[2024-01-24 13:27:40,834] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:40,836] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:40,836] [INFO] DQC Reference Directory: /var/lib/cwl/stg247ae14a-d2f7-4585-9abd-adea6e58fd02/dqc_reference
[2024-01-24 13:27:42,015] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:42,016] [INFO] Task started: Prodigal
[2024-01-24 13:27:42,016] [INFO] Running command: gunzip -c /var/lib/cwl/stg1562368b-f0e8-4b23-b5a7-e71b81c26142/GCF_000246985.2_ASM24698v3_genomic.fna.gz | prodigal -d GCF_000246985.2_ASM24698v3_genomic.fna/cds.fna -a GCF_000246985.2_ASM24698v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:27:47,010] [INFO] Task succeeded: Prodigal
[2024-01-24 13:27:47,011] [INFO] Task started: HMMsearch
[2024-01-24 13:27:47,011] [INFO] Running command: hmmsearch --tblout GCF_000246985.2_ASM24698v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg247ae14a-d2f7-4585-9abd-adea6e58fd02/dqc_reference/reference_markers.hmm GCF_000246985.2_ASM24698v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:27:47,224] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:27:47,225] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg1562368b-f0e8-4b23-b5a7-e71b81c26142/GCF_000246985.2_ASM24698v3_genomic.fna.gz]
[2024-01-24 13:27:47,252] [INFO] Query marker FASTA was written to GCF_000246985.2_ASM24698v3_genomic.fna/markers.fasta
[2024-01-24 13:27:47,253] [INFO] Task started: Blastn
[2024-01-24 13:27:47,253] [INFO] Running command: blastn -query GCF_000246985.2_ASM24698v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg247ae14a-d2f7-4585-9abd-adea6e58fd02/dqc_reference/reference_markers.fasta -out GCF_000246985.2_ASM24698v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:47,766] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:47,770] [INFO] Selected 6 target genomes.
[2024-01-24 13:27:47,770] [INFO] Target genome list was writen to GCF_000246985.2_ASM24698v3_genomic.fna/target_genomes.txt
[2024-01-24 13:27:47,799] [INFO] Task started: fastANI
[2024-01-24 13:27:47,799] [INFO] Running command: fastANI --query /var/lib/cwl/stg1562368b-f0e8-4b23-b5a7-e71b81c26142/GCF_000246985.2_ASM24698v3_genomic.fna.gz --refList GCF_000246985.2_ASM24698v3_genomic.fna/target_genomes.txt --output GCF_000246985.2_ASM24698v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:27:51,054] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:51,055] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg247ae14a-d2f7-4585-9abd-adea6e58fd02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:27:51,056] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg247ae14a-d2f7-4585-9abd-adea6e58fd02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:27:51,069] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:27:51,069] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:27:51,069] [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
Thermococcus litoralis	strain=DSM 5473	GCA_000246985.3	2265	2265	type	True	100.0	738	738	95	inconclusive
Thermococcus alcaliphilus	strain=AEDII12	GCA_024054535.1	139207	139207	type	True	95.3297	550	738	95	inconclusive
Thermococcus bergensis	strain=T7324	GCA_020386975.1	2689387	2689387	type	True	88.5853	501	738	95	below_threshold
Thermococcus aggregans	strain=TY	GCA_024022995.1	110163	110163	type	True	81.135	428	738	95	below_threshold
Thermococcus sibiricus	strain=MM 739	GCA_000022545.1	172049	172049	type	True	78.6133	251	738	95	below_threshold
Thermococcus peptonophilus	strain=OG-1	GCA_001592435.1	53952	53952	type	True	78.2871	82	738	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:27:51,071] [INFO] DFAST Taxonomy check result was written to GCF_000246985.2_ASM24698v3_genomic.fna/tc_result.tsv
[2024-01-24 13:27:51,072] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:27:51,072] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:27:51,073] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg247ae14a-d2f7-4585-9abd-adea6e58fd02/dqc_reference/checkm_data
[2024-01-24 13:27:51,075] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:27:51,103] [INFO] Task started: CheckM
[2024-01-24 13:27:51,104] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000246985.2_ASM24698v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000246985.2_ASM24698v3_genomic.fna/checkm_input GCF_000246985.2_ASM24698v3_genomic.fna/checkm_result
[2024-01-24 13:28:13,034] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:13,036] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:13,056] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:13,056] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:13,056] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000246985.2_ASM24698v3_genomic.fna/markers.fasta)
[2024-01-24 13:28:13,057] [INFO] Task started: Blastn
[2024-01-24 13:28:13,057] [INFO] Running command: blastn -query GCF_000246985.2_ASM24698v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg247ae14a-d2f7-4585-9abd-adea6e58fd02/dqc_reference/reference_markers_gtdb.fasta -out GCF_000246985.2_ASM24698v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:13,588] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:13,595] [INFO] Selected 6 target genomes.
[2024-01-24 13:28:13,595] [INFO] Target genome list was writen to GCF_000246985.2_ASM24698v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:13,620] [INFO] Task started: fastANI
[2024-01-24 13:28:13,621] [INFO] Running command: fastANI --query /var/lib/cwl/stg1562368b-f0e8-4b23-b5a7-e71b81c26142/GCF_000246985.2_ASM24698v3_genomic.fna.gz --refList GCF_000246985.2_ASM24698v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000246985.2_ASM24698v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:16,880] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:16,890] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:16,891] [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_000246985.2	s__Thermococcus_A litoralis	100.0	738	738	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_A	95.0	96.93	96.93	0.89	0.89	2	conclusive
GCF_001484685.1	s__Thermococcus_A sp001484685	90.9023	537	738	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_A	95.0	98.39	98.39	0.89	0.89	2	-
GCF_000430485.1	s__Thermococcus_A sp000430485	89.1028	510	738	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_A	95.0	96.03	95.46	0.86	0.83	4	-
GCF_000022545.1	s__Thermococcus_A sibiricus	78.6133	251	738	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_A	95.0	98.36	98.17	0.89	0.84	5	-
GCF_001592435.1	s__Thermococcus peptonophilus	78.2458	84	738	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	99.53	99.53	0.99	0.99	2	-
GCA_017656495.1	s__Thermococcus_B sp017656495	77.4271	104	738	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:16,892] [INFO] GTDB search result was written to GCF_000246985.2_ASM24698v3_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:16,893] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:16,895] [INFO] DFAST_QC result json was written to GCF_000246985.2_ASM24698v3_genomic.fna/dqc_result.json
[2024-01-24 13:28:16,896] [INFO] DFAST_QC completed!
[2024-01-24 13:28:16,896] [INFO] Total running time: 0h0m36s