[2024-01-24 14:31:00,262] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:00,266] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:00,266] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d992f26-724e-4ab9-a13a-ca42afb484d1/dqc_reference
[2024-01-24 14:31:02,105] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:02,105] [INFO] Task started: Prodigal
[2024-01-24 14:31:02,106] [INFO] Running command: gunzip -c /var/lib/cwl/stga9c8309b-a640-4e07-8be6-8fa62f5b30ce/GCF_015500095.1_ASM1550009v1_genomic.fna.gz | prodigal -d GCF_015500095.1_ASM1550009v1_genomic.fna/cds.fna -a GCF_015500095.1_ASM1550009v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:16,738] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:16,738] [INFO] Task started: HMMsearch
[2024-01-24 14:31:16,738] [INFO] Running command: hmmsearch --tblout GCF_015500095.1_ASM1550009v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d992f26-724e-4ab9-a13a-ca42afb484d1/dqc_reference/reference_markers.hmm GCF_015500095.1_ASM1550009v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:17,136] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:17,137] [INFO] Found 6/6 markers.
[2024-01-24 14:31:17,180] [INFO] Query marker FASTA was written to GCF_015500095.1_ASM1550009v1_genomic.fna/markers.fasta
[2024-01-24 14:31:17,180] [INFO] Task started: Blastn
[2024-01-24 14:31:17,180] [INFO] Running command: blastn -query GCF_015500095.1_ASM1550009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d992f26-724e-4ab9-a13a-ca42afb484d1/dqc_reference/reference_markers.fasta -out GCF_015500095.1_ASM1550009v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:17,727] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:17,730] [INFO] Selected 22 target genomes.
[2024-01-24 14:31:17,731] [INFO] Target genome list was writen to GCF_015500095.1_ASM1550009v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:17,737] [INFO] Task started: fastANI
[2024-01-24 14:31:17,738] [INFO] Running command: fastANI --query /var/lib/cwl/stga9c8309b-a640-4e07-8be6-8fa62f5b30ce/GCF_015500095.1_ASM1550009v1_genomic.fna.gz --refList GCF_015500095.1_ASM1550009v1_genomic.fna/target_genomes.txt --output GCF_015500095.1_ASM1550009v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:36,228] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:36,228] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d992f26-724e-4ab9-a13a-ca42afb484d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:36,229] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d992f26-724e-4ab9-a13a-ca42afb484d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:36,232] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:36,232] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:36,232] [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
Phototrophicus methaneseepsis	strain=ZRK33	GCA_015500095.1	2710758	2710758	type	True	100.0	1877	1877	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 14:31:36,234] [INFO] DFAST Taxonomy check result was written to GCF_015500095.1_ASM1550009v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:36,234] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:36,234] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:36,235] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d992f26-724e-4ab9-a13a-ca42afb484d1/dqc_reference/checkm_data
[2024-01-24 14:31:36,235] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:36,286] [INFO] Task started: CheckM
[2024-01-24 14:31:36,286] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015500095.1_ASM1550009v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015500095.1_ASM1550009v1_genomic.fna/checkm_input GCF_015500095.1_ASM1550009v1_genomic.fna/checkm_result
[2024-01-24 14:32:20,327] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:20,327] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:20,341] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:20,342] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:20,342] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015500095.1_ASM1550009v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:20,342] [INFO] Task started: Blastn
[2024-01-24 14:32:20,342] [INFO] Running command: blastn -query GCF_015500095.1_ASM1550009v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d992f26-724e-4ab9-a13a-ca42afb484d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_015500095.1_ASM1550009v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:21,155] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:21,158] [INFO] Selected 29 target genomes.
[2024-01-24 14:32:21,158] [INFO] Target genome list was writen to GCF_015500095.1_ASM1550009v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:21,296] [INFO] Task started: fastANI
[2024-01-24 14:32:21,296] [INFO] Running command: fastANI --query /var/lib/cwl/stga9c8309b-a640-4e07-8be6-8fa62f5b30ce/GCF_015500095.1_ASM1550009v1_genomic.fna.gz --refList GCF_015500095.1_ASM1550009v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015500095.1_ASM1550009v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:43,625] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:43,629] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:43,629] [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_015500095.1	s__GCA-2699585 sp015500095	100.0	1877	1877	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__GCA-2699585	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002699585.1	s__GCA-2699585 sp002699585	77.8994	371	1877	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__GCA-2699585	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002702065.1	s__GCA-2702065 sp002702065	75.4964	66	1877	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__GCA-2702065	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016223085.1	s__CFX2 sp016223085	75.1255	50	1877	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__CFX2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:43,630] [INFO] GTDB search result was written to GCF_015500095.1_ASM1550009v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:43,631] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:43,633] [INFO] DFAST_QC result json was written to GCF_015500095.1_ASM1550009v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:43,633] [INFO] DFAST_QC completed!
[2024-01-24 14:32:43,633] [INFO] Total running time: 0h1m43s