[2023-06-08 06:03:47,586] [INFO] DFAST_QC pipeline started.
[2023-06-08 06:03:47,639] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 06:03:47,640] [INFO] DQC Reference Directory: /var/lib/cwl/stg69794b68-968a-4683-8671-d46eeb5918c1/dqc_reference
[2023-06-08 06:03:49,955] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 06:03:49,955] [INFO] Task started: Prodigal
[2023-06-08 06:03:49,956] [INFO] Running command: gunzip -c /var/lib/cwl/stgda2e7276-898c-49cb-9dee-53707372a790/GCA_945607035.1_SRR14474043_bin.13_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945607035.1_SRR14474043_bin.13_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945607035.1_SRR14474043_bin.13_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 06:03:53,475] [INFO] Task succeeded: Prodigal
[2023-06-08 06:03:53,475] [INFO] Task started: HMMsearch
[2023-06-08 06:03:53,475] [INFO] Running command: hmmsearch --tblout GCA_945607035.1_SRR14474043_bin.13_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69794b68-968a-4683-8671-d46eeb5918c1/dqc_reference/reference_markers.hmm GCA_945607035.1_SRR14474043_bin.13_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 06:03:53,728] [INFO] Task succeeded: HMMsearch
[2023-06-08 06:03:53,730] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgda2e7276-898c-49cb-9dee-53707372a790/GCA_945607035.1_SRR14474043_bin.13_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 06:03:53,752] [INFO] Query marker FASTA was written to GCA_945607035.1_SRR14474043_bin.13_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 06:03:53,753] [INFO] Task started: Blastn
[2023-06-08 06:03:53,753] [INFO] Running command: blastn -query GCA_945607035.1_SRR14474043_bin.13_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg69794b68-968a-4683-8671-d46eeb5918c1/dqc_reference/reference_markers.fasta -out GCA_945607035.1_SRR14474043_bin.13_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 06:03:54,424] [INFO] Task succeeded: Blastn
[2023-06-08 06:03:54,428] [INFO] Selected 26 target genomes.
[2023-06-08 06:03:54,429] [INFO] Target genome list was writen to GCA_945607035.1_SRR14474043_bin.13_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 06:03:54,435] [INFO] Task started: fastANI
[2023-06-08 06:03:54,436] [INFO] Running command: fastANI --query /var/lib/cwl/stgda2e7276-898c-49cb-9dee-53707372a790/GCA_945607035.1_SRR14474043_bin.13_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945607035.1_SRR14474043_bin.13_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945607035.1_SRR14474043_bin.13_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 06:04:13,401] [INFO] Task succeeded: fastANI
[2023-06-08 06:04:13,401] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69794b68-968a-4683-8671-d46eeb5918c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 06:04:13,402] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69794b68-968a-4683-8671-d46eeb5918c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 06:04:13,408] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2023-06-08 06:04:13,408] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-08 06:04:13,409] [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
Denitrificimonas caeni	strain=DSM 24390	GCA_000421765.1	521720	521720	type	True	97.8437	384	410	95	conclusive
Thiopseudomonas alkaliphila	strain=B4199	GCA_001267175.1	1697053	1697053	type	True	76.4512	63	410	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 06:04:13,410] [INFO] DFAST Taxonomy check result was written to GCA_945607035.1_SRR14474043_bin.13_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 06:04:13,411] [INFO] ===== Taxonomy check completed =====
[2023-06-08 06:04:13,411] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 06:04:13,411] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69794b68-968a-4683-8671-d46eeb5918c1/dqc_reference/checkm_data
[2023-06-08 06:04:13,412] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 06:04:13,437] [INFO] Task started: CheckM
[2023-06-08 06:04:13,438] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945607035.1_SRR14474043_bin.13_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945607035.1_SRR14474043_bin.13_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945607035.1_SRR14474043_bin.13_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 06:04:31,281] [INFO] Task succeeded: CheckM
[2023-06-08 06:04:31,282] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 06:04:31,297] [INFO] ===== Completeness check finished =====
[2023-06-08 06:04:31,298] [INFO] ===== Start GTDB Search =====
[2023-06-08 06:04:31,298] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945607035.1_SRR14474043_bin.13_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 06:04:31,299] [INFO] Task started: Blastn
[2023-06-08 06:04:31,299] [INFO] Running command: blastn -query GCA_945607035.1_SRR14474043_bin.13_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg69794b68-968a-4683-8671-d46eeb5918c1/dqc_reference/reference_markers_gtdb.fasta -out GCA_945607035.1_SRR14474043_bin.13_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 06:04:32,356] [INFO] Task succeeded: Blastn
[2023-06-08 06:04:32,361] [INFO] Selected 8 target genomes.
[2023-06-08 06:04:32,361] [INFO] Target genome list was writen to GCA_945607035.1_SRR14474043_bin.13_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 06:04:32,369] [INFO] Task started: fastANI
[2023-06-08 06:04:32,369] [INFO] Running command: fastANI --query /var/lib/cwl/stgda2e7276-898c-49cb-9dee-53707372a790/GCA_945607035.1_SRR14474043_bin.13_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945607035.1_SRR14474043_bin.13_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945607035.1_SRR14474043_bin.13_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 06:04:36,527] [INFO] Task succeeded: fastANI
[2023-06-08 06:04:36,537] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 06:04:36,537] [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
GCF_000421765.1	s__Pseudomonas_C caeni	97.8437	384	410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_C	95.0	96.77	96.34	0.93	0.85	7	conclusive
GCA_012719655.1	s__Pseudomonas_C sp012719655	89.2119	340	410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012728315.1	s__Pseudomonas_C sp012728315	82.4292	289	410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001513025.1	s__Pseudomonas_C sp001513025	81.0281	289	410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_C	95.0	99.84	99.84	0.94	0.94	2	-
GCF_905120345.1	s__Pseudomonas_C caeni_A	80.9877	302	410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012513235.1	s__Pseudomonas_C sp012513235	80.7124	193	410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008807395.1	s__Pseudomonas_C sp002342705	80.2102	266	410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_C	95.0	99.04	98.98	0.93	0.92	7	-
GCA_012800475.1	s__Pseudomonas_C sp012800475	80.1095	192	410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 06:04:36,538] [INFO] GTDB search result was written to GCA_945607035.1_SRR14474043_bin.13_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 06:04:36,539] [INFO] ===== GTDB Search completed =====
[2023-06-08 06:04:36,541] [INFO] DFAST_QC result json was written to GCA_945607035.1_SRR14474043_bin.13_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 06:04:36,542] [INFO] DFAST_QC completed!
[2023-06-08 06:04:36,542] [INFO] Total running time: 0h0m49s