[2023-06-13 23:45:21,293] [INFO] DFAST_QC pipeline started.
[2023-06-13 23:45:21,302] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 23:45:21,302] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b609a98-27dc-41d0-af29-7c1e59444d6c/dqc_reference
[2023-06-13 23:45:22,600] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 23:45:22,601] [INFO] Task started: Prodigal
[2023-06-13 23:45:22,601] [INFO] Running command: gunzip -c /var/lib/cwl/stge9384b3c-0104-423a-af88-b5fec47da218/GCA_022820105.1_ASM2282010v1_genomic.fna.gz | prodigal -d GCA_022820105.1_ASM2282010v1_genomic.fna/cds.fna -a GCA_022820105.1_ASM2282010v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 23:45:38,402] [INFO] Task succeeded: Prodigal
[2023-06-13 23:45:38,402] [INFO] Task started: HMMsearch
[2023-06-13 23:45:38,402] [INFO] Running command: hmmsearch --tblout GCA_022820105.1_ASM2282010v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b609a98-27dc-41d0-af29-7c1e59444d6c/dqc_reference/reference_markers.hmm GCA_022820105.1_ASM2282010v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 23:45:38,731] [INFO] Task succeeded: HMMsearch
[2023-06-13 23:45:38,732] [INFO] Found 6/6 markers.
[2023-06-13 23:45:38,783] [INFO] Query marker FASTA was written to GCA_022820105.1_ASM2282010v1_genomic.fna/markers.fasta
[2023-06-13 23:45:38,784] [INFO] Task started: Blastn
[2023-06-13 23:45:38,784] [INFO] Running command: blastn -query GCA_022820105.1_ASM2282010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b609a98-27dc-41d0-af29-7c1e59444d6c/dqc_reference/reference_markers.fasta -out GCA_022820105.1_ASM2282010v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 23:45:39,363] [INFO] Task succeeded: Blastn
[2023-06-13 23:45:39,368] [INFO] Selected 6 target genomes.
[2023-06-13 23:45:39,369] [INFO] Target genome list was writen to GCA_022820105.1_ASM2282010v1_genomic.fna/target_genomes.txt
[2023-06-13 23:45:39,371] [INFO] Task started: fastANI
[2023-06-13 23:45:39,371] [INFO] Running command: fastANI --query /var/lib/cwl/stge9384b3c-0104-423a-af88-b5fec47da218/GCA_022820105.1_ASM2282010v1_genomic.fna.gz --refList GCA_022820105.1_ASM2282010v1_genomic.fna/target_genomes.txt --output GCA_022820105.1_ASM2282010v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 23:45:43,049] [INFO] Task succeeded: fastANI
[2023-06-13 23:45:43,050] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b609a98-27dc-41d0-af29-7c1e59444d6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 23:45:43,051] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b609a98-27dc-41d0-af29-7c1e59444d6c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 23:45:43,053] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 23:45:43,054] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 23:45:43,054] [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
--------------------------------------------------------------------------------
[2023-06-13 23:45:43,056] [INFO] DFAST Taxonomy check result was written to GCA_022820105.1_ASM2282010v1_genomic.fna/tc_result.tsv
[2023-06-13 23:45:43,058] [INFO] ===== Taxonomy check completed =====
[2023-06-13 23:45:43,058] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 23:45:43,058] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b609a98-27dc-41d0-af29-7c1e59444d6c/dqc_reference/checkm_data
[2023-06-13 23:45:43,063] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 23:45:43,125] [INFO] Task started: CheckM
[2023-06-13 23:45:43,125] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022820105.1_ASM2282010v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022820105.1_ASM2282010v1_genomic.fna/checkm_input GCA_022820105.1_ASM2282010v1_genomic.fna/checkm_result
[2023-06-13 23:46:31,942] [INFO] Task succeeded: CheckM
[2023-06-13 23:46:31,943] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 23:46:31,980] [INFO] ===== Completeness check finished =====
[2023-06-13 23:46:31,980] [INFO] ===== Start GTDB Search =====
[2023-06-13 23:46:31,981] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022820105.1_ASM2282010v1_genomic.fna/markers.fasta)
[2023-06-13 23:46:31,981] [INFO] Task started: Blastn
[2023-06-13 23:46:31,981] [INFO] Running command: blastn -query GCA_022820105.1_ASM2282010v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b609a98-27dc-41d0-af29-7c1e59444d6c/dqc_reference/reference_markers_gtdb.fasta -out GCA_022820105.1_ASM2282010v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 23:46:32,823] [INFO] Task succeeded: Blastn
[2023-06-13 23:46:32,831] [INFO] Selected 8 target genomes.
[2023-06-13 23:46:32,832] [INFO] Target genome list was writen to GCA_022820105.1_ASM2282010v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 23:46:32,836] [INFO] Task started: fastANI
[2023-06-13 23:46:32,837] [INFO] Running command: fastANI --query /var/lib/cwl/stge9384b3c-0104-423a-af88-b5fec47da218/GCA_022820105.1_ASM2282010v1_genomic.fna.gz --refList GCA_022820105.1_ASM2282010v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022820105.1_ASM2282010v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 23:46:43,737] [INFO] Task succeeded: fastANI
[2023-06-13 23:46:43,750] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 23:46:43,750] [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_012270865.1	s__WGA-3G sp012270865	85.5752	1273	2013	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__WGA-3G;g__WGA-3G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000406005.1	s__WGA-3G sp000406005	85.5382	1235	2013	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__WGA-3G;g__WGA-3G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007571355.1	s__WGA-3G sp007571355	83.6294	976	2013	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__WGA-3G;g__WGA-3G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009843785.1	s__WGA-3G sp009843785	81.0438	1213	2013	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__WGA-3G;g__WGA-3G	95.0	99.87	99.87	0.97	0.97	3	-
GCA_009845545.1	s__WGA-3G sp009845545	80.912	1082	2013	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__WGA-3G;g__WGA-3G	95.0	99.90	99.90	0.93	0.93	2	-
GCA_009835515.1	s__WGA-3G sp009835515	80.5611	808	2013	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__WGA-3G;g__WGA-3G	95.0	98.95	98.95	0.75	0.75	2	-
GCA_003635255.1	s__WGA-3G sp003635255	80.4293	1013	2013	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__WGA-3G;g__WGA-3G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012270875.1	s__WGA-3G sp012270875	80.3613	975	2013	d__Bacteria;p__Poribacteria;c__WGA-4E;o__WGA-4E;f__WGA-3G;g__WGA-3G	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 23:46:43,752] [INFO] GTDB search result was written to GCA_022820105.1_ASM2282010v1_genomic.fna/result_gtdb.tsv
[2023-06-13 23:46:43,753] [INFO] ===== GTDB Search completed =====
[2023-06-13 23:46:43,756] [INFO] DFAST_QC result json was written to GCA_022820105.1_ASM2282010v1_genomic.fna/dqc_result.json
[2023-06-13 23:46:43,757] [INFO] DFAST_QC completed!
[2023-06-13 23:46:43,757] [INFO] Total running time: 0h1m22s