[2024-01-24 14:19:31,832] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:31,836] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:31,836] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1383541-4d3f-471d-a5ee-bbfcc0136082/dqc_reference
[2024-01-24 14:19:33,304] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:33,304] [INFO] Task started: Prodigal
[2024-01-24 14:19:33,305] [INFO] Running command: gunzip -c /var/lib/cwl/stg57063bc7-6c69-45b0-8994-ede13931ed6c/GCF_000376965.1_ASM37696v1_genomic.fna.gz | prodigal -d GCF_000376965.1_ASM37696v1_genomic.fna/cds.fna -a GCF_000376965.1_ASM37696v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:36,618] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:36,618] [INFO] Task started: HMMsearch
[2024-01-24 14:19:36,619] [INFO] Running command: hmmsearch --tblout GCF_000376965.1_ASM37696v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1383541-4d3f-471d-a5ee-bbfcc0136082/dqc_reference/reference_markers.hmm GCF_000376965.1_ASM37696v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:36,899] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:36,901] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg57063bc7-6c69-45b0-8994-ede13931ed6c/GCF_000376965.1_ASM37696v1_genomic.fna.gz]
[2024-01-24 14:19:36,937] [INFO] Query marker FASTA was written to GCF_000376965.1_ASM37696v1_genomic.fna/markers.fasta
[2024-01-24 14:19:36,938] [INFO] Task started: Blastn
[2024-01-24 14:19:36,938] [INFO] Running command: blastn -query GCF_000376965.1_ASM37696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1383541-4d3f-471d-a5ee-bbfcc0136082/dqc_reference/reference_markers.fasta -out GCF_000376965.1_ASM37696v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:37,454] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:37,458] [INFO] Selected 3 target genomes.
[2024-01-24 14:19:37,458] [INFO] Target genome list was writen to GCF_000376965.1_ASM37696v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:37,463] [INFO] Task started: fastANI
[2024-01-24 14:19:37,464] [INFO] Running command: fastANI --query /var/lib/cwl/stg57063bc7-6c69-45b0-8994-ede13931ed6c/GCF_000376965.1_ASM37696v1_genomic.fna.gz --refList GCF_000376965.1_ASM37696v1_genomic.fna/target_genomes.txt --output GCF_000376965.1_ASM37696v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:38,899] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:38,899] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1383541-4d3f-471d-a5ee-bbfcc0136082/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:38,899] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1383541-4d3f-471d-a5ee-bbfcc0136082/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:38,904] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:38,904] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:38,904] [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
Methanothermococcus thermolithotrophicus	strain=DSM 2095	GCA_000376965.1	2186	2186	type	True	100.0	532	533	95	conclusive
Methanothermococcus okinawensis	strain=IH1	GCA_000179575.2	155863	155863	type	True	77.9759	159	533	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:38,906] [INFO] DFAST Taxonomy check result was written to GCF_000376965.1_ASM37696v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:38,906] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:38,907] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:38,907] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1383541-4d3f-471d-a5ee-bbfcc0136082/dqc_reference/checkm_data
[2024-01-24 14:19:38,908] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:38,933] [INFO] Task started: CheckM
[2024-01-24 14:19:38,933] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000376965.1_ASM37696v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000376965.1_ASM37696v1_genomic.fna/checkm_input GCF_000376965.1_ASM37696v1_genomic.fna/checkm_result
[2024-01-24 14:19:57,966] [INFO] Task succeeded: CheckM
[2024-01-24 14:19:57,967] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:19:57,982] [INFO] ===== Completeness check finished =====
[2024-01-24 14:19:57,983] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:19:57,983] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000376965.1_ASM37696v1_genomic.fna/markers.fasta)
[2024-01-24 14:19:57,984] [INFO] Task started: Blastn
[2024-01-24 14:19:57,984] [INFO] Running command: blastn -query GCF_000376965.1_ASM37696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1383541-4d3f-471d-a5ee-bbfcc0136082/dqc_reference/reference_markers_gtdb.fasta -out GCF_000376965.1_ASM37696v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:58,525] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:58,528] [INFO] Selected 4 target genomes.
[2024-01-24 14:19:58,528] [INFO] Target genome list was writen to GCF_000376965.1_ASM37696v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:19:58,536] [INFO] Task started: fastANI
[2024-01-24 14:19:58,537] [INFO] Running command: fastANI --query /var/lib/cwl/stg57063bc7-6c69-45b0-8994-ede13931ed6c/GCF_000376965.1_ASM37696v1_genomic.fna.gz --refList GCF_000376965.1_ASM37696v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000376965.1_ASM37696v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:00,140] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:00,144] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:00,144] [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_000376965.1	s__Methanothermococcus thermolithotrophicus	100.0	532	533	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanococcaceae;g__Methanothermococcus	95.0	99.60	99.39	0.95	0.95	3	conclusive
GCF_000179575.2	s__Methanothermococcus_A okinawensis	77.9759	159	533	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 14:20:00,146] [INFO] GTDB search result was written to GCF_000376965.1_ASM37696v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:00,147] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:00,150] [INFO] DFAST_QC result json was written to GCF_000376965.1_ASM37696v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:00,150] [INFO] DFAST_QC completed!
[2024-01-24 14:20:00,150] [INFO] Total running time: 0h0m28s