[2023-06-30 11:35:57,795] [INFO] DFAST_QC pipeline started.
[2023-06-30 11:35:57,797] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 11:35:57,797] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f5bb8e9-c7a1-4b38-8bad-73b62bf6c0aa/dqc_reference
[2023-06-30 11:35:59,255] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 11:35:59,256] [INFO] Task started: Prodigal
[2023-06-30 11:35:59,256] [INFO] Running command: gunzip -c /var/lib/cwl/stg3369f9c1-4547-402a-9419-920c3f9707e8/GCA_903866355.1_freshwater_MAG_---_Loclat_bin-18265_genomic.fna.gz | prodigal -d GCA_903866355.1_freshwater_MAG_---_Loclat_bin-18265_genomic.fna/cds.fna -a GCA_903866355.1_freshwater_MAG_---_Loclat_bin-18265_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 11:36:09,960] [INFO] Task succeeded: Prodigal
[2023-06-30 11:36:09,961] [INFO] Task started: HMMsearch
[2023-06-30 11:36:09,961] [INFO] Running command: hmmsearch --tblout GCA_903866355.1_freshwater_MAG_---_Loclat_bin-18265_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f5bb8e9-c7a1-4b38-8bad-73b62bf6c0aa/dqc_reference/reference_markers.hmm GCA_903866355.1_freshwater_MAG_---_Loclat_bin-18265_genomic.fna/protein.faa > /dev/null
[2023-06-30 11:36:10,225] [INFO] Task succeeded: HMMsearch
[2023-06-30 11:36:10,227] [INFO] Found 6/6 markers.
[2023-06-30 11:36:10,266] [INFO] Query marker FASTA was written to GCA_903866355.1_freshwater_MAG_---_Loclat_bin-18265_genomic.fna/markers.fasta
[2023-06-30 11:36:10,266] [INFO] Task started: Blastn
[2023-06-30 11:36:10,266] [INFO] Running command: blastn -query GCA_903866355.1_freshwater_MAG_---_Loclat_bin-18265_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f5bb8e9-c7a1-4b38-8bad-73b62bf6c0aa/dqc_reference/reference_markers.fasta -out GCA_903866355.1_freshwater_MAG_---_Loclat_bin-18265_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 11:36:10,995] [INFO] Task succeeded: Blastn
[2023-06-30 11:36:11,000] [INFO] Selected 29 target genomes.
[2023-06-30 11:36:11,001] [INFO] Target genome list was writen to GCA_903866355.1_freshwater_MAG_---_Loclat_bin-18265_genomic.fna/target_genomes.txt
[2023-06-30 11:36:11,006] [INFO] Task started: fastANI
[2023-06-30 11:36:11,006] [INFO] Running command: fastANI --query /var/lib/cwl/stg3369f9c1-4547-402a-9419-920c3f9707e8/GCA_903866355.1_freshwater_MAG_---_Loclat_bin-18265_genomic.fna.gz --refList GCA_903866355.1_freshwater_MAG_---_Loclat_bin-18265_genomic.fna/target_genomes.txt --output GCA_903866355.1_freshwater_MAG_---_Loclat_bin-18265_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 11:36:28,116] [INFO] Task succeeded: fastANI
[2023-06-30 11:36:28,117] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f5bb8e9-c7a1-4b38-8bad-73b62bf6c0aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 11:36:28,117] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f5bb8e9-c7a1-4b38-8bad-73b62bf6c0aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 11:36:28,120] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 11:36:28,120] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 11:36:28,120] [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 11:36:28,123] [INFO] DFAST Taxonomy check result was written to GCA_903866355.1_freshwater_MAG_---_Loclat_bin-18265_genomic.fna/tc_result.tsv
[2023-06-30 11:36:28,123] [INFO] ===== Taxonomy check completed =====
[2023-06-30 11:36:28,124] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 11:36:28,124] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f5bb8e9-c7a1-4b38-8bad-73b62bf6c0aa/dqc_reference/checkm_data
[2023-06-30 11:36:28,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 11:36:28,173] [INFO] Task started: CheckM
[2023-06-30 11:36:28,174] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903866355.1_freshwater_MAG_---_Loclat_bin-18265_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903866355.1_freshwater_MAG_---_Loclat_bin-18265_genomic.fna/checkm_input GCA_903866355.1_freshwater_MAG_---_Loclat_bin-18265_genomic.fna/checkm_result
[2023-06-30 11:37:03,224] [INFO] Task succeeded: CheckM
[2023-06-30 11:37:03,226] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 11:37:03,250] [INFO] ===== Completeness check finished =====
[2023-06-30 11:37:03,250] [INFO] ===== Start GTDB Search =====
[2023-06-30 11:37:03,250] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903866355.1_freshwater_MAG_---_Loclat_bin-18265_genomic.fna/markers.fasta)
[2023-06-30 11:37:03,251] [INFO] Task started: Blastn
[2023-06-30 11:37:03,251] [INFO] Running command: blastn -query GCA_903866355.1_freshwater_MAG_---_Loclat_bin-18265_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f5bb8e9-c7a1-4b38-8bad-73b62bf6c0aa/dqc_reference/reference_markers_gtdb.fasta -out GCA_903866355.1_freshwater_MAG_---_Loclat_bin-18265_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 11:37:04,401] [INFO] Task succeeded: Blastn
[2023-06-30 11:37:04,406] [INFO] Selected 16 target genomes.
[2023-06-30 11:37:04,407] [INFO] Target genome list was writen to GCA_903866355.1_freshwater_MAG_---_Loclat_bin-18265_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 11:37:04,414] [INFO] Task started: fastANI
[2023-06-30 11:37:04,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg3369f9c1-4547-402a-9419-920c3f9707e8/GCA_903866355.1_freshwater_MAG_---_Loclat_bin-18265_genomic.fna.gz --refList GCA_903866355.1_freshwater_MAG_---_Loclat_bin-18265_genomic.fna/target_genomes_gtdb.txt --output GCA_903866355.1_freshwater_MAG_---_Loclat_bin-18265_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 11:37:14,503] [INFO] Task succeeded: fastANI
[2023-06-30 11:37:14,512] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 11:37:14,512] [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_903866355.1	s__Ga0077536 sp903866355	100.0	875	890	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__Ga0077536	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009692365.1	s__Ga0077536 sp009692365	84.1306	570	890	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__Ga0077536	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464935.1	s__Ga0077536 sp001464935	75.9849	92	890	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__Ga0077536	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719885.1	s__JADJYF01 sp016719885	75.696	73	890	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__JADJYF01	95.0	97.68	97.68	0.89	0.89	2	-
GCA_016874535.1	s__CAIKBL01 sp016874535	75.6038	56	890	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077536;f__Ga0077536;g__CAIKBL01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 11:37:14,515] [INFO] GTDB search result was written to GCA_903866355.1_freshwater_MAG_---_Loclat_bin-18265_genomic.fna/result_gtdb.tsv
[2023-06-30 11:37:14,515] [INFO] ===== GTDB Search completed =====
[2023-06-30 11:37:14,518] [INFO] DFAST_QC result json was written to GCA_903866355.1_freshwater_MAG_---_Loclat_bin-18265_genomic.fna/dqc_result.json
[2023-06-30 11:37:14,518] [INFO] DFAST_QC completed!
[2023-06-30 11:37:14,519] [INFO] Total running time: 0h1m17s