[2023-06-30 22:22:18,110] [INFO] DFAST_QC pipeline started.
[2023-06-30 22:22:18,112] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 22:22:18,113] [INFO] DQC Reference Directory: /var/lib/cwl/stg81ea6b17-1bcf-49bb-a601-d002e1c98fe5/dqc_reference
[2023-06-30 22:22:20,467] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 22:22:20,468] [INFO] Task started: Prodigal
[2023-06-30 22:22:20,468] [INFO] Running command: gunzip -c /var/lib/cwl/stg299814d8-78c8-4c05-aea9-71db10189c15/GCA_903895375.1_freshwater_MAG_---_Day6-3_bin-579_genomic.fna.gz | prodigal -d GCA_903895375.1_freshwater_MAG_---_Day6-3_bin-579_genomic.fna/cds.fna -a GCA_903895375.1_freshwater_MAG_---_Day6-3_bin-579_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 22:22:34,875] [INFO] Task succeeded: Prodigal
[2023-06-30 22:22:34,876] [INFO] Task started: HMMsearch
[2023-06-30 22:22:34,876] [INFO] Running command: hmmsearch --tblout GCA_903895375.1_freshwater_MAG_---_Day6-3_bin-579_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81ea6b17-1bcf-49bb-a601-d002e1c98fe5/dqc_reference/reference_markers.hmm GCA_903895375.1_freshwater_MAG_---_Day6-3_bin-579_genomic.fna/protein.faa > /dev/null
[2023-06-30 22:22:35,128] [INFO] Task succeeded: HMMsearch
[2023-06-30 22:22:35,129] [INFO] Found 6/6 markers.
[2023-06-30 22:22:35,161] [INFO] Query marker FASTA was written to GCA_903895375.1_freshwater_MAG_---_Day6-3_bin-579_genomic.fna/markers.fasta
[2023-06-30 22:22:35,162] [INFO] Task started: Blastn
[2023-06-30 22:22:35,162] [INFO] Running command: blastn -query GCA_903895375.1_freshwater_MAG_---_Day6-3_bin-579_genomic.fna/markers.fasta -db /var/lib/cwl/stg81ea6b17-1bcf-49bb-a601-d002e1c98fe5/dqc_reference/reference_markers.fasta -out GCA_903895375.1_freshwater_MAG_---_Day6-3_bin-579_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:22:35,744] [INFO] Task succeeded: Blastn
[2023-06-30 22:22:35,749] [INFO] Selected 29 target genomes.
[2023-06-30 22:22:35,749] [INFO] Target genome list was writen to GCA_903895375.1_freshwater_MAG_---_Day6-3_bin-579_genomic.fna/target_genomes.txt
[2023-06-30 22:22:35,757] [INFO] Task started: fastANI
[2023-06-30 22:22:35,757] [INFO] Running command: fastANI --query /var/lib/cwl/stg299814d8-78c8-4c05-aea9-71db10189c15/GCA_903895375.1_freshwater_MAG_---_Day6-3_bin-579_genomic.fna.gz --refList GCA_903895375.1_freshwater_MAG_---_Day6-3_bin-579_genomic.fna/target_genomes.txt --output GCA_903895375.1_freshwater_MAG_---_Day6-3_bin-579_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 22:22:51,693] [INFO] Task succeeded: fastANI
[2023-06-30 22:22:51,694] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81ea6b17-1bcf-49bb-a601-d002e1c98fe5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 22:22:51,695] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81ea6b17-1bcf-49bb-a601-d002e1c98fe5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 22:22:51,697] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 22:22:51,697] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 22:22:51,697] [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
--------------------------------------------------------------------------------
[2023-06-30 22:22:51,700] [INFO] DFAST Taxonomy check result was written to GCA_903895375.1_freshwater_MAG_---_Day6-3_bin-579_genomic.fna/tc_result.tsv
[2023-06-30 22:22:51,700] [INFO] ===== Taxonomy check completed =====
[2023-06-30 22:22:51,701] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 22:22:51,701] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81ea6b17-1bcf-49bb-a601-d002e1c98fe5/dqc_reference/checkm_data
[2023-06-30 22:22:51,705] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 22:22:51,742] [INFO] Task started: CheckM
[2023-06-30 22:22:51,742] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903895375.1_freshwater_MAG_---_Day6-3_bin-579_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903895375.1_freshwater_MAG_---_Day6-3_bin-579_genomic.fna/checkm_input GCA_903895375.1_freshwater_MAG_---_Day6-3_bin-579_genomic.fna/checkm_result
[2023-06-30 22:23:35,921] [INFO] Task succeeded: CheckM
[2023-06-30 22:23:35,922] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.30%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 22:23:35,944] [INFO] ===== Completeness check finished =====
[2023-06-30 22:23:35,944] [INFO] ===== Start GTDB Search =====
[2023-06-30 22:23:35,944] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903895375.1_freshwater_MAG_---_Day6-3_bin-579_genomic.fna/markers.fasta)
[2023-06-30 22:23:35,945] [INFO] Task started: Blastn
[2023-06-30 22:23:35,945] [INFO] Running command: blastn -query GCA_903895375.1_freshwater_MAG_---_Day6-3_bin-579_genomic.fna/markers.fasta -db /var/lib/cwl/stg81ea6b17-1bcf-49bb-a601-d002e1c98fe5/dqc_reference/reference_markers_gtdb.fasta -out GCA_903895375.1_freshwater_MAG_---_Day6-3_bin-579_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:23:36,731] [INFO] Task succeeded: Blastn
[2023-06-30 22:23:36,736] [INFO] Selected 24 target genomes.
[2023-06-30 22:23:36,736] [INFO] Target genome list was writen to GCA_903895375.1_freshwater_MAG_---_Day6-3_bin-579_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 22:23:36,749] [INFO] Task started: fastANI
[2023-06-30 22:23:36,750] [INFO] Running command: fastANI --query /var/lib/cwl/stg299814d8-78c8-4c05-aea9-71db10189c15/GCA_903895375.1_freshwater_MAG_---_Day6-3_bin-579_genomic.fna.gz --refList GCA_903895375.1_freshwater_MAG_---_Day6-3_bin-579_genomic.fna/target_genomes_gtdb.txt --output GCA_903895375.1_freshwater_MAG_---_Day6-3_bin-579_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 22:23:51,031] [INFO] Task succeeded: fastANI
[2023-06-30 22:23:51,042] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 22:23:51,042] [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_903911435.1	s__2-12-FULL-35-15 sp903911435	99.6456	647	709	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__2-12-FULL-35-15	95.0	99.39	97.58	0.90	0.87	8	conclusive
GCA_903926385.1	s__2-12-FULL-35-15 sp903926385	82.4757	187	709	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__2-12-FULL-35-15	95.0	99.98	99.96	0.98	0.98	5	-
GCA_903881065.1	s__2-12-FULL-35-15 sp903881065	77.3684	119	709	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__2-12-FULL-35-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903870175.1	s__2-12-FULL-35-15 sp903870175	77.2655	132	709	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__2-12-FULL-35-15	95.0	99.44	99.36	0.89	0.82	6	-
GCA_903919535.1	s__2-12-FULL-35-15 sp903919535	77.2128	70	709	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__2-12-FULL-35-15	95.0	99.81	99.81	0.93	0.93	2	-
GCA_016707685.1	s__JAEUTT01 sp016707685	76.8946	59	709	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__JAEUTT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001769385.1	s__2-12-FULL-35-15 sp001769385	76.5552	68	709	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__2-12-FULL-35-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016722565.1	s__2-12-FULL-35-15 sp016722565	76.5201	71	709	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__AKYH767;f__2-12-FULL-35-15;g__2-12-FULL-35-15	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 22:23:51,044] [INFO] GTDB search result was written to GCA_903895375.1_freshwater_MAG_---_Day6-3_bin-579_genomic.fna/result_gtdb.tsv
[2023-06-30 22:23:51,045] [INFO] ===== GTDB Search completed =====
[2023-06-30 22:23:51,056] [INFO] DFAST_QC result json was written to GCA_903895375.1_freshwater_MAG_---_Day6-3_bin-579_genomic.fna/dqc_result.json
[2023-06-30 22:23:51,056] [INFO] DFAST_QC completed!
[2023-06-30 22:23:51,056] [INFO] Total running time: 0h1m33s