[2023-06-27 02:30:09,024] [INFO] DFAST_QC pipeline started.
[2023-06-27 02:30:09,059] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 02:30:09,059] [INFO] DQC Reference Directory: /var/lib/cwl/stg0adcc9d5-e5cb-49db-8422-c5454f9dd939/dqc_reference
[2023-06-27 02:30:10,280] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 02:30:10,281] [INFO] Task started: Prodigal
[2023-06-27 02:30:10,281] [INFO] Running command: gunzip -c /var/lib/cwl/stg54a091dd-ac75-46fa-ac81-051e3c8e8ce3/GCA_027074935.1_ASM2707493v1_genomic.fna.gz | prodigal -d GCA_027074935.1_ASM2707493v1_genomic.fna/cds.fna -a GCA_027074935.1_ASM2707493v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 02:30:13,372] [INFO] Task succeeded: Prodigal
[2023-06-27 02:30:13,373] [INFO] Task started: HMMsearch
[2023-06-27 02:30:13,373] [INFO] Running command: hmmsearch --tblout GCA_027074935.1_ASM2707493v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0adcc9d5-e5cb-49db-8422-c5454f9dd939/dqc_reference/reference_markers.hmm GCA_027074935.1_ASM2707493v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 02:30:13,587] [INFO] Task succeeded: HMMsearch
[2023-06-27 02:30:13,589] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg54a091dd-ac75-46fa-ac81-051e3c8e8ce3/GCA_027074935.1_ASM2707493v1_genomic.fna.gz]
[2023-06-27 02:30:13,610] [INFO] Query marker FASTA was written to GCA_027074935.1_ASM2707493v1_genomic.fna/markers.fasta
[2023-06-27 02:30:13,610] [INFO] Task started: Blastn
[2023-06-27 02:30:13,610] [INFO] Running command: blastn -query GCA_027074935.1_ASM2707493v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0adcc9d5-e5cb-49db-8422-c5454f9dd939/dqc_reference/reference_markers.fasta -out GCA_027074935.1_ASM2707493v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 02:30:14,117] [INFO] Task succeeded: Blastn
[2023-06-27 02:30:14,121] [INFO] Selected 5 target genomes.
[2023-06-27 02:30:14,122] [INFO] Target genome list was writen to GCA_027074935.1_ASM2707493v1_genomic.fna/target_genomes.txt
[2023-06-27 02:30:14,125] [INFO] Task started: fastANI
[2023-06-27 02:30:14,125] [INFO] Running command: fastANI --query /var/lib/cwl/stg54a091dd-ac75-46fa-ac81-051e3c8e8ce3/GCA_027074935.1_ASM2707493v1_genomic.fna.gz --refList GCA_027074935.1_ASM2707493v1_genomic.fna/target_genomes.txt --output GCA_027074935.1_ASM2707493v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 02:30:16,369] [INFO] Task succeeded: fastANI
[2023-06-27 02:30:16,370] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0adcc9d5-e5cb-49db-8422-c5454f9dd939/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 02:30:16,371] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0adcc9d5-e5cb-49db-8422-c5454f9dd939/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 02:30:16,382] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 02:30:16,382] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 02:30:16,382] [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 nautili	strain=30-1	GCA_000585495.1	195522	195522	type	True	82.3896	343	446	95	below_threshold
Thermococcus henrietii	strain=EXT12c	GCA_900198835.1	2016361	2016361	type	True	81.7901	334	446	95	below_threshold
Thermococcus eurythermalis	strain=A501	GCA_000769655.1	1505907	1505907	type	True	80.4165	284	446	95	below_threshold
Thermococcus gammatolerans	strain=EJ3; DSM 15229	GCA_000022365.1	187878	187878	type	True	79.8145	225	446	95	below_threshold
Thermococcus cleftensis	strain=CL1	GCA_000265525.1	163003	163003	type	True	79.1937	245	446	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 02:30:16,385] [INFO] DFAST Taxonomy check result was written to GCA_027074935.1_ASM2707493v1_genomic.fna/tc_result.tsv
[2023-06-27 02:30:16,386] [INFO] ===== Taxonomy check completed =====
[2023-06-27 02:30:16,386] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 02:30:16,386] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0adcc9d5-e5cb-49db-8422-c5454f9dd939/dqc_reference/checkm_data
[2023-06-27 02:30:16,389] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 02:30:16,413] [INFO] Task started: CheckM
[2023-06-27 02:30:16,414] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027074935.1_ASM2707493v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027074935.1_ASM2707493v1_genomic.fna/checkm_input GCA_027074935.1_ASM2707493v1_genomic.fna/checkm_result
[2023-06-27 02:30:33,726] [INFO] Task succeeded: CheckM
[2023-06-27 02:30:33,727] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 02:30:33,749] [INFO] ===== Completeness check finished =====
[2023-06-27 02:30:33,749] [INFO] ===== Start GTDB Search =====
[2023-06-27 02:30:33,750] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027074935.1_ASM2707493v1_genomic.fna/markers.fasta)
[2023-06-27 02:30:33,750] [INFO] Task started: Blastn
[2023-06-27 02:30:33,750] [INFO] Running command: blastn -query GCA_027074935.1_ASM2707493v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0adcc9d5-e5cb-49db-8422-c5454f9dd939/dqc_reference/reference_markers_gtdb.fasta -out GCA_027074935.1_ASM2707493v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 02:30:34,317] [INFO] Task succeeded: Blastn
[2023-06-27 02:30:34,324] [INFO] Selected 7 target genomes.
[2023-06-27 02:30:34,324] [INFO] Target genome list was writen to GCA_027074935.1_ASM2707493v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 02:30:34,331] [INFO] Task started: fastANI
[2023-06-27 02:30:34,332] [INFO] Running command: fastANI --query /var/lib/cwl/stg54a091dd-ac75-46fa-ac81-051e3c8e8ce3/GCA_027074935.1_ASM2707493v1_genomic.fna.gz --refList GCA_027074935.1_ASM2707493v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027074935.1_ASM2707493v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 02:30:37,158] [INFO] Task succeeded: fastANI
[2023-06-27 02:30:37,172] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 02:30:37,172] [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
GCA_015523185.1	s__Thermococcus sp015523185	99.6964	394	446	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	99.10	98.97	0.82	0.81	3	conclusive
GCF_000585495.1	s__Thermococcus nautili	82.3896	343	446	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	97.44	97.44	0.91	0.91	2	-
GCF_012027635.1	s__Thermococcus sp012027635	82.3367	338	446	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900198835.1	s__Thermococcus sp900198835	81.7901	334	446	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002214485.1	s__Thermococcus pacificus	79.5425	215	446	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265525.1	s__Thermococcus cleftensis	79.1927	245	446	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	97.89	97.89	0.92	0.92	2	-
GCA_011050175.1	s__Thermococcus sp011050175	78.3885	119	446	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Thermococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 02:30:37,175] [INFO] GTDB search result was written to GCA_027074935.1_ASM2707493v1_genomic.fna/result_gtdb.tsv
[2023-06-27 02:30:37,176] [INFO] ===== GTDB Search completed =====
[2023-06-27 02:30:37,180] [INFO] DFAST_QC result json was written to GCA_027074935.1_ASM2707493v1_genomic.fna/dqc_result.json
[2023-06-27 02:30:37,180] [INFO] DFAST_QC completed!
[2023-06-27 02:30:37,180] [INFO] Total running time: 0h0m28s