[2023-06-04 17:57:30,933] [INFO] DFAST_QC pipeline started.
[2023-06-04 17:57:30,944] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 17:57:30,944] [INFO] DQC Reference Directory: /var/lib/cwl/stga360657f-37ba-4cb8-8859-ab0b65e46cb3/dqc_reference
[2023-06-04 17:57:32,135] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 17:57:32,136] [INFO] Task started: Prodigal
[2023-06-04 17:57:32,137] [INFO] Running command: gunzip -c /var/lib/cwl/stgc34165a1-899d-43d7-8376-ddb76faf4b58/GCA_004213625.1_ASM421362v1_genomic.fna.gz | prodigal -d GCA_004213625.1_ASM421362v1_genomic.fna/cds.fna -a GCA_004213625.1_ASM421362v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 17:57:35,625] [INFO] Task succeeded: Prodigal
[2023-06-04 17:57:35,626] [INFO] Task started: HMMsearch
[2023-06-04 17:57:35,626] [INFO] Running command: hmmsearch --tblout GCA_004213625.1_ASM421362v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga360657f-37ba-4cb8-8859-ab0b65e46cb3/dqc_reference/reference_markers.hmm GCA_004213625.1_ASM421362v1_genomic.fna/protein.faa > /dev/null
[2023-06-04 17:57:35,833] [INFO] Task succeeded: HMMsearch
[2023-06-04 17:57:35,834] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc34165a1-899d-43d7-8376-ddb76faf4b58/GCA_004213625.1_ASM421362v1_genomic.fna.gz]
[2023-06-04 17:57:35,859] [INFO] Query marker FASTA was written to GCA_004213625.1_ASM421362v1_genomic.fna/markers.fasta
[2023-06-04 17:57:35,859] [INFO] Task started: Blastn
[2023-06-04 17:57:35,859] [INFO] Running command: blastn -query GCA_004213625.1_ASM421362v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga360657f-37ba-4cb8-8859-ab0b65e46cb3/dqc_reference/reference_markers.fasta -out GCA_004213625.1_ASM421362v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:57:36,433] [INFO] Task succeeded: Blastn
[2023-06-04 17:57:36,454] [INFO] Selected 20 target genomes.
[2023-06-04 17:57:36,455] [INFO] Target genome list was writen to GCA_004213625.1_ASM421362v1_genomic.fna/target_genomes.txt
[2023-06-04 17:57:37,490] [INFO] Task started: fastANI
[2023-06-04 17:57:37,491] [INFO] Running command: fastANI --query /var/lib/cwl/stgc34165a1-899d-43d7-8376-ddb76faf4b58/GCA_004213625.1_ASM421362v1_genomic.fna.gz --refList GCA_004213625.1_ASM421362v1_genomic.fna/target_genomes.txt --output GCA_004213625.1_ASM421362v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 17:57:51,047] [INFO] Task succeeded: fastANI
[2023-06-04 17:57:51,048] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga360657f-37ba-4cb8-8859-ab0b65e46cb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 17:57:51,049] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga360657f-37ba-4cb8-8859-ab0b65e46cb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 17:57:51,051] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 17:57:51,051] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 17:57:51,051] [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
--------------------------------------------------------------------------------
[2023-06-04 17:57:51,053] [INFO] DFAST Taxonomy check result was written to GCA_004213625.1_ASM421362v1_genomic.fna/tc_result.tsv
[2023-06-04 17:57:51,054] [INFO] ===== Taxonomy check completed =====
[2023-06-04 17:57:51,054] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 17:57:51,055] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga360657f-37ba-4cb8-8859-ab0b65e46cb3/dqc_reference/checkm_data
[2023-06-04 17:57:51,059] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 17:57:51,079] [INFO] Task started: CheckM
[2023-06-04 17:57:51,079] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004213625.1_ASM421362v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004213625.1_ASM421362v1_genomic.fna/checkm_input GCA_004213625.1_ASM421362v1_genomic.fna/checkm_result
[2023-06-04 17:58:08,667] [INFO] Task succeeded: CheckM
[2023-06-04 17:58:08,669] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 17:58:08,690] [INFO] ===== Completeness check finished =====
[2023-06-04 17:58:08,690] [INFO] ===== Start GTDB Search =====
[2023-06-04 17:58:08,691] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004213625.1_ASM421362v1_genomic.fna/markers.fasta)
[2023-06-04 17:58:08,691] [INFO] Task started: Blastn
[2023-06-04 17:58:08,692] [INFO] Running command: blastn -query GCA_004213625.1_ASM421362v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga360657f-37ba-4cb8-8859-ab0b65e46cb3/dqc_reference/reference_markers_gtdb.fasta -out GCA_004213625.1_ASM421362v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 17:58:09,441] [INFO] Task succeeded: Blastn
[2023-06-04 17:58:09,446] [INFO] Selected 14 target genomes.
[2023-06-04 17:58:09,447] [INFO] Target genome list was writen to GCA_004213625.1_ASM421362v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 17:58:09,948] [INFO] Task started: fastANI
[2023-06-04 17:58:09,948] [INFO] Running command: fastANI --query /var/lib/cwl/stgc34165a1-899d-43d7-8376-ddb76faf4b58/GCA_004213625.1_ASM421362v1_genomic.fna.gz --refList GCA_004213625.1_ASM421362v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004213625.1_ASM421362v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 17:58:17,982] [INFO] Task succeeded: fastANI
[2023-06-04 17:58:17,989] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 17:58:17,989] [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_002477465.1	s__UBA9145 sp002477465	99.8095	417	426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.95	97.46	0.90	0.76	11	conclusive
GCA_002684935.1	s__UBA9145 sp002684935	91.7919	354	426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.47	98.41	0.83	0.81	3	-
GCA_008081045.1	s__UBA9145 sp008081045	77.0251	62	426	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.92	98.40	0.89	0.82	4	-
--------------------------------------------------------------------------------
[2023-06-04 17:58:17,991] [INFO] GTDB search result was written to GCA_004213625.1_ASM421362v1_genomic.fna/result_gtdb.tsv
[2023-06-04 17:58:17,992] [INFO] ===== GTDB Search completed =====
[2023-06-04 17:58:17,994] [INFO] DFAST_QC result json was written to GCA_004213625.1_ASM421362v1_genomic.fna/dqc_result.json
[2023-06-04 17:58:17,994] [INFO] DFAST_QC completed!
[2023-06-04 17:58:17,994] [INFO] Total running time: 0h0m47s