[2023-06-18 20:29:33,412] [INFO] DFAST_QC pipeline started.
[2023-06-18 20:29:33,415] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 20:29:33,415] [INFO] DQC Reference Directory: /var/lib/cwl/stg97923154-4f33-41b9-a530-3f3461e8b2b8/dqc_reference
[2023-06-18 20:29:35,678] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 20:29:35,679] [INFO] Task started: Prodigal
[2023-06-18 20:29:35,679] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d41bcd9-9647-44af-88e4-498305ae0ba9/GCA_018607795.1_ASM1860779v1_genomic.fna.gz | prodigal -d GCA_018607795.1_ASM1860779v1_genomic.fna/cds.fna -a GCA_018607795.1_ASM1860779v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 20:29:42,565] [INFO] Task succeeded: Prodigal
[2023-06-18 20:29:42,566] [INFO] Task started: HMMsearch
[2023-06-18 20:29:42,566] [INFO] Running command: hmmsearch --tblout GCA_018607795.1_ASM1860779v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97923154-4f33-41b9-a530-3f3461e8b2b8/dqc_reference/reference_markers.hmm GCA_018607795.1_ASM1860779v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 20:29:42,817] [INFO] Task succeeded: HMMsearch
[2023-06-18 20:29:42,818] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5d41bcd9-9647-44af-88e4-498305ae0ba9/GCA_018607795.1_ASM1860779v1_genomic.fna.gz]
[2023-06-18 20:29:42,847] [INFO] Query marker FASTA was written to GCA_018607795.1_ASM1860779v1_genomic.fna/markers.fasta
[2023-06-18 20:29:42,847] [INFO] Task started: Blastn
[2023-06-18 20:29:42,848] [INFO] Running command: blastn -query GCA_018607795.1_ASM1860779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97923154-4f33-41b9-a530-3f3461e8b2b8/dqc_reference/reference_markers.fasta -out GCA_018607795.1_ASM1860779v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:29:43,482] [INFO] Task succeeded: Blastn
[2023-06-18 20:29:43,486] [INFO] Selected 25 target genomes.
[2023-06-18 20:29:43,487] [INFO] Target genome list was writen to GCA_018607795.1_ASM1860779v1_genomic.fna/target_genomes.txt
[2023-06-18 20:29:43,493] [INFO] Task started: fastANI
[2023-06-18 20:29:43,494] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d41bcd9-9647-44af-88e4-498305ae0ba9/GCA_018607795.1_ASM1860779v1_genomic.fna.gz --refList GCA_018607795.1_ASM1860779v1_genomic.fna/target_genomes.txt --output GCA_018607795.1_ASM1860779v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 20:30:01,648] [INFO] Task succeeded: fastANI
[2023-06-18 20:30:01,648] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97923154-4f33-41b9-a530-3f3461e8b2b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 20:30:01,648] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97923154-4f33-41b9-a530-3f3461e8b2b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 20:30:01,650] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 20:30:01,650] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 20:30:01,650] [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
--------------------------------------------------------------------------------
[2023-06-18 20:30:01,651] [INFO] DFAST Taxonomy check result was written to GCA_018607795.1_ASM1860779v1_genomic.fna/tc_result.tsv
[2023-06-18 20:30:01,652] [INFO] ===== Taxonomy check completed =====
[2023-06-18 20:30:01,652] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 20:30:01,652] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97923154-4f33-41b9-a530-3f3461e8b2b8/dqc_reference/checkm_data
[2023-06-18 20:30:01,655] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 20:30:01,684] [INFO] Task started: CheckM
[2023-06-18 20:30:01,684] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018607795.1_ASM1860779v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018607795.1_ASM1860779v1_genomic.fna/checkm_input GCA_018607795.1_ASM1860779v1_genomic.fna/checkm_result
[2023-06-18 20:30:28,900] [INFO] Task succeeded: CheckM
[2023-06-18 20:30:28,902] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.41%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 20:30:28,919] [INFO] ===== Completeness check finished =====
[2023-06-18 20:30:28,919] [INFO] ===== Start GTDB Search =====
[2023-06-18 20:30:28,920] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018607795.1_ASM1860779v1_genomic.fna/markers.fasta)
[2023-06-18 20:30:28,920] [INFO] Task started: Blastn
[2023-06-18 20:30:28,920] [INFO] Running command: blastn -query GCA_018607795.1_ASM1860779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97923154-4f33-41b9-a530-3f3461e8b2b8/dqc_reference/reference_markers_gtdb.fasta -out GCA_018607795.1_ASM1860779v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:30:29,856] [INFO] Task succeeded: Blastn
[2023-06-18 20:30:29,859] [INFO] Selected 19 target genomes.
[2023-06-18 20:30:29,859] [INFO] Target genome list was writen to GCA_018607795.1_ASM1860779v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 20:30:29,918] [INFO] Task started: fastANI
[2023-06-18 20:30:29,919] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d41bcd9-9647-44af-88e4-498305ae0ba9/GCA_018607795.1_ASM1860779v1_genomic.fna.gz --refList GCA_018607795.1_ASM1860779v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018607795.1_ASM1860779v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 20:30:38,628] [INFO] Task succeeded: fastANI
[2023-06-18 20:30:38,634] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 20:30:38,635] [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_009886815.1	s__Luminiphilus sp009886815	98.1582	585	844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	98.45	98.43	0.82	0.81	3	conclusive
GCA_000169115.1	s__Luminiphilus sp000169115	81.0915	538	844	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	96.96	96.76	0.93	0.91	5	-
--------------------------------------------------------------------------------
[2023-06-18 20:30:38,637] [INFO] GTDB search result was written to GCA_018607795.1_ASM1860779v1_genomic.fna/result_gtdb.tsv
[2023-06-18 20:30:38,637] [INFO] ===== GTDB Search completed =====
[2023-06-18 20:30:38,639] [INFO] DFAST_QC result json was written to GCA_018607795.1_ASM1860779v1_genomic.fna/dqc_result.json
[2023-06-18 20:30:38,639] [INFO] DFAST_QC completed!
[2023-06-18 20:30:38,640] [INFO] Total running time: 0h1m5s