[2023-06-13 01:02:19,783] [INFO] DFAST_QC pipeline started.
[2023-06-13 01:02:19,789] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 01:02:19,789] [INFO] DQC Reference Directory: /var/lib/cwl/stg35b58cac-502c-4202-a872-791e5f2e7eff/dqc_reference
[2023-06-13 01:02:21,110] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 01:02:21,111] [INFO] Task started: Prodigal
[2023-06-13 01:02:21,111] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb80e3d7-7162-46ae-b529-fac78c1ba47e/GCA_947448335.1_Jr-11may16-188_genomic.fna.gz | prodigal -d GCA_947448335.1_Jr-11may16-188_genomic.fna/cds.fna -a GCA_947448335.1_Jr-11may16-188_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 01:02:25,407] [INFO] Task succeeded: Prodigal
[2023-06-13 01:02:25,407] [INFO] Task started: HMMsearch
[2023-06-13 01:02:25,407] [INFO] Running command: hmmsearch --tblout GCA_947448335.1_Jr-11may16-188_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35b58cac-502c-4202-a872-791e5f2e7eff/dqc_reference/reference_markers.hmm GCA_947448335.1_Jr-11may16-188_genomic.fna/protein.faa > /dev/null
[2023-06-13 01:02:25,641] [INFO] Task succeeded: HMMsearch
[2023-06-13 01:02:25,643] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdb80e3d7-7162-46ae-b529-fac78c1ba47e/GCA_947448335.1_Jr-11may16-188_genomic.fna.gz]
[2023-06-13 01:02:25,670] [INFO] Query marker FASTA was written to GCA_947448335.1_Jr-11may16-188_genomic.fna/markers.fasta
[2023-06-13 01:02:25,670] [INFO] Task started: Blastn
[2023-06-13 01:02:25,670] [INFO] Running command: blastn -query GCA_947448335.1_Jr-11may16-188_genomic.fna/markers.fasta -db /var/lib/cwl/stg35b58cac-502c-4202-a872-791e5f2e7eff/dqc_reference/reference_markers.fasta -out GCA_947448335.1_Jr-11may16-188_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:02:26,222] [INFO] Task succeeded: Blastn
[2023-06-13 01:02:26,225] [INFO] Selected 13 target genomes.
[2023-06-13 01:02:26,226] [INFO] Target genome list was writen to GCA_947448335.1_Jr-11may16-188_genomic.fna/target_genomes.txt
[2023-06-13 01:02:26,231] [INFO] Task started: fastANI
[2023-06-13 01:02:26,232] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb80e3d7-7162-46ae-b529-fac78c1ba47e/GCA_947448335.1_Jr-11may16-188_genomic.fna.gz --refList GCA_947448335.1_Jr-11may16-188_genomic.fna/target_genomes.txt --output GCA_947448335.1_Jr-11may16-188_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 01:02:31,824] [INFO] Task succeeded: fastANI
[2023-06-13 01:02:31,825] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35b58cac-502c-4202-a872-791e5f2e7eff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 01:02:31,825] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35b58cac-502c-4202-a872-791e5f2e7eff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 01:02:31,832] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 01:02:31,832] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 01:02:31,832] [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
Polynucleobacter rarus	strain=MT-CBb6A5	GCA_003072505.1	556055	556055	type	True	77.5328	110	635	95	below_threshold
Polynucleobacter kasalickyi	strain=VK13	GCA_900176405.1	1938817	1938817	type	True	76.8827	102	635	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 01:02:31,834] [INFO] DFAST Taxonomy check result was written to GCA_947448335.1_Jr-11may16-188_genomic.fna/tc_result.tsv
[2023-06-13 01:02:31,835] [INFO] ===== Taxonomy check completed =====
[2023-06-13 01:02:31,835] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 01:02:31,835] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35b58cac-502c-4202-a872-791e5f2e7eff/dqc_reference/checkm_data
[2023-06-13 01:02:31,837] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 01:02:31,863] [INFO] Task started: CheckM
[2023-06-13 01:02:31,864] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947448335.1_Jr-11may16-188_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947448335.1_Jr-11may16-188_genomic.fna/checkm_input GCA_947448335.1_Jr-11may16-188_genomic.fna/checkm_result
[2023-06-13 01:02:52,907] [INFO] Task succeeded: CheckM
[2023-06-13 01:02:52,909] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 01:02:52,931] [INFO] ===== Completeness check finished =====
[2023-06-13 01:02:52,931] [INFO] ===== Start GTDB Search =====
[2023-06-13 01:02:52,932] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947448335.1_Jr-11may16-188_genomic.fna/markers.fasta)
[2023-06-13 01:02:52,932] [INFO] Task started: Blastn
[2023-06-13 01:02:52,932] [INFO] Running command: blastn -query GCA_947448335.1_Jr-11may16-188_genomic.fna/markers.fasta -db /var/lib/cwl/stg35b58cac-502c-4202-a872-791e5f2e7eff/dqc_reference/reference_markers_gtdb.fasta -out GCA_947448335.1_Jr-11may16-188_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:02:53,628] [INFO] Task succeeded: Blastn
[2023-06-13 01:02:53,633] [INFO] Selected 18 target genomes.
[2023-06-13 01:02:53,633] [INFO] Target genome list was writen to GCA_947448335.1_Jr-11may16-188_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 01:02:53,635] [INFO] Task started: fastANI
[2023-06-13 01:02:53,635] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb80e3d7-7162-46ae-b529-fac78c1ba47e/GCA_947448335.1_Jr-11may16-188_genomic.fna.gz --refList GCA_947448335.1_Jr-11may16-188_genomic.fna/target_genomes_gtdb.txt --output GCA_947448335.1_Jr-11may16-188_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 01:03:00,393] [INFO] Task succeeded: fastANI
[2023-06-13 01:03:00,402] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 01:03:00,403] [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_903875135.1	s__Polynucleobacter sp903875135	78.4338	203	635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.93	99.91	0.96	0.95	4	-
GCA_903867305.1	s__Polynucleobacter sp903867305	77.9917	196	635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.81	99.77	0.91	0.90	6	-
GCF_003072505.1	s__Polynucleobacter rarus	77.5328	110	635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903889595.1	s__Polynucleobacter sp903889595	77.4452	97	635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.49	99.49	0.84	0.84	2	-
GCF_900176405.1	s__Polynucleobacter sp900176405	76.9059	101	635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	98.69	98.69	0.92	0.91	3	-
GCA_903821995.1	s__Polynucleobacter sp903821995	76.7254	62	635	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polynucleobacter	95.0	99.83	99.77	0.91	0.85	9	-
--------------------------------------------------------------------------------
[2023-06-13 01:03:00,405] [INFO] GTDB search result was written to GCA_947448335.1_Jr-11may16-188_genomic.fna/result_gtdb.tsv
[2023-06-13 01:03:00,406] [INFO] ===== GTDB Search completed =====
[2023-06-13 01:03:00,408] [INFO] DFAST_QC result json was written to GCA_947448335.1_Jr-11may16-188_genomic.fna/dqc_result.json
[2023-06-13 01:03:00,408] [INFO] DFAST_QC completed!
[2023-06-13 01:03:00,409] [INFO] Total running time: 0h0m41s