[2023-06-19 08:34:24,239] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:34:24,242] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:34:24,242] [INFO] DQC Reference Directory: /var/lib/cwl/stg2985af3f-6e51-4655-816b-5aaf96b77c98/dqc_reference
[2023-06-19 08:34:25,502] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:34:25,503] [INFO] Task started: Prodigal
[2023-06-19 08:34:25,503] [INFO] Running command: gunzip -c /var/lib/cwl/stg299833b6-2ac0-490e-854b-486a0a02c487/GCA_018334975.1_ASM1833497v1_genomic.fna.gz | prodigal -d GCA_018334975.1_ASM1833497v1_genomic.fna/cds.fna -a GCA_018334975.1_ASM1833497v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:34:28,238] [INFO] Task succeeded: Prodigal
[2023-06-19 08:34:28,239] [INFO] Task started: HMMsearch
[2023-06-19 08:34:28,239] [INFO] Running command: hmmsearch --tblout GCA_018334975.1_ASM1833497v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2985af3f-6e51-4655-816b-5aaf96b77c98/dqc_reference/reference_markers.hmm GCA_018334975.1_ASM1833497v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:34:28,500] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:34:28,501] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg299833b6-2ac0-490e-854b-486a0a02c487/GCA_018334975.1_ASM1833497v1_genomic.fna.gz]
[2023-06-19 08:34:28,525] [INFO] Query marker FASTA was written to GCA_018334975.1_ASM1833497v1_genomic.fna/markers.fasta
[2023-06-19 08:34:28,525] [INFO] Task started: Blastn
[2023-06-19 08:34:28,526] [INFO] Running command: blastn -query GCA_018334975.1_ASM1833497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2985af3f-6e51-4655-816b-5aaf96b77c98/dqc_reference/reference_markers.fasta -out GCA_018334975.1_ASM1833497v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:34:29,080] [INFO] Task succeeded: Blastn
[2023-06-19 08:34:29,085] [INFO] Selected 7 target genomes.
[2023-06-19 08:34:29,085] [INFO] Target genome list was writen to GCA_018334975.1_ASM1833497v1_genomic.fna/target_genomes.txt
[2023-06-19 08:34:29,089] [INFO] Task started: fastANI
[2023-06-19 08:34:29,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg299833b6-2ac0-490e-854b-486a0a02c487/GCA_018334975.1_ASM1833497v1_genomic.fna.gz --refList GCA_018334975.1_ASM1833497v1_genomic.fna/target_genomes.txt --output GCA_018334975.1_ASM1833497v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:34:33,608] [INFO] Task succeeded: fastANI
[2023-06-19 08:34:33,609] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2985af3f-6e51-4655-816b-5aaf96b77c98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:34:33,610] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2985af3f-6e51-4655-816b-5aaf96b77c98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:34:33,613] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:34:33,613] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 08:34:33,613] [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 08:34:33,615] [INFO] DFAST Taxonomy check result was written to GCA_018334975.1_ASM1833497v1_genomic.fna/tc_result.tsv
[2023-06-19 08:34:33,616] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:34:33,617] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:34:33,617] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2985af3f-6e51-4655-816b-5aaf96b77c98/dqc_reference/checkm_data
[2023-06-19 08:34:33,622] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:34:33,647] [INFO] Task started: CheckM
[2023-06-19 08:34:33,647] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018334975.1_ASM1833497v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018334975.1_ASM1833497v1_genomic.fna/checkm_input GCA_018334975.1_ASM1833497v1_genomic.fna/checkm_result
[2023-06-19 08:34:50,122] [INFO] Task succeeded: CheckM
[2023-06-19 08:34:50,123] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.51%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 08:34:50,151] [INFO] ===== Completeness check finished =====
[2023-06-19 08:34:50,151] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:34:50,152] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018334975.1_ASM1833497v1_genomic.fna/markers.fasta)
[2023-06-19 08:34:50,152] [INFO] Task started: Blastn
[2023-06-19 08:34:50,152] [INFO] Running command: blastn -query GCA_018334975.1_ASM1833497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2985af3f-6e51-4655-816b-5aaf96b77c98/dqc_reference/reference_markers_gtdb.fasta -out GCA_018334975.1_ASM1833497v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:34:50,869] [INFO] Task succeeded: Blastn
[2023-06-19 08:34:50,875] [INFO] Selected 12 target genomes.
[2023-06-19 08:34:50,875] [INFO] Target genome list was writen to GCA_018334975.1_ASM1833497v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:34:50,904] [INFO] Task started: fastANI
[2023-06-19 08:34:50,904] [INFO] Running command: fastANI --query /var/lib/cwl/stg299833b6-2ac0-490e-854b-486a0a02c487/GCA_018334975.1_ASM1833497v1_genomic.fna.gz --refList GCA_018334975.1_ASM1833497v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018334975.1_ASM1833497v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:34:56,388] [INFO] Task succeeded: fastANI
[2023-06-19 08:34:56,395] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 08:34:56,395] [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	79.2174	56	385	d__Bacteria;p__Bipolaricaulota;c__Bipolaricaulia;o__M55B111;f__M55B111;g__JAGXLP01	95.0	99.44	99.44	0.87	0.87	2	-
GCA_018334915.1	s__JAGXLP01 sp018334915	79.0665	66	385	d__Bacteria;p__Bipolaricaulota;c__Bipolaricaulia;o__M55B111;f__M55B111;g__JAGXLP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 08:34:56,398] [INFO] GTDB search result was written to GCA_018334975.1_ASM1833497v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:34:56,399] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:34:56,403] [INFO] DFAST_QC result json was written to GCA_018334975.1_ASM1833497v1_genomic.fna/dqc_result.json
[2023-06-19 08:34:56,403] [INFO] DFAST_QC completed!
[2023-06-19 08:34:56,403] [INFO] Total running time: 0h0m32s