[2023-06-30 20:54:52,296] [INFO] DFAST_QC pipeline started.
[2023-06-30 20:54:52,299] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 20:54:52,300] [INFO] DQC Reference Directory: /var/lib/cwl/stgef07cc5e-930a-413d-aeb6-e7d69f3c384e/dqc_reference
[2023-06-30 20:54:53,697] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 20:54:53,698] [INFO] Task started: Prodigal
[2023-06-30 20:54:53,698] [INFO] Running command: gunzip -c /var/lib/cwl/stga7c96bc4-851e-413f-b30f-32b83b99961d/GCA_903856325.1_freshwater_MAG_---_LaPlata-5m-a_bin-440_genomic.fna.gz | prodigal -d GCA_903856325.1_freshwater_MAG_---_LaPlata-5m-a_bin-440_genomic.fna/cds.fna -a GCA_903856325.1_freshwater_MAG_---_LaPlata-5m-a_bin-440_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 20:54:55,291] [INFO] Task succeeded: Prodigal
[2023-06-30 20:54:55,292] [INFO] Task started: HMMsearch
[2023-06-30 20:54:55,292] [INFO] Running command: hmmsearch --tblout GCA_903856325.1_freshwater_MAG_---_LaPlata-5m-a_bin-440_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef07cc5e-930a-413d-aeb6-e7d69f3c384e/dqc_reference/reference_markers.hmm GCA_903856325.1_freshwater_MAG_---_LaPlata-5m-a_bin-440_genomic.fna/protein.faa > /dev/null
[2023-06-30 20:54:55,531] [INFO] Task succeeded: HMMsearch
[2023-06-30 20:54:55,533] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga7c96bc4-851e-413f-b30f-32b83b99961d/GCA_903856325.1_freshwater_MAG_---_LaPlata-5m-a_bin-440_genomic.fna.gz]
[2023-06-30 20:54:55,553] [INFO] Query marker FASTA was written to GCA_903856325.1_freshwater_MAG_---_LaPlata-5m-a_bin-440_genomic.fna/markers.fasta
[2023-06-30 20:54:55,554] [INFO] Task started: Blastn
[2023-06-30 20:54:55,554] [INFO] Running command: blastn -query GCA_903856325.1_freshwater_MAG_---_LaPlata-5m-a_bin-440_genomic.fna/markers.fasta -db /var/lib/cwl/stgef07cc5e-930a-413d-aeb6-e7d69f3c384e/dqc_reference/reference_markers.fasta -out GCA_903856325.1_freshwater_MAG_---_LaPlata-5m-a_bin-440_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:54:56,135] [INFO] Task succeeded: Blastn
[2023-06-30 20:54:56,139] [INFO] Selected 21 target genomes.
[2023-06-30 20:54:56,140] [INFO] Target genome list was writen to GCA_903856325.1_freshwater_MAG_---_LaPlata-5m-a_bin-440_genomic.fna/target_genomes.txt
[2023-06-30 20:54:56,144] [INFO] Task started: fastANI
[2023-06-30 20:54:56,144] [INFO] Running command: fastANI --query /var/lib/cwl/stga7c96bc4-851e-413f-b30f-32b83b99961d/GCA_903856325.1_freshwater_MAG_---_LaPlata-5m-a_bin-440_genomic.fna.gz --refList GCA_903856325.1_freshwater_MAG_---_LaPlata-5m-a_bin-440_genomic.fna/target_genomes.txt --output GCA_903856325.1_freshwater_MAG_---_LaPlata-5m-a_bin-440_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 20:55:09,369] [INFO] Task succeeded: fastANI
[2023-06-30 20:55:09,369] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef07cc5e-930a-413d-aeb6-e7d69f3c384e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 20:55:09,370] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef07cc5e-930a-413d-aeb6-e7d69f3c384e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 20:55:09,371] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 20:55:09,372] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 20:55:09,372] [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 20:55:09,374] [INFO] DFAST Taxonomy check result was written to GCA_903856325.1_freshwater_MAG_---_LaPlata-5m-a_bin-440_genomic.fna/tc_result.tsv
[2023-06-30 20:55:09,374] [INFO] ===== Taxonomy check completed =====
[2023-06-30 20:55:09,375] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 20:55:09,375] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef07cc5e-930a-413d-aeb6-e7d69f3c384e/dqc_reference/checkm_data
[2023-06-30 20:55:09,378] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 20:55:09,391] [INFO] Task started: CheckM
[2023-06-30 20:55:09,391] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903856325.1_freshwater_MAG_---_LaPlata-5m-a_bin-440_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903856325.1_freshwater_MAG_---_LaPlata-5m-a_bin-440_genomic.fna/checkm_input GCA_903856325.1_freshwater_MAG_---_LaPlata-5m-a_bin-440_genomic.fna/checkm_result
[2023-06-30 20:55:23,269] [INFO] Task succeeded: CheckM
[2023-06-30 20:55:23,270] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.83%
Contamintation: 6.25%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 20:55:23,301] [INFO] ===== Completeness check finished =====
[2023-06-30 20:55:23,302] [INFO] ===== Start GTDB Search =====
[2023-06-30 20:55:23,302] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903856325.1_freshwater_MAG_---_LaPlata-5m-a_bin-440_genomic.fna/markers.fasta)
[2023-06-30 20:55:23,303] [INFO] Task started: Blastn
[2023-06-30 20:55:23,303] [INFO] Running command: blastn -query GCA_903856325.1_freshwater_MAG_---_LaPlata-5m-a_bin-440_genomic.fna/markers.fasta -db /var/lib/cwl/stgef07cc5e-930a-413d-aeb6-e7d69f3c384e/dqc_reference/reference_markers_gtdb.fasta -out GCA_903856325.1_freshwater_MAG_---_LaPlata-5m-a_bin-440_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:55:24,123] [INFO] Task succeeded: Blastn
[2023-06-30 20:55:24,128] [INFO] Selected 6 target genomes.
[2023-06-30 20:55:24,128] [INFO] Target genome list was writen to GCA_903856325.1_freshwater_MAG_---_LaPlata-5m-a_bin-440_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 20:55:24,131] [INFO] Task started: fastANI
[2023-06-30 20:55:24,131] [INFO] Running command: fastANI --query /var/lib/cwl/stga7c96bc4-851e-413f-b30f-32b83b99961d/GCA_903856325.1_freshwater_MAG_---_LaPlata-5m-a_bin-440_genomic.fna.gz --refList GCA_903856325.1_freshwater_MAG_---_LaPlata-5m-a_bin-440_genomic.fna/target_genomes_gtdb.txt --output GCA_903856325.1_freshwater_MAG_---_LaPlata-5m-a_bin-440_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 20:55:25,195] [INFO] Task succeeded: fastANI
[2023-06-30 20:55:25,200] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 20:55:25,201] [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_009926035.1	s__Methylopumilus sp009926035	97.6297	59	81	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006364615.1	s__Methylopumilus rimovensis	91.5092	69	81	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus	95.0	98.38	98.38	0.95	0.95	2	-
GCA_016868195.1	s__Methylopumilus sp016868195	89.7294	62	81	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903849185.1	s__Methylopumilus sp903849185	88.5106	61	81	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Methylophilaceae;g__Methylopumilus	95.0	98.91	98.07	0.83	0.78	5	-
--------------------------------------------------------------------------------
[2023-06-30 20:55:25,203] [INFO] GTDB search result was written to GCA_903856325.1_freshwater_MAG_---_LaPlata-5m-a_bin-440_genomic.fna/result_gtdb.tsv
[2023-06-30 20:55:25,204] [INFO] ===== GTDB Search completed =====
[2023-06-30 20:55:25,207] [INFO] DFAST_QC result json was written to GCA_903856325.1_freshwater_MAG_---_LaPlata-5m-a_bin-440_genomic.fna/dqc_result.json
[2023-06-30 20:55:25,207] [INFO] DFAST_QC completed!
[2023-06-30 20:55:25,207] [INFO] Total running time: 0h0m33s