[2023-03-15 17:46:31,706] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:46:31,706] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:46:31,706] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d4b6904-8d67-4446-a83b-c61968673f05/dqc_reference
[2023-03-15 17:46:32,797] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:46:32,797] [INFO] Task started: Prodigal
[2023-03-15 17:46:32,797] [INFO] Running command: cat /var/lib/cwl/stga26c931d-fad4-4992-9a65-4738ab541f95/OceanDNA-b5109.fa | prodigal -d OceanDNA-b5109/cds.fna -a OceanDNA-b5109/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:46:40,964] [INFO] Task succeeded: Prodigal
[2023-03-15 17:46:40,965] [INFO] Task started: HMMsearch
[2023-03-15 17:46:40,965] [INFO] Running command: hmmsearch --tblout OceanDNA-b5109/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d4b6904-8d67-4446-a83b-c61968673f05/dqc_reference/reference_markers.hmm OceanDNA-b5109/protein.faa > /dev/null
[2023-03-15 17:46:41,128] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:46:41,128] [INFO] Found 6/6 markers.
[2023-03-15 17:46:41,143] [INFO] Query marker FASTA was written to OceanDNA-b5109/markers.fasta
[2023-03-15 17:46:41,144] [INFO] Task started: Blastn
[2023-03-15 17:46:41,144] [INFO] Running command: blastn -query OceanDNA-b5109/markers.fasta -db /var/lib/cwl/stg6d4b6904-8d67-4446-a83b-c61968673f05/dqc_reference/reference_markers.fasta -out OceanDNA-b5109/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:46:41,687] [INFO] Task succeeded: Blastn
[2023-03-15 17:46:41,688] [INFO] Selected 27 target genomes.
[2023-03-15 17:46:41,689] [INFO] Target genome list was writen to OceanDNA-b5109/target_genomes.txt
[2023-03-15 17:46:41,709] [INFO] Task started: fastANI
[2023-03-15 17:46:41,709] [INFO] Running command: fastANI --query /var/lib/cwl/stga26c931d-fad4-4992-9a65-4738ab541f95/OceanDNA-b5109.fa --refList OceanDNA-b5109/target_genomes.txt --output OceanDNA-b5109/fastani_result.tsv --threads 1
[2023-03-15 17:46:55,924] [INFO] Task succeeded: fastANI
[2023-03-15 17:46:55,925] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d4b6904-8d67-4446-a83b-c61968673f05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:46:55,925] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d4b6904-8d67-4446-a83b-c61968673f05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:46:55,925] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:46:55,925] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 17:46:55,925] [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
--------------------------------------------------------------------------------
[2023-03-15 17:46:55,927] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5109/tc_result.tsv
[2023-03-15 17:46:55,928] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:46:55,928] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:46:55,928] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d4b6904-8d67-4446-a83b-c61968673f05/dqc_reference/checkm_data
[2023-03-15 17:46:55,930] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:46:55,937] [INFO] Task started: CheckM
[2023-03-15 17:46:55,937] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5109/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5109/checkm_input OceanDNA-b5109/checkm_result
[2023-03-15 17:47:21,371] [INFO] Task succeeded: CheckM
[2023-03-15 17:47:21,371] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:47:21,375] [INFO] ===== Completeness check finished =====
[2023-03-15 17:47:21,375] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:47:21,375] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5109/markers.fasta)
[2023-03-15 17:47:21,376] [INFO] Task started: Blastn
[2023-03-15 17:47:21,376] [INFO] Running command: blastn -query OceanDNA-b5109/markers.fasta -db /var/lib/cwl/stg6d4b6904-8d67-4446-a83b-c61968673f05/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5109/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:47:22,164] [INFO] Task succeeded: Blastn
[2023-03-15 17:47:22,165] [INFO] Selected 28 target genomes.
[2023-03-15 17:47:22,165] [INFO] Target genome list was writen to OceanDNA-b5109/target_genomes_gtdb.txt
[2023-03-15 17:47:22,195] [INFO] Task started: fastANI
[2023-03-15 17:47:22,196] [INFO] Running command: fastANI --query /var/lib/cwl/stga26c931d-fad4-4992-9a65-4738ab541f95/OceanDNA-b5109.fa --refList OceanDNA-b5109/target_genomes_gtdb.txt --output OceanDNA-b5109/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:47:31,365] [INFO] Task succeeded: fastANI
[2023-03-15 17:47:31,372] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:47:31,373] [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_902627575.1	s__GCA-2711125 sp902627575	77.637	96	453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2711125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002711125.1	s__GCA-2711125 sp002711125	77.0725	136	453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2711125	95.0	97.93	96.61	0.96	0.94	3	-
GCA_018652335.1	s__GCA-2683775 sp018652335	76.6849	77	453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2683775	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002693745.1	s__BACL11 sp002693745	76.6084	70	453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__BACL11	95.0	98.58	98.58	0.90	0.90	2	-
GCA_002683775.1	s__GCA-2683775 sp002683775	76.5769	67	453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2683775	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002730985.1	s__BACL11 sp002730985	76.5271	57	453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__BACL11	95.0	97.22	97.22	0.84	0.84	2	-
GCA_905479165.1	s__UWMA-0277 sp905479165	76.5116	76	453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724895.1	s__GCA-2693335 sp002724895	76.3992	77	453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2693335	95.0	97.78	97.48	0.81	0.76	3	-
GCA_905181585.1	s__CAJIYG01 sp905181585	76.3419	72	453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__CAJIYG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478185.1	s__UWMA-0277 sp905478185	76.1505	74	453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	96.67	96.67	0.88	0.88	2	-
GCA_002715565.1	s__GCA-2715565 sp002715565	76.1246	52	453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2715565	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478765.1	s__UWMA-0277 sp905478765	76.016	83	453	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:47:31,374] [INFO] GTDB search result was written to OceanDNA-b5109/result_gtdb.tsv
[2023-03-15 17:47:31,374] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:47:31,376] [INFO] DFAST_QC result json was written to OceanDNA-b5109/dqc_result.json
[2023-03-15 17:47:31,376] [INFO] DFAST_QC completed!
[2023-03-15 17:47:31,376] [INFO] Total running time: 0h0m60s