[2023-06-30 23:48:34,538] [INFO] DFAST_QC pipeline started.
[2023-06-30 23:48:34,540] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 23:48:34,540] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3b33e43-c655-4900-9d82-74f723557ee2/dqc_reference
[2023-06-30 23:48:35,805] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 23:48:35,806] [INFO] Task started: Prodigal
[2023-06-30 23:48:35,807] [INFO] Running command: gunzip -c /var/lib/cwl/stg5569bb1a-cdd2-4496-81eb-a995834dcc9a/GCA_943841735.1_20200310_Bin_Bin_75_2-contigs.fa_genomic.fna.gz | prodigal -d GCA_943841735.1_20200310_Bin_Bin_75_2-contigs.fa_genomic.fna/cds.fna -a GCA_943841735.1_20200310_Bin_Bin_75_2-contigs.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 23:48:39,432] [INFO] Task succeeded: Prodigal
[2023-06-30 23:48:39,433] [INFO] Task started: HMMsearch
[2023-06-30 23:48:39,433] [INFO] Running command: hmmsearch --tblout GCA_943841735.1_20200310_Bin_Bin_75_2-contigs.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3b33e43-c655-4900-9d82-74f723557ee2/dqc_reference/reference_markers.hmm GCA_943841735.1_20200310_Bin_Bin_75_2-contigs.fa_genomic.fna/protein.faa > /dev/null
[2023-06-30 23:48:39,661] [INFO] Task succeeded: HMMsearch
[2023-06-30 23:48:39,662] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5569bb1a-cdd2-4496-81eb-a995834dcc9a/GCA_943841735.1_20200310_Bin_Bin_75_2-contigs.fa_genomic.fna.gz]
[2023-06-30 23:48:39,686] [INFO] Query marker FASTA was written to GCA_943841735.1_20200310_Bin_Bin_75_2-contigs.fa_genomic.fna/markers.fasta
[2023-06-30 23:48:39,686] [INFO] Task started: Blastn
[2023-06-30 23:48:39,687] [INFO] Running command: blastn -query GCA_943841735.1_20200310_Bin_Bin_75_2-contigs.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3b33e43-c655-4900-9d82-74f723557ee2/dqc_reference/reference_markers.fasta -out GCA_943841735.1_20200310_Bin_Bin_75_2-contigs.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 23:48:40,265] [INFO] Task succeeded: Blastn
[2023-06-30 23:48:40,269] [INFO] Selected 16 target genomes.
[2023-06-30 23:48:40,269] [INFO] Target genome list was writen to GCA_943841735.1_20200310_Bin_Bin_75_2-contigs.fa_genomic.fna/target_genomes.txt
[2023-06-30 23:48:40,271] [INFO] Task started: fastANI
[2023-06-30 23:48:40,271] [INFO] Running command: fastANI --query /var/lib/cwl/stg5569bb1a-cdd2-4496-81eb-a995834dcc9a/GCA_943841735.1_20200310_Bin_Bin_75_2-contigs.fa_genomic.fna.gz --refList GCA_943841735.1_20200310_Bin_Bin_75_2-contigs.fa_genomic.fna/target_genomes.txt --output GCA_943841735.1_20200310_Bin_Bin_75_2-contigs.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 23:48:50,070] [INFO] Task succeeded: fastANI
[2023-06-30 23:48:50,071] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3b33e43-c655-4900-9d82-74f723557ee2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 23:48:50,071] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3b33e43-c655-4900-9d82-74f723557ee2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 23:48:50,072] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 23:48:50,072] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 23:48:50,073] [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 23:48:50,074] [INFO] DFAST Taxonomy check result was written to GCA_943841735.1_20200310_Bin_Bin_75_2-contigs.fa_genomic.fna/tc_result.tsv
[2023-06-30 23:48:50,075] [INFO] ===== Taxonomy check completed =====
[2023-06-30 23:48:50,075] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 23:48:50,075] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3b33e43-c655-4900-9d82-74f723557ee2/dqc_reference/checkm_data
[2023-06-30 23:48:50,078] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 23:48:50,100] [INFO] Task started: CheckM
[2023-06-30 23:48:50,101] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_943841735.1_20200310_Bin_Bin_75_2-contigs.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_943841735.1_20200310_Bin_Bin_75_2-contigs.fa_genomic.fna/checkm_input GCA_943841735.1_20200310_Bin_Bin_75_2-contigs.fa_genomic.fna/checkm_result
[2023-06-30 23:49:08,590] [INFO] Task succeeded: CheckM
[2023-06-30 23:49:08,592] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 23:49:08,613] [INFO] ===== Completeness check finished =====
[2023-06-30 23:49:08,614] [INFO] ===== Start GTDB Search =====
[2023-06-30 23:49:08,614] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_943841735.1_20200310_Bin_Bin_75_2-contigs.fa_genomic.fna/markers.fasta)
[2023-06-30 23:49:08,614] [INFO] Task started: Blastn
[2023-06-30 23:49:08,615] [INFO] Running command: blastn -query GCA_943841735.1_20200310_Bin_Bin_75_2-contigs.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3b33e43-c655-4900-9d82-74f723557ee2/dqc_reference/reference_markers_gtdb.fasta -out GCA_943841735.1_20200310_Bin_Bin_75_2-contigs.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 23:49:09,377] [INFO] Task succeeded: Blastn
[2023-06-30 23:49:09,381] [INFO] Selected 12 target genomes.
[2023-06-30 23:49:09,382] [INFO] Target genome list was writen to GCA_943841735.1_20200310_Bin_Bin_75_2-contigs.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 23:49:09,389] [INFO] Task started: fastANI
[2023-06-30 23:49:09,389] [INFO] Running command: fastANI --query /var/lib/cwl/stg5569bb1a-cdd2-4496-81eb-a995834dcc9a/GCA_943841735.1_20200310_Bin_Bin_75_2-contigs.fa_genomic.fna.gz --refList GCA_943841735.1_20200310_Bin_Bin_75_2-contigs.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_943841735.1_20200310_Bin_Bin_75_2-contigs.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 23:49:14,989] [INFO] Task succeeded: fastANI
[2023-06-30 23:49:14,994] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 23:49:14,994] [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_017854255.1	s__UBA9926 sp003451575	99.2788	411	432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	99.03	98.40	0.91	0.88	11	conclusive
GCA_018645765.1	s__UBA9926 sp018645765	90.1115	263	432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018647445.1	s__UBA9926 sp018647445	86.5667	335	432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	99.28	99.28	0.84	0.84	2	-
GCA_905182155.1	s__UBA9926 sp905182155	81.4564	259	432	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9926	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 23:49:14,996] [INFO] GTDB search result was written to GCA_943841735.1_20200310_Bin_Bin_75_2-contigs.fa_genomic.fna/result_gtdb.tsv
[2023-06-30 23:49:14,997] [INFO] ===== GTDB Search completed =====
[2023-06-30 23:49:14,999] [INFO] DFAST_QC result json was written to GCA_943841735.1_20200310_Bin_Bin_75_2-contigs.fa_genomic.fna/dqc_result.json
[2023-06-30 23:49:14,999] [INFO] DFAST_QC completed!
[2023-06-30 23:49:14,999] [INFO] Total running time: 0h0m40s