[2023-06-19 02:24:56,385] [INFO] DFAST_QC pipeline started.
[2023-06-19 02:24:56,387] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 02:24:56,387] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf7f65c5-448b-4012-bea2-59a9d905e69a/dqc_reference
[2023-06-19 02:24:57,628] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 02:24:57,628] [INFO] Task started: Prodigal
[2023-06-19 02:24:57,629] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a93c6d2-dc64-4426-94e2-83edfa19a6ce/GCA_018664515.1_ASM1866451v1_genomic.fna.gz | prodigal -d GCA_018664515.1_ASM1866451v1_genomic.fna/cds.fna -a GCA_018664515.1_ASM1866451v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 02:25:12,619] [INFO] Task succeeded: Prodigal
[2023-06-19 02:25:12,620] [INFO] Task started: HMMsearch
[2023-06-19 02:25:12,620] [INFO] Running command: hmmsearch --tblout GCA_018664515.1_ASM1866451v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf7f65c5-448b-4012-bea2-59a9d905e69a/dqc_reference/reference_markers.hmm GCA_018664515.1_ASM1866451v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 02:25:12,934] [INFO] Task succeeded: HMMsearch
[2023-06-19 02:25:12,936] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg3a93c6d2-dc64-4426-94e2-83edfa19a6ce/GCA_018664515.1_ASM1866451v1_genomic.fna.gz]
[2023-06-19 02:25:12,981] [INFO] Query marker FASTA was written to GCA_018664515.1_ASM1866451v1_genomic.fna/markers.fasta
[2023-06-19 02:25:12,982] [INFO] Task started: Blastn
[2023-06-19 02:25:12,982] [INFO] Running command: blastn -query GCA_018664515.1_ASM1866451v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf7f65c5-448b-4012-bea2-59a9d905e69a/dqc_reference/reference_markers.fasta -out GCA_018664515.1_ASM1866451v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:25:13,470] [INFO] Task succeeded: Blastn
[2023-06-19 02:25:13,474] [INFO] Selected 16 target genomes.
[2023-06-19 02:25:13,474] [INFO] Target genome list was writen to GCA_018664515.1_ASM1866451v1_genomic.fna/target_genomes.txt
[2023-06-19 02:25:13,477] [INFO] Task started: fastANI
[2023-06-19 02:25:13,477] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a93c6d2-dc64-4426-94e2-83edfa19a6ce/GCA_018664515.1_ASM1866451v1_genomic.fna.gz --refList GCA_018664515.1_ASM1866451v1_genomic.fna/target_genomes.txt --output GCA_018664515.1_ASM1866451v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 02:25:27,362] [INFO] Task succeeded: fastANI
[2023-06-19 02:25:27,362] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf7f65c5-448b-4012-bea2-59a9d905e69a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 02:25:27,363] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf7f65c5-448b-4012-bea2-59a9d905e69a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 02:25:27,366] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 02:25:27,366] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 02:25:27,366] [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
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	75.4507	80	1322	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 02:25:27,369] [INFO] DFAST Taxonomy check result was written to GCA_018664515.1_ASM1866451v1_genomic.fna/tc_result.tsv
[2023-06-19 02:25:27,369] [INFO] ===== Taxonomy check completed =====
[2023-06-19 02:25:27,369] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 02:25:27,370] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf7f65c5-448b-4012-bea2-59a9d905e69a/dqc_reference/checkm_data
[2023-06-19 02:25:27,371] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 02:25:27,437] [INFO] Task started: CheckM
[2023-06-19 02:25:27,437] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018664515.1_ASM1866451v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018664515.1_ASM1866451v1_genomic.fna/checkm_input GCA_018664515.1_ASM1866451v1_genomic.fna/checkm_result
[2023-06-19 02:26:14,254] [INFO] Task succeeded: CheckM
[2023-06-19 02:26:14,256] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.66%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 02:26:14,282] [INFO] ===== Completeness check finished =====
[2023-06-19 02:26:14,283] [INFO] ===== Start GTDB Search =====
[2023-06-19 02:26:14,283] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018664515.1_ASM1866451v1_genomic.fna/markers.fasta)
[2023-06-19 02:26:14,284] [INFO] Task started: Blastn
[2023-06-19 02:26:14,284] [INFO] Running command: blastn -query GCA_018664515.1_ASM1866451v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf7f65c5-448b-4012-bea2-59a9d905e69a/dqc_reference/reference_markers_gtdb.fasta -out GCA_018664515.1_ASM1866451v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:26:14,739] [INFO] Task succeeded: Blastn
[2023-06-19 02:26:14,744] [INFO] Selected 16 target genomes.
[2023-06-19 02:26:14,744] [INFO] Target genome list was writen to GCA_018664515.1_ASM1866451v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 02:26:14,752] [INFO] Task started: fastANI
[2023-06-19 02:26:14,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a93c6d2-dc64-4426-94e2-83edfa19a6ce/GCA_018664515.1_ASM1866451v1_genomic.fna.gz --refList GCA_018664515.1_ASM1866451v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018664515.1_ASM1866451v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 02:26:29,067] [INFO] Task succeeded: fastANI
[2023-06-19 02:26:29,078] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 02:26:29,078] [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_018699955.1	s__JABISG01 sp018699955	99.9135	1268	1322	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JABISG01	95.0	99.95	99.95	0.96	0.96	3	conclusive
GCF_007747795.1	s__Maioricimonas rarisocia	75.4507	80	1322	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Maioricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724315.1	s__UBA8437 sp002724315	75.4102	65	1322	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__UBA8437	95.0	97.85	97.85	0.87	0.87	2	-
GCA_009691905.1	s__SIAF01 sp009691905	75.2327	70	1322	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__UBA10511;g__SIAF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 02:26:29,081] [INFO] GTDB search result was written to GCA_018664515.1_ASM1866451v1_genomic.fna/result_gtdb.tsv
[2023-06-19 02:26:29,081] [INFO] ===== GTDB Search completed =====
[2023-06-19 02:26:29,085] [INFO] DFAST_QC result json was written to GCA_018664515.1_ASM1866451v1_genomic.fna/dqc_result.json
[2023-06-19 02:26:29,085] [INFO] DFAST_QC completed!
[2023-06-19 02:26:29,085] [INFO] Total running time: 0h1m33s