[2023-06-29 19:13:39,456] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:13:39,457] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:13:39,457] [INFO] DQC Reference Directory: /var/lib/cwl/stgefaaa471-eb98-44d6-ab3e-8d6aa4cf6ac5/dqc_reference
[2023-06-29 19:13:40,707] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:13:40,708] [INFO] Task started: Prodigal
[2023-06-29 19:13:40,708] [INFO] Running command: gunzip -c /var/lib/cwl/stg219f47d2-1fda-49d2-823d-42f5f1f5df7c/GCA_937866945.1_SRR5676473_bin.100_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937866945.1_SRR5676473_bin.100_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937866945.1_SRR5676473_bin.100_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:13:46,773] [INFO] Task succeeded: Prodigal
[2023-06-29 19:13:46,773] [INFO] Task started: HMMsearch
[2023-06-29 19:13:46,773] [INFO] Running command: hmmsearch --tblout GCA_937866945.1_SRR5676473_bin.100_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefaaa471-eb98-44d6-ab3e-8d6aa4cf6ac5/dqc_reference/reference_markers.hmm GCA_937866945.1_SRR5676473_bin.100_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:13:46,966] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:13:46,967] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg219f47d2-1fda-49d2-823d-42f5f1f5df7c/GCA_937866945.1_SRR5676473_bin.100_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-29 19:13:46,992] [INFO] Query marker FASTA was written to GCA_937866945.1_SRR5676473_bin.100_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 19:13:46,993] [INFO] Task started: Blastn
[2023-06-29 19:13:46,993] [INFO] Running command: blastn -query GCA_937866945.1_SRR5676473_bin.100_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgefaaa471-eb98-44d6-ab3e-8d6aa4cf6ac5/dqc_reference/reference_markers.fasta -out GCA_937866945.1_SRR5676473_bin.100_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:13:47,715] [INFO] Task succeeded: Blastn
[2023-06-29 19:13:47,719] [INFO] Selected 21 target genomes.
[2023-06-29 19:13:47,719] [INFO] Target genome list was writen to GCA_937866945.1_SRR5676473_bin.100_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 19:13:47,721] [INFO] Task started: fastANI
[2023-06-29 19:13:47,722] [INFO] Running command: fastANI --query /var/lib/cwl/stg219f47d2-1fda-49d2-823d-42f5f1f5df7c/GCA_937866945.1_SRR5676473_bin.100_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937866945.1_SRR5676473_bin.100_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937866945.1_SRR5676473_bin.100_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:14:01,735] [INFO] Task succeeded: fastANI
[2023-06-29 19:14:01,736] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefaaa471-eb98-44d6-ab3e-8d6aa4cf6ac5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:14:01,736] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefaaa471-eb98-44d6-ab3e-8d6aa4cf6ac5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:14:01,742] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 19:14:01,742] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 19:14:01,742] [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
Tolumonas auensis	strain=DSM 9187	GCA_000023065.1	43948	43948	type	True	83.3358	488	707	95	below_threshold
Tolumonas osonensis	strain=DSM 22975	GCA_014202415.1	675874	675874	type	True	81.3733	444	707	95	below_threshold
Tolumonas lignilytica	strain=BRL6-1	GCA_000527035.1	1283284	1283284	type	True	81.0076	432	707	95	below_threshold
Rahnella inusitata	strain=DSM 30078	GCA_003263515.1	58169	58169	type	True	76.4654	53	707	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 19:14:01,744] [INFO] DFAST Taxonomy check result was written to GCA_937866945.1_SRR5676473_bin.100_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 19:14:01,745] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:14:01,745] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:14:01,745] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefaaa471-eb98-44d6-ab3e-8d6aa4cf6ac5/dqc_reference/checkm_data
[2023-06-29 19:14:01,746] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:14:01,775] [INFO] Task started: CheckM
[2023-06-29 19:14:01,775] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937866945.1_SRR5676473_bin.100_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937866945.1_SRR5676473_bin.100_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937866945.1_SRR5676473_bin.100_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 19:14:26,120] [INFO] Task succeeded: CheckM
[2023-06-29 19:14:26,121] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.01%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 19:14:26,136] [INFO] ===== Completeness check finished =====
[2023-06-29 19:14:26,137] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:14:26,137] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937866945.1_SRR5676473_bin.100_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 19:14:26,137] [INFO] Task started: Blastn
[2023-06-29 19:14:26,137] [INFO] Running command: blastn -query GCA_937866945.1_SRR5676473_bin.100_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgefaaa471-eb98-44d6-ab3e-8d6aa4cf6ac5/dqc_reference/reference_markers_gtdb.fasta -out GCA_937866945.1_SRR5676473_bin.100_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:14:27,128] [INFO] Task succeeded: Blastn
[2023-06-29 19:14:27,131] [INFO] Selected 11 target genomes.
[2023-06-29 19:14:27,132] [INFO] Target genome list was writen to GCA_937866945.1_SRR5676473_bin.100_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:14:27,146] [INFO] Task started: fastANI
[2023-06-29 19:14:27,146] [INFO] Running command: fastANI --query /var/lib/cwl/stg219f47d2-1fda-49d2-823d-42f5f1f5df7c/GCA_937866945.1_SRR5676473_bin.100_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937866945.1_SRR5676473_bin.100_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937866945.1_SRR5676473_bin.100_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:14:33,953] [INFO] Task succeeded: fastANI
[2023-06-29 19:14:33,961] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 19:14:33,961] [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_903931645.1	s__Tolumonas sp903931645	89.8067	373	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Tolumonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023065.1	s__Tolumonas auensis	83.3175	489	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Tolumonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202415.1	s__Tolumonas osonensis	81.358	445	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Tolumonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000527035.1	s__Tolumonas lignilytica	81.0116	432	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Tolumonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008015085.1	s__Tolumonas sp008015085	80.8254	253	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Tolumonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003251455.1	s__Tolumonas sp003251455	78.4317	188	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Tolumonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010231475.1	s__Citrobacter sp010231475	76.6068	50	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Citrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018199995.1	s__Photobacterium sp018199995	76.0097	51	707	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 19:14:33,963] [INFO] GTDB search result was written to GCA_937866945.1_SRR5676473_bin.100_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 19:14:33,963] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:14:33,966] [INFO] DFAST_QC result json was written to GCA_937866945.1_SRR5676473_bin.100_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 19:14:33,966] [INFO] DFAST_QC completed!
[2023-06-29 19:14:33,966] [INFO] Total running time: 0h0m55s