[2024-01-24 12:52:26,488] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:26,510] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:26,510] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d0b1fe1-fd13-488d-bc91-74f3778c5fee/dqc_reference
[2024-01-24 12:52:27,866] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:27,867] [INFO] Task started: Prodigal
[2024-01-24 12:52:27,868] [INFO] Running command: gunzip -c /var/lib/cwl/stgbae8f654-d8a9-41de-b057-09d45ace2d34/GCF_902827225.1_Methanocaldococcus_lauensis_SG7_genomic.fna.gz | prodigal -d GCF_902827225.1_Methanocaldococcus_lauensis_SG7_genomic.fna/cds.fna -a GCF_902827225.1_Methanocaldococcus_lauensis_SG7_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:52:30,414] [INFO] Task succeeded: Prodigal
[2024-01-24 12:52:30,415] [INFO] Task started: HMMsearch
[2024-01-24 12:52:30,415] [INFO] Running command: hmmsearch --tblout GCF_902827225.1_Methanocaldococcus_lauensis_SG7_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d0b1fe1-fd13-488d-bc91-74f3778c5fee/dqc_reference/reference_markers.hmm GCF_902827225.1_Methanocaldococcus_lauensis_SG7_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:52:30,689] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:52:30,691] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgbae8f654-d8a9-41de-b057-09d45ace2d34/GCF_902827225.1_Methanocaldococcus_lauensis_SG7_genomic.fna.gz]
[2024-01-24 12:52:30,709] [INFO] Query marker FASTA was written to GCF_902827225.1_Methanocaldococcus_lauensis_SG7_genomic.fna/markers.fasta
[2024-01-24 12:52:30,709] [INFO] Task started: Blastn
[2024-01-24 12:52:30,709] [INFO] Running command: blastn -query GCF_902827225.1_Methanocaldococcus_lauensis_SG7_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d0b1fe1-fd13-488d-bc91-74f3778c5fee/dqc_reference/reference_markers.fasta -out GCF_902827225.1_Methanocaldococcus_lauensis_SG7_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:31,322] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:31,325] [INFO] Selected 6 target genomes.
[2024-01-24 12:52:31,326] [INFO] Target genome list was writen to GCF_902827225.1_Methanocaldococcus_lauensis_SG7_genomic.fna/target_genomes.txt
[2024-01-24 12:52:31,382] [INFO] Task started: fastANI
[2024-01-24 12:52:31,383] [INFO] Running command: fastANI --query /var/lib/cwl/stgbae8f654-d8a9-41de-b057-09d45ace2d34/GCF_902827225.1_Methanocaldococcus_lauensis_SG7_genomic.fna.gz --refList GCF_902827225.1_Methanocaldococcus_lauensis_SG7_genomic.fna/target_genomes.txt --output GCF_902827225.1_Methanocaldococcus_lauensis_SG7_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:52:33,400] [INFO] Task succeeded: fastANI
[2024-01-24 12:52:33,401] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d0b1fe1-fd13-488d-bc91-74f3778c5fee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:52:33,401] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d0b1fe1-fd13-488d-bc91-74f3778c5fee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:52:33,408] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:52:33,408] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:52:33,408] [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
Methanocaldococcus bathoardescens	strain=JH146	GCA_000739065.1	1301915	1301915	type	True	81.9299	368	511	95	below_threshold
Methanocaldococcus jannaschii	strain=DSM 2661	GCA_000091665.1	2190	2190	type	True	80.2472	354	511	95	below_threshold
Methanocaldococcus villosus	strain=KIN24-T80	GCA_000371805.1	667126	667126	type	True	77.5415	136	511	95	below_threshold
Methanocaldococcus villosus	strain=KIN24-T80	GCA_000363885.1	667126	667126	type	True	77.3442	122	511	95	below_threshold
Methanocaldococcus infernus	strain=ME	GCA_000092305.1	67760	67760	type	True	77.2024	106	511	95	below_threshold
Methanothermococcus okinawensis	strain=IH1	GCA_000179575.2	155863	155863	type	True	76.159	93	511	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:52:33,410] [INFO] DFAST Taxonomy check result was written to GCF_902827225.1_Methanocaldococcus_lauensis_SG7_genomic.fna/tc_result.tsv
[2024-01-24 12:52:33,410] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:52:33,410] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:52:33,410] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d0b1fe1-fd13-488d-bc91-74f3778c5fee/dqc_reference/checkm_data
[2024-01-24 12:52:33,411] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:52:33,428] [INFO] Task started: CheckM
[2024-01-24 12:52:33,429] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902827225.1_Methanocaldococcus_lauensis_SG7_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902827225.1_Methanocaldococcus_lauensis_SG7_genomic.fna/checkm_input GCF_902827225.1_Methanocaldococcus_lauensis_SG7_genomic.fna/checkm_result
[2024-01-24 12:52:49,793] [INFO] Task succeeded: CheckM
[2024-01-24 12:52:49,799] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:52:49,820] [INFO] ===== Completeness check finished =====
[2024-01-24 12:52:49,820] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:52:49,821] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902827225.1_Methanocaldococcus_lauensis_SG7_genomic.fna/markers.fasta)
[2024-01-24 12:52:49,821] [INFO] Task started: Blastn
[2024-01-24 12:52:49,821] [INFO] Running command: blastn -query GCF_902827225.1_Methanocaldococcus_lauensis_SG7_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d0b1fe1-fd13-488d-bc91-74f3778c5fee/dqc_reference/reference_markers_gtdb.fasta -out GCF_902827225.1_Methanocaldococcus_lauensis_SG7_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:50,336] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:50,339] [INFO] Selected 6 target genomes.
[2024-01-24 12:52:50,339] [INFO] Target genome list was writen to GCF_902827225.1_Methanocaldococcus_lauensis_SG7_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:52:50,351] [INFO] Task started: fastANI
[2024-01-24 12:52:50,351] [INFO] Running command: fastANI --query /var/lib/cwl/stgbae8f654-d8a9-41de-b057-09d45ace2d34/GCF_902827225.1_Methanocaldococcus_lauensis_SG7_genomic.fna.gz --refList GCF_902827225.1_Methanocaldococcus_lauensis_SG7_genomic.fna/target_genomes_gtdb.txt --output GCF_902827225.1_Methanocaldococcus_lauensis_SG7_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:52:52,442] [INFO] Task succeeded: fastANI
[2024-01-24 12:52:52,448] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:52:52,448] [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_902827205.1	s__Methanocaldococcus sp902827205	97.4303	466	511	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanocaldococcaceae;g__Methanocaldococcus	95.0	97.43	97.43	0.94	0.94	2	conclusive
GCF_000739065.1	s__Methanocaldococcus bathoardescens	81.9351	365	511	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanocaldococcaceae;g__Methanocaldococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000091665.1	s__Methanocaldococcus jannaschii	80.2522	353	511	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanocaldococcaceae;g__Methanocaldococcus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000371805.1	s__Methanocaldococcus_A villosus	77.4976	138	511	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanocaldococcaceae;g__Methanocaldococcus_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000092305.1	s__Methanocaldococcus_A infernus	77.2171	107	511	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanocaldococcaceae;g__Methanocaldococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000179575.2	s__Methanothermococcus_A okinawensis	76.114	93	511	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanococcaceae;g__Methanothermococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:52:52,451] [INFO] GTDB search result was written to GCF_902827225.1_Methanocaldococcus_lauensis_SG7_genomic.fna/result_gtdb.tsv
[2024-01-24 12:52:52,451] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:52:52,454] [INFO] DFAST_QC result json was written to GCF_902827225.1_Methanocaldococcus_lauensis_SG7_genomic.fna/dqc_result.json
[2024-01-24 12:52:52,454] [INFO] DFAST_QC completed!
[2024-01-24 12:52:52,454] [INFO] Total running time: 0h0m26s