[2023-06-30 23:29:03,755] [INFO] DFAST_QC pipeline started.
[2023-06-30 23:29:03,759] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 23:29:03,760] [INFO] DQC Reference Directory: /var/lib/cwl/stg5fc5688b-ad03-42c9-835a-84c2bcd4b5b2/dqc_reference
[2023-06-30 23:29:05,066] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 23:29:05,068] [INFO] Task started: Prodigal
[2023-06-30 23:29:05,068] [INFO] Running command: gunzip -c /var/lib/cwl/stge9d1913f-e2a5-45ec-b62e-8e75c39e4276/GCA_903862855.1_freshwater_MAG_---_LaPlata_bin-2064_genomic.fna.gz | prodigal -d GCA_903862855.1_freshwater_MAG_---_LaPlata_bin-2064_genomic.fna/cds.fna -a GCA_903862855.1_freshwater_MAG_---_LaPlata_bin-2064_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 23:29:15,770] [INFO] Task succeeded: Prodigal
[2023-06-30 23:29:15,771] [INFO] Task started: HMMsearch
[2023-06-30 23:29:15,771] [INFO] Running command: hmmsearch --tblout GCA_903862855.1_freshwater_MAG_---_LaPlata_bin-2064_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5fc5688b-ad03-42c9-835a-84c2bcd4b5b2/dqc_reference/reference_markers.hmm GCA_903862855.1_freshwater_MAG_---_LaPlata_bin-2064_genomic.fna/protein.faa > /dev/null
[2023-06-30 23:29:16,064] [INFO] Task succeeded: HMMsearch
[2023-06-30 23:29:16,066] [INFO] Found 6/6 markers.
[2023-06-30 23:29:16,101] [INFO] Query marker FASTA was written to GCA_903862855.1_freshwater_MAG_---_LaPlata_bin-2064_genomic.fna/markers.fasta
[2023-06-30 23:29:16,101] [INFO] Task started: Blastn
[2023-06-30 23:29:16,102] [INFO] Running command: blastn -query GCA_903862855.1_freshwater_MAG_---_LaPlata_bin-2064_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fc5688b-ad03-42c9-835a-84c2bcd4b5b2/dqc_reference/reference_markers.fasta -out GCA_903862855.1_freshwater_MAG_---_LaPlata_bin-2064_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 23:29:16,710] [INFO] Task succeeded: Blastn
[2023-06-30 23:29:16,714] [INFO] Selected 21 target genomes.
[2023-06-30 23:29:16,714] [INFO] Target genome list was writen to GCA_903862855.1_freshwater_MAG_---_LaPlata_bin-2064_genomic.fna/target_genomes.txt
[2023-06-30 23:29:16,719] [INFO] Task started: fastANI
[2023-06-30 23:29:16,719] [INFO] Running command: fastANI --query /var/lib/cwl/stge9d1913f-e2a5-45ec-b62e-8e75c39e4276/GCA_903862855.1_freshwater_MAG_---_LaPlata_bin-2064_genomic.fna.gz --refList GCA_903862855.1_freshwater_MAG_---_LaPlata_bin-2064_genomic.fna/target_genomes.txt --output GCA_903862855.1_freshwater_MAG_---_LaPlata_bin-2064_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 23:29:32,288] [INFO] Task succeeded: fastANI
[2023-06-30 23:29:32,289] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5fc5688b-ad03-42c9-835a-84c2bcd4b5b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 23:29:32,289] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5fc5688b-ad03-42c9-835a-84c2bcd4b5b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 23:29:32,291] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 23:29:32,291] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 23:29:32,292] [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 23:29:32,294] [INFO] DFAST Taxonomy check result was written to GCA_903862855.1_freshwater_MAG_---_LaPlata_bin-2064_genomic.fna/tc_result.tsv
[2023-06-30 23:29:32,295] [INFO] ===== Taxonomy check completed =====
[2023-06-30 23:29:32,295] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 23:29:32,296] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5fc5688b-ad03-42c9-835a-84c2bcd4b5b2/dqc_reference/checkm_data
[2023-06-30 23:29:32,300] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 23:29:32,346] [INFO] Task started: CheckM
[2023-06-30 23:29:32,346] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903862855.1_freshwater_MAG_---_LaPlata_bin-2064_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903862855.1_freshwater_MAG_---_LaPlata_bin-2064_genomic.fna/checkm_input GCA_903862855.1_freshwater_MAG_---_LaPlata_bin-2064_genomic.fna/checkm_result
[2023-06-30 23:30:09,541] [INFO] Task succeeded: CheckM
[2023-06-30 23:30:09,543] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 23:30:09,564] [INFO] ===== Completeness check finished =====
[2023-06-30 23:30:09,565] [INFO] ===== Start GTDB Search =====
[2023-06-30 23:30:09,565] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903862855.1_freshwater_MAG_---_LaPlata_bin-2064_genomic.fna/markers.fasta)
[2023-06-30 23:30:09,566] [INFO] Task started: Blastn
[2023-06-30 23:30:09,566] [INFO] Running command: blastn -query GCA_903862855.1_freshwater_MAG_---_LaPlata_bin-2064_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fc5688b-ad03-42c9-835a-84c2bcd4b5b2/dqc_reference/reference_markers_gtdb.fasta -out GCA_903862855.1_freshwater_MAG_---_LaPlata_bin-2064_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 23:30:10,408] [INFO] Task succeeded: Blastn
[2023-06-30 23:30:10,414] [INFO] Selected 17 target genomes.
[2023-06-30 23:30:10,414] [INFO] Target genome list was writen to GCA_903862855.1_freshwater_MAG_---_LaPlata_bin-2064_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 23:30:10,427] [INFO] Task started: fastANI
[2023-06-30 23:30:10,428] [INFO] Running command: fastANI --query /var/lib/cwl/stge9d1913f-e2a5-45ec-b62e-8e75c39e4276/GCA_903862855.1_freshwater_MAG_---_LaPlata_bin-2064_genomic.fna.gz --refList GCA_903862855.1_freshwater_MAG_---_LaPlata_bin-2064_genomic.fna/target_genomes_gtdb.txt --output GCA_903862855.1_freshwater_MAG_---_LaPlata_bin-2064_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 23:30:24,311] [INFO] Task succeeded: fastANI
[2023-06-30 23:30:24,319] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 23:30:24,319] [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_903862855.1	s__CAIOZW01 sp903862855	100.0	1260	1274	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__RBC074;f__RBC074;g__CAIOZW01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903828635.1	s__CAIOZW01 sp903828635	77.1984	226	1274	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__RBC074;f__RBC074;g__CAIOZW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016700195.1	s__JADJXM01 sp016700195	76.5639	140	1274	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__RBC074;f__RBC074;g__JADJXM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710075.1	s__JADJLO01 sp016710075	75.8463	83	1274	d__Bacteria;p__Acidobacteriota;c__Blastocatellia;o__RBC074;f__RBC074;g__JADJLO01	95.0	97.43	96.49	0.92	0.87	4	-
--------------------------------------------------------------------------------
[2023-06-30 23:30:24,321] [INFO] GTDB search result was written to GCA_903862855.1_freshwater_MAG_---_LaPlata_bin-2064_genomic.fna/result_gtdb.tsv
[2023-06-30 23:30:24,322] [INFO] ===== GTDB Search completed =====
[2023-06-30 23:30:24,324] [INFO] DFAST_QC result json was written to GCA_903862855.1_freshwater_MAG_---_LaPlata_bin-2064_genomic.fna/dqc_result.json
[2023-06-30 23:30:24,324] [INFO] DFAST_QC completed!
[2023-06-30 23:30:24,324] [INFO] Total running time: 0h1m21s