Task succeeded: Prodigal
[2024-01-25 18:51:01,312] [INFO] Task started: HMMsearch
[2024-01-25 18:51:01,312] [INFO] Running command: hmmsearch --tblout GCF_000091545.1_ASM9154v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg373316ce-2a10-4d7e-bbcf-a1978d327b65/dqc_reference/reference_markers.hmm GCF_000091545.1_ASM9154v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:51:01,503] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:51:01,504] [INFO] Found 6/6 markers.
[2024-01-25 18:51:01,524] [INFO] Query marker FASTA was written to GCF_000091545.1_ASM9154v1_genomic.fna/markers.fasta
[2024-01-25 18:51:01,524] [INFO] Task started: Blastn
[2024-01-25 18:51:01,524] [INFO] Running command: blastn -query GCF_000091545.1_ASM9154v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg373316ce-2a10-4d7e-bbcf-a1978d327b65/dqc_reference/reference_markers.fasta -out GCF_000091545.1_ASM9154v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:02,077] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:02,080] [INFO] Selected 7 target genomes.
[2024-01-25 18:51:02,081] [INFO] Target genome list was writen to GCF_000091545.1_ASM9154v1_genomic.fna/target_genomes.txt
[2024-01-25 18:51:02,084] [INFO] Task started: fastANI
[2024-01-25 18:51:02,084] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7a291a6-f6c4-4cb5-9d6d-9376e801c449/GCF_000091545.1_ASM9154v1_genomic.fna.gz --refList GCF_000091545.1_ASM9154v1_genomic.fna/target_genomes.txt --output GCF_000091545.1_ASM9154v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:51:06,839] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:06,840] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg373316ce-2a10-4d7e-bbcf-a1978d327b65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:51:06,840] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg373316ce-2a10-4d7e-bbcf-a1978d327b65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:51:06,846] [INFO] Found 7 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 18:51:06,847] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 18:51:06,847] [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=HB8	GCA_000091545.1	274	274	type	True	100.0	704	704	95	inconclusive
Thermus thermophilus	strain=JCM10941	GCA_019973715.1	274	274	type	True	99.9984	702	704	95	inconclusive
Thermus parvatiensis	strain=RL	GCA_000252835.2	456163	456163	type	True	95.7643	579	704	95	inconclusive
Thermus parvatiensis	strain=RL	GCA_001535545.1	456163	456163	type	True	95.7364	591	704	95	inconclusive
Thermus arciformis	strain=CGMCC 1.6992	GCA_900102145.1	482827	482827	type	True	91.1488	572	704	95	below_threshold
Thermus arciformis	strain=JCM 15153	GCA_022556335.1	482827	482827	type	True	91.0216	581	704	95	below_threshold
Thermus thermamylovorans	strain=CFH 72773T	GCA_004307015.1	2509362	2509362	type	True	84.997	530	704	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:51:06,848] [INFO] DFAST Taxonomy check result was written to GCF_000091545.1_ASM9154v1_genomic.fna/tc_result.tsv
[2024-01-25 18:51:06,848] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:51:06,848] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:51:06,849] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg373316ce-2a10-4d7e-bbcf-a1978d327b65/dqc_reference/checkm_data
[2024-01-25 18:51:06,849] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:51:06,872] [INFO] Task started: CheckM
[2024-01-25 18:51:06,872] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000091545.1_ASM9154v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000091545.1_ASM9154v1_genomic.fna/checkm_input GCF_000091545.1_ASM9154v1_genomic.fna/checkm_result
[2024-01-25 18:51:35,802] [INFO] Task succeeded: CheckM
[2024-01-25 18:51:35,803] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:51:35,822] [INFO] ===== Completeness check finished =====
[2024-01-25 18:51:35,822] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:51:35,822] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000091545.1_ASM9154v1_genomic.fna/markers.fasta)
[2024-01-25 18:51:35,823] [INFO] Task started: Blastn
[2024-01-25 18:51:35,823] [INFO] Running command: blastn -query GCF_000091545.1_ASM9154v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg373316ce-2a10-4d7e-bbcf-a1978d327b65/dqc_reference/reference_markers_gtdb.fasta -out GCF_000091545.1_ASM9154v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:36,655] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:36,658] [INFO] Selected 10 target genomes.
[2024-01-25 18:51:36,658] [INFO] Target genome list was writen to GCF_000091545.1_ASM9154v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:51:36,673] [INFO] Task started: fastANI
[2024-01-25 18:51:36,673] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7a291a6-f6c4-4cb5-9d6d-9376e801c449/GCF_000091545.1_ASM9154v1_genomic.fna.gz --refList GCF_000091545.1_ASM9154v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000091545.1_ASM9154v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:51:43,257] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:43,265] [INFO] Found 10 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-25 18:51:43,265] [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	100.0	704	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	95.6896	621	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	95.6657	593	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	91.1681	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	-
GCF_014647535.1	s__Thermus composti	88.8783	536	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	88.6128	376	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	87.9604	346	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	86.3405	528	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	86.0082	545	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	85.544	558	704	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Thermaceae;g__Thermus	95.0	98.40	98.40	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:51:43,267] [INFO] GTDB search result was written to GCF_000091545.1_ASM9154v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:51:43,267] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:51:43,272] [INFO] DFAST_QC result json was written to GCF_000091545.1_ASM9154v1_genomic.fna/dqc_result.json
[2024-01-25 18:51:43,272] [INFO] DFAST_QC completed!
[2024-01-25 18:51:43,272] [INFO] Total running time: 0h0m53s