[2024-01-24 13:57:32,097] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:32,099] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:32,099] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a77b400-bd40-4c8d-9193-814cea04b3f5/dqc_reference
[2024-01-24 13:57:33,415] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:33,416] [INFO] Task started: Prodigal
[2024-01-24 13:57:33,416] [INFO] Running command: gunzip -c /var/lib/cwl/stgda2320ae-2b24-4fef-86fc-ccdc5d1528cb/GCF_024807035.1_ASM2480703v1_genomic.fna.gz | prodigal -d GCF_024807035.1_ASM2480703v1_genomic.fna/cds.fna -a GCF_024807035.1_ASM2480703v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:36,524] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:36,524] [INFO] Task started: HMMsearch
[2024-01-24 13:57:36,524] [INFO] Running command: hmmsearch --tblout GCF_024807035.1_ASM2480703v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a77b400-bd40-4c8d-9193-814cea04b3f5/dqc_reference/reference_markers.hmm GCF_024807035.1_ASM2480703v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:36,666] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:36,667] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgda2320ae-2b24-4fef-86fc-ccdc5d1528cb/GCF_024807035.1_ASM2480703v1_genomic.fna.gz]
[2024-01-24 13:57:36,684] [INFO] Query marker FASTA was written to GCF_024807035.1_ASM2480703v1_genomic.fna/markers.fasta
[2024-01-24 13:57:36,685] [INFO] Task started: Blastn
[2024-01-24 13:57:36,685] [INFO] Running command: blastn -query GCF_024807035.1_ASM2480703v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a77b400-bd40-4c8d-9193-814cea04b3f5/dqc_reference/reference_markers.fasta -out GCF_024807035.1_ASM2480703v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:37,194] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:37,198] [INFO] Selected 7 target genomes.
[2024-01-24 13:57:37,199] [INFO] Target genome list was writen to GCF_024807035.1_ASM2480703v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:37,207] [INFO] Task started: fastANI
[2024-01-24 13:57:37,208] [INFO] Running command: fastANI --query /var/lib/cwl/stgda2320ae-2b24-4fef-86fc-ccdc5d1528cb/GCF_024807035.1_ASM2480703v1_genomic.fna.gz --refList GCF_024807035.1_ASM2480703v1_genomic.fna/target_genomes.txt --output GCF_024807035.1_ASM2480703v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:39,522] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:39,523] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a77b400-bd40-4c8d-9193-814cea04b3f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:39,523] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a77b400-bd40-4c8d-9193-814cea04b3f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:39,526] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:57:39,526] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:57:39,527] [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
Methanobrevibacter olleyae	strain=DSM 16632	GCA_900114585.1	294671	294671	type	True	74.6476	59	588	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:39,528] [INFO] DFAST Taxonomy check result was written to GCF_024807035.1_ASM2480703v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:39,528] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:39,528] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:39,529] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a77b400-bd40-4c8d-9193-814cea04b3f5/dqc_reference/checkm_data
[2024-01-24 13:57:39,530] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:39,554] [INFO] Task started: CheckM
[2024-01-24 13:57:39,555] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024807035.1_ASM2480703v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024807035.1_ASM2480703v1_genomic.fna/checkm_input GCF_024807035.1_ASM2480703v1_genomic.fna/checkm_result
[2024-01-24 13:57:56,402] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:56,403] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:56,421] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:56,422] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:56,422] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024807035.1_ASM2480703v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:56,422] [INFO] Task started: Blastn
[2024-01-24 13:57:56,422] [INFO] Running command: blastn -query GCF_024807035.1_ASM2480703v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a77b400-bd40-4c8d-9193-814cea04b3f5/dqc_reference/reference_markers_gtdb.fasta -out GCF_024807035.1_ASM2480703v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:56,917] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:56,920] [INFO] Selected 8 target genomes.
[2024-01-24 13:57:56,921] [INFO] Target genome list was writen to GCF_024807035.1_ASM2480703v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:56,928] [INFO] Task started: fastANI
[2024-01-24 13:57:56,928] [INFO] Running command: fastANI --query /var/lib/cwl/stgda2320ae-2b24-4fef-86fc-ccdc5d1528cb/GCF_024807035.1_ASM2480703v1_genomic.fna.gz --refList GCF_024807035.1_ASM2480703v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024807035.1_ASM2480703v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:00,430] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:00,436] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:00,437] [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_017875625.1	s__Methanococcus voltae_B	99.5257	559	588	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanococcaceae;g__Methanococcus	95.0	99.48	99.48	0.97	0.97	2	conclusive
GCF_017875395.1	s__Methanococcus voltae_C	92.4558	557	588	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanococcaceae;g__Methanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000006175.1	s__Methanococcus voltae_A	84.7616	508	588	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanococcaceae;g__Methanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000018485.1	s__Methanococcus maripaludis_C	77.5622	99	588	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanococcaceae;g__Methanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017225.1	s__Methanococcus maripaludis_A	77.4692	104	588	d__Archaea;p__Methanobacteriota_A;c__Methanococci;o__Methanococcales;f__Methanococcaceae;g__Methanococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900114585.1	s__Methanobrevibacter olleyae	74.6573	54	588	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	99.51	99.51	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:00,438] [INFO] GTDB search result was written to GCF_024807035.1_ASM2480703v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:00,439] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:00,441] [INFO] DFAST_QC result json was written to GCF_024807035.1_ASM2480703v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:00,441] [INFO] DFAST_QC completed!
[2024-01-24 13:58:00,441] [INFO] Total running time: 0h0m28s