[2023-06-28 23:29:02,639] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:29:02,642] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:29:02,642] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e0ac21c-3a0c-431e-9cce-8cce807c6abd/dqc_reference
[2023-06-28 23:29:03,869] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:29:03,870] [INFO] Task started: Prodigal
[2023-06-28 23:29:03,870] [INFO] Running command: gunzip -c /var/lib/cwl/stg66de60f7-0f95-4d80-9779-4b9150de9db6/GCA_020403895.1_ASM2040389v1_genomic.fna.gz | prodigal -d GCA_020403895.1_ASM2040389v1_genomic.fna/cds.fna -a GCA_020403895.1_ASM2040389v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:29:12,021] [INFO] Task succeeded: Prodigal
[2023-06-28 23:29:12,021] [INFO] Task started: HMMsearch
[2023-06-28 23:29:12,021] [INFO] Running command: hmmsearch --tblout GCA_020403895.1_ASM2040389v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e0ac21c-3a0c-431e-9cce-8cce807c6abd/dqc_reference/reference_markers.hmm GCA_020403895.1_ASM2040389v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:29:12,309] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:29:12,311] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg66de60f7-0f95-4d80-9779-4b9150de9db6/GCA_020403895.1_ASM2040389v1_genomic.fna.gz]
[2023-06-28 23:29:12,347] [INFO] Query marker FASTA was written to GCA_020403895.1_ASM2040389v1_genomic.fna/markers.fasta
[2023-06-28 23:29:12,348] [INFO] Task started: Blastn
[2023-06-28 23:29:12,348] [INFO] Running command: blastn -query GCA_020403895.1_ASM2040389v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e0ac21c-3a0c-431e-9cce-8cce807c6abd/dqc_reference/reference_markers.fasta -out GCA_020403895.1_ASM2040389v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:29:12,911] [INFO] Task succeeded: Blastn
[2023-06-28 23:29:12,916] [INFO] Selected 23 target genomes.
[2023-06-28 23:29:12,916] [INFO] Target genome list was writen to GCA_020403895.1_ASM2040389v1_genomic.fna/target_genomes.txt
[2023-06-28 23:29:12,920] [INFO] Task started: fastANI
[2023-06-28 23:29:12,920] [INFO] Running command: fastANI --query /var/lib/cwl/stg66de60f7-0f95-4d80-9779-4b9150de9db6/GCA_020403895.1_ASM2040389v1_genomic.fna.gz --refList GCA_020403895.1_ASM2040389v1_genomic.fna/target_genomes.txt --output GCA_020403895.1_ASM2040389v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:29:27,875] [INFO] Task succeeded: fastANI
[2023-06-28 23:29:27,876] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e0ac21c-3a0c-431e-9cce-8cce807c6abd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:29:27,876] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e0ac21c-3a0c-431e-9cce-8cce807c6abd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:29:27,878] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:29:27,878] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 23:29:27,879] [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
--------------------------------------------------------------------------------
[2023-06-28 23:29:27,881] [INFO] DFAST Taxonomy check result was written to GCA_020403895.1_ASM2040389v1_genomic.fna/tc_result.tsv
[2023-06-28 23:29:27,882] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:29:27,882] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:29:27,882] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e0ac21c-3a0c-431e-9cce-8cce807c6abd/dqc_reference/checkm_data
[2023-06-28 23:29:27,886] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:29:27,926] [INFO] Task started: CheckM
[2023-06-28 23:29:27,926] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020403895.1_ASM2040389v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020403895.1_ASM2040389v1_genomic.fna/checkm_input GCA_020403895.1_ASM2040389v1_genomic.fna/checkm_result
[2023-06-28 23:29:58,166] [INFO] Task succeeded: CheckM
[2023-06-28 23:29:58,167] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 23:29:58,188] [INFO] ===== Completeness check finished =====
[2023-06-28 23:29:58,188] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:29:58,189] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020403895.1_ASM2040389v1_genomic.fna/markers.fasta)
[2023-06-28 23:29:58,189] [INFO] Task started: Blastn
[2023-06-28 23:29:58,189] [INFO] Running command: blastn -query GCA_020403895.1_ASM2040389v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4e0ac21c-3a0c-431e-9cce-8cce807c6abd/dqc_reference/reference_markers_gtdb.fasta -out GCA_020403895.1_ASM2040389v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:29:58,909] [INFO] Task succeeded: Blastn
[2023-06-28 23:29:58,914] [INFO] Selected 11 target genomes.
[2023-06-28 23:29:58,914] [INFO] Target genome list was writen to GCA_020403895.1_ASM2040389v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:29:58,917] [INFO] Task started: fastANI
[2023-06-28 23:29:58,917] [INFO] Running command: fastANI --query /var/lib/cwl/stg66de60f7-0f95-4d80-9779-4b9150de9db6/GCA_020403895.1_ASM2040389v1_genomic.fna.gz --refList GCA_020403895.1_ASM2040389v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020403895.1_ASM2040389v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:30:13,043] [INFO] Task succeeded: fastANI
[2023-06-28 23:30:13,060] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 23:30:13,060] [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
GCF_006937785.1	s__Pseudanabaena sp006937785	91.8536	1042	1281	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002914585.1	s__Pseudanabaena sp002914585	89.4934	1023	1281	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016584665.1	s__Pseudanabaena sp016584665	88.3782	990	1281	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003249035.1	s__Pseudanabaena sp003249035	85.76	856	1281	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014696925.1	s__Pseudanabaena sp014696925	84.3477	946	1281	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002251945.1	s__Pseudanabaena sp002251945	84.0522	906	1281	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242085.1	s__Pseudanabaena frigida	80.9068	793	1281	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967015.1	s__Pseudanabaena sp003967015	80.7151	780	1281	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012863495.1	s__Pseudanabaena yagii	80.6225	766	1281	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903819605.1	s__Pseudanabaena sp903819605	80.5839	608	1281	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	97.61	97.57	0.80	0.79	3	-
GCF_014696355.1	s__Pseudanabaena sp014696355	80.1852	684	1281	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Pseudanabaenales;f__Pseudanabaenaceae;g__Pseudanabaena	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 23:30:13,063] [INFO] GTDB search result was written to GCA_020403895.1_ASM2040389v1_genomic.fna/result_gtdb.tsv
[2023-06-28 23:30:13,064] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:30:13,069] [INFO] DFAST_QC result json was written to GCA_020403895.1_ASM2040389v1_genomic.fna/dqc_result.json
[2023-06-28 23:30:13,070] [INFO] DFAST_QC completed!
[2023-06-28 23:30:13,070] [INFO] Total running time: 0h1m10s