[2023-03-14 11:49:17,073] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:49:17,076] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:49:17,076] [INFO] DQC Reference Directory: /var/lib/cwl/stgbafcc430-da18-4490-bd1b-f0b1c25cab19/dqc_reference
[2023-03-14 11:49:18,155] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:49:18,155] [INFO] Task started: Prodigal
[2023-03-14 11:49:18,155] [INFO] Running command: cat /var/lib/cwl/stg31cb07a7-09c6-4c82-948d-4a05713b053b/OceanDNA-b4966.fa | prodigal -d OceanDNA-b4966/cds.fna -a OceanDNA-b4966/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:49:26,839] [INFO] Task succeeded: Prodigal
[2023-03-14 11:49:26,839] [INFO] Task started: HMMsearch
[2023-03-14 11:49:26,839] [INFO] Running command: hmmsearch --tblout OceanDNA-b4966/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbafcc430-da18-4490-bd1b-f0b1c25cab19/dqc_reference/reference_markers.hmm OceanDNA-b4966/protein.faa > /dev/null
[2023-03-14 11:49:27,010] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:49:27,011] [INFO] Found 6/6 markers.
[2023-03-14 11:49:27,043] [INFO] Query marker FASTA was written to OceanDNA-b4966/markers.fasta
[2023-03-14 11:49:27,043] [INFO] Task started: Blastn
[2023-03-14 11:49:27,043] [INFO] Running command: blastn -query OceanDNA-b4966/markers.fasta -db /var/lib/cwl/stgbafcc430-da18-4490-bd1b-f0b1c25cab19/dqc_reference/reference_markers.fasta -out OceanDNA-b4966/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:49:27,602] [INFO] Task succeeded: Blastn
[2023-03-14 11:49:27,608] [INFO] Selected 25 target genomes.
[2023-03-14 11:49:27,608] [INFO] Target genome list was writen to OceanDNA-b4966/target_genomes.txt
[2023-03-14 11:49:27,623] [INFO] Task started: fastANI
[2023-03-14 11:49:27,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg31cb07a7-09c6-4c82-948d-4a05713b053b/OceanDNA-b4966.fa --refList OceanDNA-b4966/target_genomes.txt --output OceanDNA-b4966/fastani_result.tsv --threads 1
[2023-03-14 11:49:39,919] [INFO] Task succeeded: fastANI
[2023-03-14 11:49:39,919] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbafcc430-da18-4490-bd1b-f0b1c25cab19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:49:39,920] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbafcc430-da18-4490-bd1b-f0b1c25cab19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:49:39,920] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:49:39,920] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:49:39,920] [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
--------------------------------------------------------------------------------
[2023-03-14 11:49:39,923] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4966/tc_result.tsv
[2023-03-14 11:49:39,926] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:49:39,926] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:49:39,926] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbafcc430-da18-4490-bd1b-f0b1c25cab19/dqc_reference/checkm_data
[2023-03-14 11:49:39,929] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:49:39,949] [INFO] Task started: CheckM
[2023-03-14 11:49:39,950] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4966/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4966/checkm_input OceanDNA-b4966/checkm_result
[2023-03-14 11:50:06,195] [INFO] Task succeeded: CheckM
[2023-03-14 11:50:06,196] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:50:06,278] [INFO] ===== Completeness check finished =====
[2023-03-14 11:50:06,278] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:50:06,278] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4966/markers.fasta)
[2023-03-14 11:50:06,279] [INFO] Task started: Blastn
[2023-03-14 11:50:06,280] [INFO] Running command: blastn -query OceanDNA-b4966/markers.fasta -db /var/lib/cwl/stgbafcc430-da18-4490-bd1b-f0b1c25cab19/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4966/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:50:07,185] [INFO] Task succeeded: Blastn
[2023-03-14 11:50:07,189] [INFO] Selected 20 target genomes.
[2023-03-14 11:50:07,189] [INFO] Target genome list was writen to OceanDNA-b4966/target_genomes_gtdb.txt
[2023-03-14 11:50:07,257] [INFO] Task started: fastANI
[2023-03-14 11:50:07,257] [INFO] Running command: fastANI --query /var/lib/cwl/stg31cb07a7-09c6-4c82-948d-4a05713b053b/OceanDNA-b4966.fa --refList OceanDNA-b4966/target_genomes_gtdb.txt --output OceanDNA-b4966/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:50:13,208] [INFO] Task succeeded: fastANI
[2023-03-14 11:50:13,216] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:50:13,216] [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_002696275.1	s__GCA-002697625 sp002696275	99.8333	468	484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002697625.1	s__GCA-002697625 sp002697625	80.6087	293	484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478555.1	s__GCA-002697625 sp905478555	78.286	192	484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	96.63	96.63	0.87	0.87	2	-
GCA_902514225.1	s__GCA-002697625 sp902514225	77.5175	129	484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018647945.1	s__GCA-002697625 sp018647945	77.2321	162	484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	99.64	99.58	0.90	0.90	3	-
GCA_018695965.1	s__GCA-002697625 sp018695965	77.211	144	484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002697625	95.0	98.45	97.65	0.78	0.72	6	-
GCA_905478765.1	s__UWMA-0277 sp905478765	76.5081	87	484	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_018652335.1	s__GCA-2683775 sp018652335	76.4497	61	484	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_018664745.1	s__UWMA-0277 sp018664745	76.3922	55	484	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_014381465.1	s__DUAL01 sp014381465	76.2651	73	484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__DUAL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002711125.1	s__GCA-2711125 sp002711125	76.1566	75	484	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_902579065.1	s__GCA-002715885 sp902579065	76.085	56	484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018675825.1	s__GCA-002715885 sp018675825	75.7225	52	484	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:50:13,221] [INFO] GTDB search result was written to OceanDNA-b4966/result_gtdb.tsv
[2023-03-14 11:50:13,223] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:50:13,229] [INFO] DFAST_QC result json was written to OceanDNA-b4966/dqc_result.json
[2023-03-14 11:50:13,229] [INFO] DFAST_QC completed!
[2023-03-14 11:50:13,229] [INFO] Total running time: 0h0m56s