[2023-06-19 08:39:07,014] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:39:07,018] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:39:07,018] [INFO] DQC Reference Directory: /var/lib/cwl/stg6427aa6c-55f2-4072-8932-431e6a7ddccc/dqc_reference
[2023-06-19 08:39:08,261] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:39:08,262] [INFO] Task started: Prodigal
[2023-06-19 08:39:08,262] [INFO] Running command: gunzip -c /var/lib/cwl/stg5fddb342-82b4-4c7c-bbac-2fdd33626ff3/GCA_018822925.1_ASM1882292v1_genomic.fna.gz | prodigal -d GCA_018822925.1_ASM1882292v1_genomic.fna/cds.fna -a GCA_018822925.1_ASM1882292v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:39:14,103] [INFO] Task succeeded: Prodigal
[2023-06-19 08:39:14,103] [INFO] Task started: HMMsearch
[2023-06-19 08:39:14,103] [INFO] Running command: hmmsearch --tblout GCA_018822925.1_ASM1882292v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6427aa6c-55f2-4072-8932-431e6a7ddccc/dqc_reference/reference_markers.hmm GCA_018822925.1_ASM1882292v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:39:14,276] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:39:14,277] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5fddb342-82b4-4c7c-bbac-2fdd33626ff3/GCA_018822925.1_ASM1882292v1_genomic.fna.gz]
[2023-06-19 08:39:14,297] [INFO] Query marker FASTA was written to GCA_018822925.1_ASM1882292v1_genomic.fna/markers.fasta
[2023-06-19 08:39:14,297] [INFO] Task started: Blastn
[2023-06-19 08:39:14,297] [INFO] Running command: blastn -query GCA_018822925.1_ASM1882292v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6427aa6c-55f2-4072-8932-431e6a7ddccc/dqc_reference/reference_markers.fasta -out GCA_018822925.1_ASM1882292v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:39:14,842] [INFO] Task succeeded: Blastn
[2023-06-19 08:39:14,845] [INFO] Selected 15 target genomes.
[2023-06-19 08:39:14,845] [INFO] Target genome list was writen to GCA_018822925.1_ASM1882292v1_genomic.fna/target_genomes.txt
[2023-06-19 08:39:14,848] [INFO] Task started: fastANI
[2023-06-19 08:39:14,849] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fddb342-82b4-4c7c-bbac-2fdd33626ff3/GCA_018822925.1_ASM1882292v1_genomic.fna.gz --refList GCA_018822925.1_ASM1882292v1_genomic.fna/target_genomes.txt --output GCA_018822925.1_ASM1882292v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:39:24,340] [INFO] Task succeeded: fastANI
[2023-06-19 08:39:24,341] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6427aa6c-55f2-4072-8932-431e6a7ddccc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:39:24,341] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6427aa6c-55f2-4072-8932-431e6a7ddccc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:39:24,343] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:39:24,343] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 08:39:24,343] [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
--------------------------------------------------------------------------------
[2023-06-19 08:39:24,347] [INFO] DFAST Taxonomy check result was written to GCA_018822925.1_ASM1882292v1_genomic.fna/tc_result.tsv
[2023-06-19 08:39:24,348] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:39:24,349] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:39:24,349] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6427aa6c-55f2-4072-8932-431e6a7ddccc/dqc_reference/checkm_data
[2023-06-19 08:39:24,352] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:39:24,374] [INFO] Task started: CheckM
[2023-06-19 08:39:24,375] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018822925.1_ASM1882292v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018822925.1_ASM1882292v1_genomic.fna/checkm_input GCA_018822925.1_ASM1882292v1_genomic.fna/checkm_result
[2023-06-19 08:39:46,846] [INFO] Task succeeded: CheckM
[2023-06-19 08:39:46,847] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:39:46,867] [INFO] ===== Completeness check finished =====
[2023-06-19 08:39:46,867] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:39:46,867] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018822925.1_ASM1882292v1_genomic.fna/markers.fasta)
[2023-06-19 08:39:46,867] [INFO] Task started: Blastn
[2023-06-19 08:39:46,867] [INFO] Running command: blastn -query GCA_018822925.1_ASM1882292v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6427aa6c-55f2-4072-8932-431e6a7ddccc/dqc_reference/reference_markers_gtdb.fasta -out GCA_018822925.1_ASM1882292v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:39:47,571] [INFO] Task succeeded: Blastn
[2023-06-19 08:39:47,576] [INFO] Selected 17 target genomes.
[2023-06-19 08:39:47,576] [INFO] Target genome list was writen to GCA_018822925.1_ASM1882292v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:39:47,615] [INFO] Task started: fastANI
[2023-06-19 08:39:47,616] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fddb342-82b4-4c7c-bbac-2fdd33626ff3/GCA_018822925.1_ASM1882292v1_genomic.fna.gz --refList GCA_018822925.1_ASM1882292v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018822925.1_ASM1882292v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:39:52,464] [INFO] Task succeeded: fastANI
[2023-06-19 08:39:52,471] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:39:52,471] [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_018813295.1	s__JAHJBZ01 sp018813295	99.8824	390	441	d__Bacteria;p__Patescibacteria;c__Gracilibacteria;o__UM-FILTER-43-11;f__UM-FILTER-43-11;g__JAHJBZ01	95.0	99.80	99.72	0.90	0.88	3	conclusive
GCA_018814945.1	s__JAHIYT01 sp018814945	76.8895	60	441	d__Bacteria;p__Patescibacteria;c__Gracilibacteria;o__UM-FILTER-43-11;f__UM-FILTER-43-11;g__JAHIYT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016932505.1	s__JAFGCT01 sp016932505	76.5276	55	441	d__Bacteria;p__Patescibacteria;c__Gracilibacteria;o__UM-FILTER-43-11;f__UM-FILTER-43-11;g__JAFGCT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 08:39:52,473] [INFO] GTDB search result was written to GCA_018822925.1_ASM1882292v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:39:52,476] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:39:52,480] [INFO] DFAST_QC result json was written to GCA_018822925.1_ASM1882292v1_genomic.fna/dqc_result.json
[2023-06-19 08:39:52,480] [INFO] DFAST_QC completed!
[2023-06-19 08:39:52,480] [INFO] Total running time: 0h0m45s