[2023-06-13 21:20:32,838] [INFO] DFAST_QC pipeline started.
[2023-06-13 21:20:32,844] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 21:20:32,844] [INFO] DQC Reference Directory: /var/lib/cwl/stge325df6c-3f41-4d77-bd06-5bb38612f809/dqc_reference
[2023-06-13 21:20:34,596] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 21:20:34,597] [INFO] Task started: Prodigal
[2023-06-13 21:20:34,597] [INFO] Running command: gunzip -c /var/lib/cwl/stga28cc6ba-1ea9-4152-8e18-99b98839ddd8/GCA_938075845.1_S2_Bin_METABAT_260_sub_1_genomic.fna.gz | prodigal -d GCA_938075845.1_S2_Bin_METABAT_260_sub_1_genomic.fna/cds.fna -a GCA_938075845.1_S2_Bin_METABAT_260_sub_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 21:20:41,436] [INFO] Task succeeded: Prodigal
[2023-06-13 21:20:41,437] [INFO] Task started: HMMsearch
[2023-06-13 21:20:41,437] [INFO] Running command: hmmsearch --tblout GCA_938075845.1_S2_Bin_METABAT_260_sub_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge325df6c-3f41-4d77-bd06-5bb38612f809/dqc_reference/reference_markers.hmm GCA_938075845.1_S2_Bin_METABAT_260_sub_1_genomic.fna/protein.faa > /dev/null
[2023-06-13 21:20:41,660] [INFO] Task succeeded: HMMsearch
[2023-06-13 21:20:41,661] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga28cc6ba-1ea9-4152-8e18-99b98839ddd8/GCA_938075845.1_S2_Bin_METABAT_260_sub_1_genomic.fna.gz]
[2023-06-13 21:20:41,692] [INFO] Query marker FASTA was written to GCA_938075845.1_S2_Bin_METABAT_260_sub_1_genomic.fna/markers.fasta
[2023-06-13 21:20:41,692] [INFO] Task started: Blastn
[2023-06-13 21:20:41,692] [INFO] Running command: blastn -query GCA_938075845.1_S2_Bin_METABAT_260_sub_1_genomic.fna/markers.fasta -db /var/lib/cwl/stge325df6c-3f41-4d77-bd06-5bb38612f809/dqc_reference/reference_markers.fasta -out GCA_938075845.1_S2_Bin_METABAT_260_sub_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:20:42,273] [INFO] Task succeeded: Blastn
[2023-06-13 21:20:42,279] [INFO] Selected 14 target genomes.
[2023-06-13 21:20:42,279] [INFO] Target genome list was writen to GCA_938075845.1_S2_Bin_METABAT_260_sub_1_genomic.fna/target_genomes.txt
[2023-06-13 21:20:42,308] [INFO] Task started: fastANI
[2023-06-13 21:20:42,308] [INFO] Running command: fastANI --query /var/lib/cwl/stga28cc6ba-1ea9-4152-8e18-99b98839ddd8/GCA_938075845.1_S2_Bin_METABAT_260_sub_1_genomic.fna.gz --refList GCA_938075845.1_S2_Bin_METABAT_260_sub_1_genomic.fna/target_genomes.txt --output GCA_938075845.1_S2_Bin_METABAT_260_sub_1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 21:20:50,708] [INFO] Task succeeded: fastANI
[2023-06-13 21:20:50,708] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge325df6c-3f41-4d77-bd06-5bb38612f809/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 21:20:50,709] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge325df6c-3f41-4d77-bd06-5bb38612f809/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 21:20:50,710] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 21:20:50,710] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 21:20:50,710] [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
--------------------------------------------------------------------------------
[2023-06-13 21:20:50,712] [INFO] DFAST Taxonomy check result was written to GCA_938075845.1_S2_Bin_METABAT_260_sub_1_genomic.fna/tc_result.tsv
[2023-06-13 21:20:50,712] [INFO] ===== Taxonomy check completed =====
[2023-06-13 21:20:50,712] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 21:20:50,713] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge325df6c-3f41-4d77-bd06-5bb38612f809/dqc_reference/checkm_data
[2023-06-13 21:20:50,715] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 21:20:50,755] [INFO] Task started: CheckM
[2023-06-13 21:20:50,755] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938075845.1_S2_Bin_METABAT_260_sub_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938075845.1_S2_Bin_METABAT_260_sub_1_genomic.fna/checkm_input GCA_938075845.1_S2_Bin_METABAT_260_sub_1_genomic.fna/checkm_result
[2023-06-13 21:21:15,389] [INFO] Task succeeded: CheckM
[2023-06-13 21:21:15,390] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 21:21:15,410] [INFO] ===== Completeness check finished =====
[2023-06-13 21:21:15,411] [INFO] ===== Start GTDB Search =====
[2023-06-13 21:21:15,411] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938075845.1_S2_Bin_METABAT_260_sub_1_genomic.fna/markers.fasta)
[2023-06-13 21:21:15,411] [INFO] Task started: Blastn
[2023-06-13 21:21:15,411] [INFO] Running command: blastn -query GCA_938075845.1_S2_Bin_METABAT_260_sub_1_genomic.fna/markers.fasta -db /var/lib/cwl/stge325df6c-3f41-4d77-bd06-5bb38612f809/dqc_reference/reference_markers_gtdb.fasta -out GCA_938075845.1_S2_Bin_METABAT_260_sub_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 21:21:16,160] [INFO] Task succeeded: Blastn
[2023-06-13 21:21:16,164] [INFO] Selected 10 target genomes.
[2023-06-13 21:21:16,164] [INFO] Target genome list was writen to GCA_938075845.1_S2_Bin_METABAT_260_sub_1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 21:21:16,169] [INFO] Task started: fastANI
[2023-06-13 21:21:16,170] [INFO] Running command: fastANI --query /var/lib/cwl/stga28cc6ba-1ea9-4152-8e18-99b98839ddd8/GCA_938075845.1_S2_Bin_METABAT_260_sub_1_genomic.fna.gz --refList GCA_938075845.1_S2_Bin_METABAT_260_sub_1_genomic.fna/target_genomes_gtdb.txt --output GCA_938075845.1_S2_Bin_METABAT_260_sub_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 21:21:21,829] [INFO] Task succeeded: fastANI
[2023-06-13 21:21:21,834] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 21:21:21,835] [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_002401885.1	s__UBA9145 sp002401885	84.7902	664	1061	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016762975.1	s__UBA9145 sp016762975	82.7618	512	1061	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016762995.1	s__UBA9145 sp016762995	82.5592	544	1061	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	96.79	96.79	0.78	0.78	2	-
GCA_905478195.1	s__UBA9145 sp003483155	78.3935	287	1061	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	99.23	98.96	0.87	0.81	6	-
GCA_012960305.1	s__UBA9145 sp012960305	77.9894	82	1061	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	99.98	99.98	0.97	0.97	2	-
GCA_002402175.1	s__UBA9145 sp002402175	76.8171	78	1061	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 21:21:21,838] [INFO] GTDB search result was written to GCA_938075845.1_S2_Bin_METABAT_260_sub_1_genomic.fna/result_gtdb.tsv
[2023-06-13 21:21:21,838] [INFO] ===== GTDB Search completed =====
[2023-06-13 21:21:21,841] [INFO] DFAST_QC result json was written to GCA_938075845.1_S2_Bin_METABAT_260_sub_1_genomic.fna/dqc_result.json
[2023-06-13 21:21:21,841] [INFO] DFAST_QC completed!
[2023-06-13 21:21:21,841] [INFO] Total running time: 0h0m49s