[2023-06-28 01:45:55,286] [INFO] DFAST_QC pipeline started.
[2023-06-28 01:45:55,288] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 01:45:55,288] [INFO] DQC Reference Directory: /var/lib/cwl/stg95b705e3-bf92-4e99-9417-678aed530d74/dqc_reference
[2023-06-28 01:45:56,494] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 01:45:56,495] [INFO] Task started: Prodigal
[2023-06-28 01:45:56,495] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe603521-24da-4a9b-8409-54d07350f043/GCA_002708695.1_ASM270869v1_genomic.fna.gz | prodigal -d GCA_002708695.1_ASM270869v1_genomic.fna/cds.fna -a GCA_002708695.1_ASM270869v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 01:46:00,350] [INFO] Task succeeded: Prodigal
[2023-06-28 01:46:00,351] [INFO] Task started: HMMsearch
[2023-06-28 01:46:00,351] [INFO] Running command: hmmsearch --tblout GCA_002708695.1_ASM270869v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95b705e3-bf92-4e99-9417-678aed530d74/dqc_reference/reference_markers.hmm GCA_002708695.1_ASM270869v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 01:46:00,587] [INFO] Task succeeded: HMMsearch
[2023-06-28 01:46:00,589] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgfe603521-24da-4a9b-8409-54d07350f043/GCA_002708695.1_ASM270869v1_genomic.fna.gz]
[2023-06-28 01:46:00,620] [INFO] Query marker FASTA was written to GCA_002708695.1_ASM270869v1_genomic.fna/markers.fasta
[2023-06-28 01:46:00,621] [INFO] Task started: Blastn
[2023-06-28 01:46:00,621] [INFO] Running command: blastn -query GCA_002708695.1_ASM270869v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95b705e3-bf92-4e99-9417-678aed530d74/dqc_reference/reference_markers.fasta -out GCA_002708695.1_ASM270869v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:46:01,172] [INFO] Task succeeded: Blastn
[2023-06-28 01:46:01,176] [INFO] Selected 5 target genomes.
[2023-06-28 01:46:01,177] [INFO] Target genome list was writen to GCA_002708695.1_ASM270869v1_genomic.fna/target_genomes.txt
[2023-06-28 01:46:01,179] [INFO] Task started: fastANI
[2023-06-28 01:46:01,179] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe603521-24da-4a9b-8409-54d07350f043/GCA_002708695.1_ASM270869v1_genomic.fna.gz --refList GCA_002708695.1_ASM270869v1_genomic.fna/target_genomes.txt --output GCA_002708695.1_ASM270869v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 01:46:02,835] [INFO] Task succeeded: fastANI
[2023-06-28 01:46:02,836] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95b705e3-bf92-4e99-9417-678aed530d74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 01:46:02,836] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95b705e3-bf92-4e99-9417-678aed530d74/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 01:46:02,838] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 01:46:02,838] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 01:46:02,838] [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
--------------------------------------------------------------------------------
[2023-06-28 01:46:02,840] [INFO] DFAST Taxonomy check result was written to GCA_002708695.1_ASM270869v1_genomic.fna/tc_result.tsv
[2023-06-28 01:46:02,841] [INFO] ===== Taxonomy check completed =====
[2023-06-28 01:46:02,841] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 01:46:02,841] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95b705e3-bf92-4e99-9417-678aed530d74/dqc_reference/checkm_data
[2023-06-28 01:46:02,845] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 01:46:02,867] [INFO] Task started: CheckM
[2023-06-28 01:46:02,867] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002708695.1_ASM270869v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002708695.1_ASM270869v1_genomic.fna/checkm_input GCA_002708695.1_ASM270869v1_genomic.fna/checkm_result
[2023-06-28 01:46:22,298] [INFO] Task succeeded: CheckM
[2023-06-28 01:46:22,299] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 01:46:22,319] [INFO] ===== Completeness check finished =====
[2023-06-28 01:46:22,319] [INFO] ===== Start GTDB Search =====
[2023-06-28 01:46:22,320] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002708695.1_ASM270869v1_genomic.fna/markers.fasta)
[2023-06-28 01:46:22,320] [INFO] Task started: Blastn
[2023-06-28 01:46:22,320] [INFO] Running command: blastn -query GCA_002708695.1_ASM270869v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95b705e3-bf92-4e99-9417-678aed530d74/dqc_reference/reference_markers_gtdb.fasta -out GCA_002708695.1_ASM270869v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 01:46:22,985] [INFO] Task succeeded: Blastn
[2023-06-28 01:46:22,989] [INFO] Selected 6 target genomes.
[2023-06-28 01:46:22,989] [INFO] Target genome list was writen to GCA_002708695.1_ASM270869v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 01:46:22,996] [INFO] Task started: fastANI
[2023-06-28 01:46:22,996] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe603521-24da-4a9b-8409-54d07350f043/GCA_002708695.1_ASM270869v1_genomic.fna.gz --refList GCA_002708695.1_ASM270869v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002708695.1_ASM270869v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 01:46:25,160] [INFO] Task succeeded: fastANI
[2023-06-28 01:46:25,168] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 01:46:25,169] [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
GCA_002708695.1	s__MGIIb-N2 sp002708695	100.0	557	562	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002502625.1	s__MGIIb-N2 sp002502625	80.749	352	562	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	99.71	99.70	0.87	0.83	3	-
GCA_002708015.1	s__MGIIb-N2 sp002708015	80.6559	296	562	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002503665.1	s__MGIIb-N2 sp002503665	79.4604	142	562	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-N2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 01:46:25,171] [INFO] GTDB search result was written to GCA_002708695.1_ASM270869v1_genomic.fna/result_gtdb.tsv
[2023-06-28 01:46:25,172] [INFO] ===== GTDB Search completed =====
[2023-06-28 01:46:25,175] [INFO] DFAST_QC result json was written to GCA_002708695.1_ASM270869v1_genomic.fna/dqc_result.json
[2023-06-28 01:46:25,176] [INFO] DFAST_QC completed!
[2023-06-28 01:46:25,176] [INFO] Total running time: 0h0m30s