[2024-01-24 14:03:08,538] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:08,541] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:08,541] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ac455ae-e9a5-42d9-8e72-a28319de5e05/dqc_reference
[2024-01-24 14:03:09,910] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:09,911] [INFO] Task started: Prodigal
[2024-01-24 14:03:09,911] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0d5a1c4-839e-43cb-acae-ef8c4bc7b93f/GCF_000023985.1_ASM2398v1_genomic.fna.gz | prodigal -d GCF_000023985.1_ASM2398v1_genomic.fna/cds.fna -a GCF_000023985.1_ASM2398v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:12,835] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:12,836] [INFO] Task started: HMMsearch
[2024-01-24 14:03:12,836] [INFO] Running command: hmmsearch --tblout GCF_000023985.1_ASM2398v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ac455ae-e9a5-42d9-8e72-a28319de5e05/dqc_reference/reference_markers.hmm GCF_000023985.1_ASM2398v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:13,084] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:13,086] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgc0d5a1c4-839e-43cb-acae-ef8c4bc7b93f/GCF_000023985.1_ASM2398v1_genomic.fna.gz]
[2024-01-24 14:03:13,106] [INFO] Query marker FASTA was written to GCF_000023985.1_ASM2398v1_genomic.fna/markers.fasta
[2024-01-24 14:03:13,107] [INFO] Task started: Blastn
[2024-01-24 14:03:13,107] [INFO] Running command: blastn -query GCF_000023985.1_ASM2398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ac455ae-e9a5-42d9-8e72-a28319de5e05/dqc_reference/reference_markers.fasta -out GCF_000023985.1_ASM2398v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:13,622] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:13,625] [INFO] Selected 6 target genomes.
[2024-01-24 14:03:13,625] [INFO] Target genome list was writen to GCF_000023985.1_ASM2398v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:13,635] [INFO] Task started: fastANI
[2024-01-24 14:03:13,636] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0d5a1c4-839e-43cb-acae-ef8c4bc7b93f/GCF_000023985.1_ASM2398v1_genomic.fna.gz --refList GCF_000023985.1_ASM2398v1_genomic.fna/target_genomes.txt --output GCF_000023985.1_ASM2398v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:16,048] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:16,049] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ac455ae-e9a5-42d9-8e72-a28319de5e05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:16,049] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ac455ae-e9a5-42d9-8e72-a28319de5e05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:16,056] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:03:16,056] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:16,056] [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 fervens	strain=AG86	GCA_000023985.1	83171	83171	type	True	100.0	501	502	95	conclusive
Methanocaldococcus bathoardescens	strain=JH146	GCA_000739065.1	1301915	1301915	type	True	84.5949	394	502	95	below_threshold
Methanocaldococcus jannaschii	strain=DSM 2661	GCA_000091665.1	2190	2190	type	True	83.3214	392	502	95	below_threshold
Methanocaldococcus vulcanius	strain=M7	GCA_000024625.1	73913	73913	type	True	79.4425	254	502	95	below_threshold
Methanotorris formicicus	strain=Mc-S-70	GCA_000243455.2	213185	213185	type	True	78.1557	123	502	95	below_threshold
Methanocaldococcus infernus	strain=ME	GCA_000092305.1	67760	67760	type	True	77.3142	92	502	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:16,058] [INFO] DFAST Taxonomy check result was written to GCF_000023985.1_ASM2398v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:16,058] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:16,059] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:16,059] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ac455ae-e9a5-42d9-8e72-a28319de5e05/dqc_reference/checkm_data
[2024-01-24 14:03:16,060] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:16,082] [INFO] Task started: CheckM
[2024-01-24 14:03:16,082] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000023985.1_ASM2398v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000023985.1_ASM2398v1_genomic.fna/checkm_input GCF_000023985.1_ASM2398v1_genomic.fna/checkm_result
[2024-01-24 14:03:33,290] [INFO] Task succeeded: CheckM
[2024-01-24 14:03:33,291] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:03:33,312] [INFO] ===== Completeness check finished =====
[2024-01-24 14:03:33,312] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:03:33,313] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000023985.1_ASM2398v1_genomic.fna/markers.fasta)
[2024-01-24 14:03:33,313] [INFO] Task started: Blastn
[2024-01-24 14:03:33,313] [INFO] Running command: blastn -query GCF_000023985.1_ASM2398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ac455ae-e9a5-42d9-8e72-a28319de5e05/dqc_reference/reference_markers_gtdb.fasta -out GCF_000023985.1_ASM2398v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:33,834] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:33,837] [INFO] Selected 6 target genomes.
[2024-01-24 14:03:33,838] [INFO] Target genome list was writen to GCF_000023985.1_ASM2398v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:03:33,846] [INFO] Task started: fastANI
[2024-01-24 14:03:33,847] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0d5a1c4-839e-43cb-acae-ef8c4bc7b93f/GCF_000023985.1_ASM2398v1_genomic.fna.gz --refList GCF_000023985.1_ASM2398v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000023985.1_ASM2398v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:03:36,588] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:36,598] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:03:36,598] [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_000023985.1	s__Methanocaldococcus fervens	100.0	501	502	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanocaldococcaceae;g__Methanocaldococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000739065.1	s__Methanocaldococcus bathoardescens	84.6261	393	502	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	83.3049	393	502	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_000025525.1	s__Methanocaldococcus sp000025525	82.9751	400	502	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanocaldococcaceae;g__Methanocaldococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902827205.1	s__Methanocaldococcus sp902827205	79.5833	307	502	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanocaldococcaceae;g__Methanocaldococcus	95.0	97.43	97.43	0.94	0.94	2	-
GCA_013153845.1	s__Methanocaldococcus sp013153845	79.1773	211	502	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanocaldococcaceae;g__Methanocaldococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:03:36,600] [INFO] GTDB search result was written to GCF_000023985.1_ASM2398v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:03:36,601] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:03:36,604] [INFO] DFAST_QC result json was written to GCF_000023985.1_ASM2398v1_genomic.fna/dqc_result.json
[2024-01-24 14:03:36,604] [INFO] DFAST_QC completed!
[2024-01-24 14:03:36,604] [INFO] Total running time: 0h0m28s