[2024-01-24 13:49:15,273] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:15,275] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:15,275] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f806712-9b2b-4267-bd1d-ccc75454faab/dqc_reference
[2024-01-24 13:49:16,520] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:16,521] [INFO] Task started: Prodigal
[2024-01-24 13:49:16,521] [INFO] Running command: gunzip -c /var/lib/cwl/stge691a6d9-9b17-4920-8037-e75c2b88e3b6/GCF_032050975.1_ASM3205097v1_genomic.fna.gz | prodigal -d GCF_032050975.1_ASM3205097v1_genomic.fna/cds.fna -a GCF_032050975.1_ASM3205097v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:31,698] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:31,699] [INFO] Task started: HMMsearch
[2024-01-24 13:49:31,699] [INFO] Running command: hmmsearch --tblout GCF_032050975.1_ASM3205097v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f806712-9b2b-4267-bd1d-ccc75454faab/dqc_reference/reference_markers.hmm GCF_032050975.1_ASM3205097v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:32,014] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:32,016] [INFO] Found 6/6 markers.
[2024-01-24 13:49:32,053] [INFO] Query marker FASTA was written to GCF_032050975.1_ASM3205097v1_genomic.fna/markers.fasta
[2024-01-24 13:49:32,053] [INFO] Task started: Blastn
[2024-01-24 13:49:32,054] [INFO] Running command: blastn -query GCF_032050975.1_ASM3205097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f806712-9b2b-4267-bd1d-ccc75454faab/dqc_reference/reference_markers.fasta -out GCF_032050975.1_ASM3205097v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:32,642] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:32,646] [INFO] Selected 16 target genomes.
[2024-01-24 13:49:32,647] [INFO] Target genome list was writen to GCF_032050975.1_ASM3205097v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:32,654] [INFO] Task started: fastANI
[2024-01-24 13:49:32,655] [INFO] Running command: fastANI --query /var/lib/cwl/stge691a6d9-9b17-4920-8037-e75c2b88e3b6/GCF_032050975.1_ASM3205097v1_genomic.fna.gz --refList GCF_032050975.1_ASM3205097v1_genomic.fna/target_genomes.txt --output GCF_032050975.1_ASM3205097v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:40,891] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:40,892] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f806712-9b2b-4267-bd1d-ccc75454faab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:40,892] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f806712-9b2b-4267-bd1d-ccc75454faab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:40,893] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:49:40,894] [INFO] The taxonomy check result is classified as 'no_hit'.
[2024-01-24 13:49:40,894] [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
--------------------------------------------------------------------------------
[2024-01-24 13:49:40,895] [INFO] DFAST Taxonomy check result was written to GCF_032050975.1_ASM3205097v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:40,896] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:40,896] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:40,897] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f806712-9b2b-4267-bd1d-ccc75454faab/dqc_reference/checkm_data
[2024-01-24 13:49:40,900] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:40,949] [INFO] Task started: CheckM
[2024-01-24 13:49:40,949] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_032050975.1_ASM3205097v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_032050975.1_ASM3205097v1_genomic.fna/checkm_input GCF_032050975.1_ASM3205097v1_genomic.fna/checkm_result
[2024-01-24 13:50:31,544] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:31,546] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:31,565] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:31,565] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:31,566] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_032050975.1_ASM3205097v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:31,566] [INFO] Task started: Blastn
[2024-01-24 13:50:31,566] [INFO] Running command: blastn -query GCF_032050975.1_ASM3205097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f806712-9b2b-4267-bd1d-ccc75454faab/dqc_reference/reference_markers_gtdb.fasta -out GCF_032050975.1_ASM3205097v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:32,336] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:32,339] [INFO] Selected 11 target genomes.
[2024-01-24 13:50:32,340] [INFO] Target genome list was writen to GCF_032050975.1_ASM3205097v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:32,349] [INFO] Task started: fastANI
[2024-01-24 13:50:32,349] [INFO] Running command: fastANI --query /var/lib/cwl/stge691a6d9-9b17-4920-8037-e75c2b88e3b6/GCF_032050975.1_ASM3205097v1_genomic.fna.gz --refList GCF_032050975.1_ASM3205097v1_genomic.fna/target_genomes_gtdb.txt --output GCF_032050975.1_ASM3205097v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:38,729] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:38,740] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:50:38,741] [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_902500695.1	s__UBA8639 sp902500695	85.8625	1072	1517	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__UBA8639;g__UBA8639	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013817135.1	s__UBA8639 sp013817135	85.8563	613	1517	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__UBA8639;g__UBA8639	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003523945.1	s__UBA8639 sp003523945	84.1958	822	1517	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__UBA8639;g__UBA8639	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377845.1	s__UBA8639 sp009377845	80.1743	589	1517	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__UBA8639;g__UBA8639	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003235785.1	s__UBA8639 sp003235785	77.3548	133	1517	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__UBA8639;g__UBA8639	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003228495.1	s__UBA8639 sp003228495	76.833	100	1517	d__Bacteria;p__Nitrospirota;c__Nitrospiria;o__Nitrospirales;f__UBA8639;g__UBA8639	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:38,742] [INFO] GTDB search result was written to GCF_032050975.1_ASM3205097v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:38,742] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:38,745] [INFO] DFAST_QC result json was written to GCF_032050975.1_ASM3205097v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:38,745] [INFO] DFAST_QC completed!
[2024-01-24 13:50:38,745] [INFO] Total running time: 0h1m23s