[2024-01-25 19:31:51,655] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:31:51,657] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:31:51,657] [INFO] DQC Reference Directory: /var/lib/cwl/stg9cc894f1-b107-48d6-80fe-df7d83eb44dc/dqc_reference
[2024-01-25 19:31:52,774] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:31:52,775] [INFO] Task started: Prodigal
[2024-01-25 19:31:52,775] [INFO] Running command: gunzip -c /var/lib/cwl/stg71b64de0-b94a-49ed-a643-1a0424bacfe6/GCF_000024625.1_ASM2462v1_genomic.fna.gz | prodigal -d GCF_000024625.1_ASM2462v1_genomic.fna/cds.fna -a GCF_000024625.1_ASM2462v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:31:55,593] [INFO] Task succeeded: Prodigal
[2024-01-25 19:31:55,593] [INFO] Task started: HMMsearch
[2024-01-25 19:31:55,593] [INFO] Running command: hmmsearch --tblout GCF_000024625.1_ASM2462v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9cc894f1-b107-48d6-80fe-df7d83eb44dc/dqc_reference/reference_markers.hmm GCF_000024625.1_ASM2462v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:31:55,731] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:31:55,732] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg71b64de0-b94a-49ed-a643-1a0424bacfe6/GCF_000024625.1_ASM2462v1_genomic.fna.gz]
[2024-01-25 19:31:55,749] [INFO] Query marker FASTA was written to GCF_000024625.1_ASM2462v1_genomic.fna/markers.fasta
[2024-01-25 19:31:55,749] [INFO] Task started: Blastn
[2024-01-25 19:31:55,749] [INFO] Running command: blastn -query GCF_000024625.1_ASM2462v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9cc894f1-b107-48d6-80fe-df7d83eb44dc/dqc_reference/reference_markers.fasta -out GCF_000024625.1_ASM2462v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:31:56,189] [INFO] Task succeeded: Blastn
[2024-01-25 19:31:56,193] [INFO] Selected 6 target genomes.
[2024-01-25 19:31:56,193] [INFO] Target genome list was writen to GCF_000024625.1_ASM2462v1_genomic.fna/target_genomes.txt
[2024-01-25 19:31:56,202] [INFO] Task started: fastANI
[2024-01-25 19:31:56,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg71b64de0-b94a-49ed-a643-1a0424bacfe6/GCF_000024625.1_ASM2462v1_genomic.fna.gz --refList GCF_000024625.1_ASM2462v1_genomic.fna/target_genomes.txt --output GCF_000024625.1_ASM2462v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:31:58,460] [INFO] Task succeeded: fastANI
[2024-01-25 19:31:58,461] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9cc894f1-b107-48d6-80fe-df7d83eb44dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:31:58,461] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9cc894f1-b107-48d6-80fe-df7d83eb44dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:31:58,467] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:31:58,467] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:31:58,467] [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 vulcanius	strain=M7	GCA_000024625.1	73913	73913	type	True	100.0	586	586	95	conclusive
Methanocaldococcus jannaschii	strain=DSM 2661	GCA_000091665.1	2190	2190	type	True	81.6467	312	586	95	below_threshold
Methanocaldococcus bathoardescens	strain=JH146	GCA_000739065.1	1301915	1301915	type	True	80.0225	301	586	95	below_threshold
Methanocaldococcus fervens	strain=AG86	GCA_000023985.1	83171	83171	type	True	79.2606	255	586	95	below_threshold
Methanotorris formicicus	strain=Mc-S-70	GCA_000243455.2	213185	213185	type	True	77.7085	123	586	95	below_threshold
Methanotorris igneus	strain=Kol 5	GCA_000214415.1	2189	2189	type	True	77.0836	122	586	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:31:58,469] [INFO] DFAST Taxonomy check result was written to GCF_000024625.1_ASM2462v1_genomic.fna/tc_result.tsv
[2024-01-25 19:31:58,470] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:31:58,470] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:31:58,470] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9cc894f1-b107-48d6-80fe-df7d83eb44dc/dqc_reference/checkm_data
[2024-01-25 19:31:58,471] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:31:58,492] [INFO] Task started: CheckM
[2024-01-25 19:31:58,492] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000024625.1_ASM2462v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000024625.1_ASM2462v1_genomic.fna/checkm_input GCF_000024625.1_ASM2462v1_genomic.fna/checkm_result
[2024-01-25 19:32:12,903] [INFO] Task succeeded: CheckM
[2024-01-25 19:32:12,904] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:32:12,921] [INFO] ===== Completeness check finished =====
[2024-01-25 19:32:12,921] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:32:12,922] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000024625.1_ASM2462v1_genomic.fna/markers.fasta)
[2024-01-25 19:32:12,922] [INFO] Task started: Blastn
[2024-01-25 19:32:12,922] [INFO] Running command: blastn -query GCF_000024625.1_ASM2462v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9cc894f1-b107-48d6-80fe-df7d83eb44dc/dqc_reference/reference_markers_gtdb.fasta -out GCF_000024625.1_ASM2462v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:32:13,370] [INFO] Task succeeded: Blastn
[2024-01-25 19:32:13,373] [INFO] Selected 6 target genomes.
[2024-01-25 19:32:13,373] [INFO] Target genome list was writen to GCF_000024625.1_ASM2462v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:32:13,388] [INFO] Task started: fastANI
[2024-01-25 19:32:13,388] [INFO] Running command: fastANI --query /var/lib/cwl/stg71b64de0-b94a-49ed-a643-1a0424bacfe6/GCF_000024625.1_ASM2462v1_genomic.fna.gz --refList GCF_000024625.1_ASM2462v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000024625.1_ASM2462v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:32:15,911] [INFO] Task succeeded: fastANI
[2024-01-25 19:32:15,916] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:32:15,916] [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_000024625.1	s__Methanocaldococcus vulcanius	100.0	586	586	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
GCA_013153845.1	s__Methanocaldococcus sp013153845	94.5705	391	586	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	81.6467	312	586	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_000739065.1	s__Methanocaldococcus bathoardescens	80.0223	301	586	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_000025525.1	s__Methanocaldococcus sp000025525	79.6784	300	586	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_000023985.1	s__Methanocaldococcus fervens	79.251	250	586	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanocaldococcaceae;g__Methanocaldococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:32:15,917] [INFO] GTDB search result was written to GCF_000024625.1_ASM2462v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:32:15,918] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:32:15,921] [INFO] DFAST_QC result json was written to GCF_000024625.1_ASM2462v1_genomic.fna/dqc_result.json
[2024-01-25 19:32:15,921] [INFO] DFAST_QC completed!
[2024-01-25 19:32:15,921] [INFO] Total running time: 0h0m24s