[2023-06-18 18:09:58,340] [INFO] DFAST_QC pipeline started.
[2023-06-18 18:09:58,343] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 18:09:58,343] [INFO] DQC Reference Directory: /var/lib/cwl/stgebb18d6f-920b-4dde-8831-39425ed2aed1/dqc_reference
[2023-06-18 18:10:01,323] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 18:10:01,324] [INFO] Task started: Prodigal
[2023-06-18 18:10:01,324] [INFO] Running command: gunzip -c /var/lib/cwl/stg7868741e-2dbc-4c1f-a46b-812083955e17/GCA_018335315.1_ASM1833531v1_genomic.fna.gz | prodigal -d GCA_018335315.1_ASM1833531v1_genomic.fna/cds.fna -a GCA_018335315.1_ASM1833531v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 18:10:05,667] [INFO] Task succeeded: Prodigal
[2023-06-18 18:10:05,667] [INFO] Task started: HMMsearch
[2023-06-18 18:10:05,668] [INFO] Running command: hmmsearch --tblout GCA_018335315.1_ASM1833531v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgebb18d6f-920b-4dde-8831-39425ed2aed1/dqc_reference/reference_markers.hmm GCA_018335315.1_ASM1833531v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 18:10:05,913] [INFO] Task succeeded: HMMsearch
[2023-06-18 18:10:05,914] [INFO] Found 6/6 markers.
[2023-06-18 18:10:05,941] [INFO] Query marker FASTA was written to GCA_018335315.1_ASM1833531v1_genomic.fna/markers.fasta
[2023-06-18 18:10:05,941] [INFO] Task started: Blastn
[2023-06-18 18:10:05,941] [INFO] Running command: blastn -query GCA_018335315.1_ASM1833531v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebb18d6f-920b-4dde-8831-39425ed2aed1/dqc_reference/reference_markers.fasta -out GCA_018335315.1_ASM1833531v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:10:08,231] [INFO] Task succeeded: Blastn
[2023-06-18 18:10:08,238] [INFO] Selected 7 target genomes.
[2023-06-18 18:10:08,239] [INFO] Target genome list was writen to GCA_018335315.1_ASM1833531v1_genomic.fna/target_genomes.txt
[2023-06-18 18:10:08,241] [INFO] Task started: fastANI
[2023-06-18 18:10:08,242] [INFO] Running command: fastANI --query /var/lib/cwl/stg7868741e-2dbc-4c1f-a46b-812083955e17/GCA_018335315.1_ASM1833531v1_genomic.fna.gz --refList GCA_018335315.1_ASM1833531v1_genomic.fna/target_genomes.txt --output GCA_018335315.1_ASM1833531v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 18:10:12,247] [INFO] Task succeeded: fastANI
[2023-06-18 18:10:12,252] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgebb18d6f-920b-4dde-8831-39425ed2aed1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 18:10:12,253] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgebb18d6f-920b-4dde-8831-39425ed2aed1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 18:10:12,255] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 18:10:12,256] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 18:10:12,256] [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 18:10:12,259] [INFO] DFAST Taxonomy check result was written to GCA_018335315.1_ASM1833531v1_genomic.fna/tc_result.tsv
[2023-06-18 18:10:12,264] [INFO] ===== Taxonomy check completed =====
[2023-06-18 18:10:12,264] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 18:10:12,265] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgebb18d6f-920b-4dde-8831-39425ed2aed1/dqc_reference/checkm_data
[2023-06-18 18:10:12,277] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 18:10:12,313] [INFO] Task started: CheckM
[2023-06-18 18:10:12,313] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018335315.1_ASM1833531v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018335315.1_ASM1833531v1_genomic.fna/checkm_input GCA_018335315.1_ASM1833531v1_genomic.fna/checkm_result
[2023-06-18 18:10:32,754] [INFO] Task succeeded: CheckM
[2023-06-18 18:10:32,755] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 18:10:32,782] [INFO] ===== Completeness check finished =====
[2023-06-18 18:10:32,783] [INFO] ===== Start GTDB Search =====
[2023-06-18 18:10:32,783] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018335315.1_ASM1833531v1_genomic.fna/markers.fasta)
[2023-06-18 18:10:32,784] [INFO] Task started: Blastn
[2023-06-18 18:10:32,784] [INFO] Running command: blastn -query GCA_018335315.1_ASM1833531v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgebb18d6f-920b-4dde-8831-39425ed2aed1/dqc_reference/reference_markers_gtdb.fasta -out GCA_018335315.1_ASM1833531v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:10:33,624] [INFO] Task succeeded: Blastn
[2023-06-18 18:10:33,630] [INFO] Selected 14 target genomes.
[2023-06-18 18:10:33,631] [INFO] Target genome list was writen to GCA_018335315.1_ASM1833531v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 18:10:33,638] [INFO] Task started: fastANI
[2023-06-18 18:10:33,639] [INFO] Running command: fastANI --query /var/lib/cwl/stg7868741e-2dbc-4c1f-a46b-812083955e17/GCA_018335315.1_ASM1833531v1_genomic.fna.gz --refList GCA_018335315.1_ASM1833531v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018335315.1_ASM1833531v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 18:10:39,503] [INFO] Task succeeded: fastANI
[2023-06-18 18:10:39,507] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 18:10:39,508] [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_018335015.1	s__JAGXLP01 sp018335015	99.2158	509	694	d__Bacteria;p__Bipolaricaulota;c__Bipolaricaulia;o__M55B111;f__M55B111;g__JAGXLP01	95.0	99.44	99.44	0.87	0.87	2	conclusive
GCA_018334915.1	s__JAGXLP01 sp018334915	84.0789	398	694	d__Bacteria;p__Bipolaricaulota;c__Bipolaricaulia;o__M55B111;f__M55B111;g__JAGXLP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018334615.1	s__JAGXLP01 sp018334615	80.057	80	694	d__Bacteria;p__Bipolaricaulota;c__Bipolaricaulia;o__M55B111;f__M55B111;g__JAGXLP01	95.0	99.41	99.39	0.84	0.80	3	-
--------------------------------------------------------------------------------
[2023-06-18 18:10:39,510] [INFO] GTDB search result was written to GCA_018335315.1_ASM1833531v1_genomic.fna/result_gtdb.tsv
[2023-06-18 18:10:39,513] [INFO] ===== GTDB Search completed =====
[2023-06-18 18:10:39,517] [INFO] DFAST_QC result json was written to GCA_018335315.1_ASM1833531v1_genomic.fna/dqc_result.json
[2023-06-18 18:10:39,517] [INFO] DFAST_QC completed!
[2023-06-18 18:10:39,517] [INFO] Total running time: 0h0m41s