[2023-06-28 08:56:10,818] [INFO] DFAST_QC pipeline started.
[2023-06-28 08:56:10,823] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 08:56:10,824] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9d7f897-7651-4971-9a12-cf8e991a08bd/dqc_reference
[2023-06-28 08:56:12,829] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 08:56:12,830] [INFO] Task started: Prodigal
[2023-06-28 08:56:12,831] [INFO] Running command: gunzip -c /var/lib/cwl/stg386524b3-5321-42fa-a6df-717278ee406a/GCA_017438385.1_ASM1743838v1_genomic.fna.gz | prodigal -d GCA_017438385.1_ASM1743838v1_genomic.fna/cds.fna -a GCA_017438385.1_ASM1743838v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 08:56:22,714] [INFO] Task succeeded: Prodigal
[2023-06-28 08:56:22,715] [INFO] Task started: HMMsearch
[2023-06-28 08:56:22,715] [INFO] Running command: hmmsearch --tblout GCA_017438385.1_ASM1743838v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9d7f897-7651-4971-9a12-cf8e991a08bd/dqc_reference/reference_markers.hmm GCA_017438385.1_ASM1743838v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 08:56:22,896] [INFO] Task succeeded: HMMsearch
[2023-06-28 08:56:22,898] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg386524b3-5321-42fa-a6df-717278ee406a/GCA_017438385.1_ASM1743838v1_genomic.fna.gz]
[2023-06-28 08:56:22,919] [INFO] Query marker FASTA was written to GCA_017438385.1_ASM1743838v1_genomic.fna/markers.fasta
[2023-06-28 08:56:22,920] [INFO] Task started: Blastn
[2023-06-28 08:56:22,920] [INFO] Running command: blastn -query GCA_017438385.1_ASM1743838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9d7f897-7651-4971-9a12-cf8e991a08bd/dqc_reference/reference_markers.fasta -out GCA_017438385.1_ASM1743838v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:56:23,499] [INFO] Task succeeded: Blastn
[2023-06-28 08:56:23,504] [INFO] Selected 19 target genomes.
[2023-06-28 08:56:23,504] [INFO] Target genome list was writen to GCA_017438385.1_ASM1743838v1_genomic.fna/target_genomes.txt
[2023-06-28 08:56:23,525] [INFO] Task started: fastANI
[2023-06-28 08:56:23,525] [INFO] Running command: fastANI --query /var/lib/cwl/stg386524b3-5321-42fa-a6df-717278ee406a/GCA_017438385.1_ASM1743838v1_genomic.fna.gz --refList GCA_017438385.1_ASM1743838v1_genomic.fna/target_genomes.txt --output GCA_017438385.1_ASM1743838v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 08:56:32,444] [INFO] Task succeeded: fastANI
[2023-06-28 08:56:32,445] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9d7f897-7651-4971-9a12-cf8e991a08bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 08:56:32,445] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9d7f897-7651-4971-9a12-cf8e991a08bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 08:56:32,447] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 08:56:32,447] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 08:56:32,448] [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 08:56:32,450] [INFO] DFAST Taxonomy check result was written to GCA_017438385.1_ASM1743838v1_genomic.fna/tc_result.tsv
[2023-06-28 08:56:32,450] [INFO] ===== Taxonomy check completed =====
[2023-06-28 08:56:32,451] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 08:56:32,451] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9d7f897-7651-4971-9a12-cf8e991a08bd/dqc_reference/checkm_data
[2023-06-28 08:56:32,455] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 08:56:32,503] [INFO] Task started: CheckM
[2023-06-28 08:56:32,503] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017438385.1_ASM1743838v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017438385.1_ASM1743838v1_genomic.fna/checkm_input GCA_017438385.1_ASM1743838v1_genomic.fna/checkm_result
[2023-06-28 08:57:04,447] [INFO] Task succeeded: CheckM
[2023-06-28 08:57:04,448] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 33.71%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 08:57:04,476] [INFO] ===== Completeness check finished =====
[2023-06-28 08:57:04,476] [INFO] ===== Start GTDB Search =====
[2023-06-28 08:57:04,477] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017438385.1_ASM1743838v1_genomic.fna/markers.fasta)
[2023-06-28 08:57:04,477] [INFO] Task started: Blastn
[2023-06-28 08:57:04,477] [INFO] Running command: blastn -query GCA_017438385.1_ASM1743838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9d7f897-7651-4971-9a12-cf8e991a08bd/dqc_reference/reference_markers_gtdb.fasta -out GCA_017438385.1_ASM1743838v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:57:05,267] [INFO] Task succeeded: Blastn
[2023-06-28 08:57:05,272] [INFO] Selected 10 target genomes.
[2023-06-28 08:57:05,272] [INFO] Target genome list was writen to GCA_017438385.1_ASM1743838v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 08:57:05,274] [INFO] Task started: fastANI
[2023-06-28 08:57:05,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg386524b3-5321-42fa-a6df-717278ee406a/GCA_017438385.1_ASM1743838v1_genomic.fna.gz --refList GCA_017438385.1_ASM1743838v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017438385.1_ASM1743838v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 08:57:09,390] [INFO] Task succeeded: fastANI
[2023-06-28 08:57:09,403] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 08:57:09,403] [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_902789445.1	s__Bact-11 sp902789445	88.6699	346	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-11	95.0	97.70	97.46	0.83	0.81	3	-
GCA_017509755.1	s__Bact-11 sp017509755	82.3721	325	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-11	95.0	97.30	97.26	0.83	0.77	3	-
GCA_017548335.1	s__Bact-11 sp017548335	80.647	228	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002361615.1	s__Bact-11 sp002361615	80.4717	290	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-11	95.0	97.07	96.21	0.85	0.79	8	-
GCA_016284265.1	s__Bact-11 sp016284265	80.1242	259	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902784965.1	s__Bact-11 sp902784965	80.1003	206	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017619655.1	s__Bact-11 sp017619655	79.9865	165	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001602845.1	s__Bact-11 sp001602845	79.9031	221	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-11	95.0	98.09	98.09	0.77	0.77	2	-
GCA_905233345.1	s__Bact-11 sp905233345	79.7292	247	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016290385.1	s__Bact-11 sp016290385	79.5947	243	477	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Bact-11	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 08:57:09,405] [INFO] GTDB search result was written to GCA_017438385.1_ASM1743838v1_genomic.fna/result_gtdb.tsv
[2023-06-28 08:57:09,405] [INFO] ===== GTDB Search completed =====
[2023-06-28 08:57:09,408] [INFO] DFAST_QC result json was written to GCA_017438385.1_ASM1743838v1_genomic.fna/dqc_result.json
[2023-06-28 08:57:09,408] [INFO] DFAST_QC completed!
[2023-06-28 08:57:09,408] [INFO] Total running time: 0h0m59s