[2023-03-16 10:46:24,063] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:46:24,063] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:46:24,064] [INFO] DQC Reference Directory: /var/lib/cwl/stge0a0944c-b432-4573-acea-8f0bb2d87501/dqc_reference
[2023-03-16 10:46:25,192] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:46:25,193] [INFO] Task started: Prodigal
[2023-03-16 10:46:25,193] [INFO] Running command: cat /var/lib/cwl/stg1d293986-d5f4-4cc3-af89-8e3aaa3ef184/OceanDNA-b4842.fa | prodigal -d OceanDNA-b4842/cds.fna -a OceanDNA-b4842/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:46:32,651] [INFO] Task succeeded: Prodigal
[2023-03-16 10:46:32,651] [INFO] Task started: HMMsearch
[2023-03-16 10:46:32,651] [INFO] Running command: hmmsearch --tblout OceanDNA-b4842/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0a0944c-b432-4573-acea-8f0bb2d87501/dqc_reference/reference_markers.hmm OceanDNA-b4842/protein.faa > /dev/null
[2023-03-16 10:46:32,847] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:46:32,848] [INFO] Found 6/6 markers.
[2023-03-16 10:46:32,858] [INFO] Query marker FASTA was written to OceanDNA-b4842/markers.fasta
[2023-03-16 10:46:32,858] [INFO] Task started: Blastn
[2023-03-16 10:46:32,858] [INFO] Running command: blastn -query OceanDNA-b4842/markers.fasta -db /var/lib/cwl/stge0a0944c-b432-4573-acea-8f0bb2d87501/dqc_reference/reference_markers.fasta -out OceanDNA-b4842/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:46:33,419] [INFO] Task succeeded: Blastn
[2023-03-16 10:46:33,420] [INFO] Selected 33 target genomes.
[2023-03-16 10:46:33,420] [INFO] Target genome list was writen to OceanDNA-b4842/target_genomes.txt
[2023-03-16 10:46:33,542] [INFO] Task started: fastANI
[2023-03-16 10:46:33,542] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d293986-d5f4-4cc3-af89-8e3aaa3ef184/OceanDNA-b4842.fa --refList OceanDNA-b4842/target_genomes.txt --output OceanDNA-b4842/fastani_result.tsv --threads 1
[2023-03-16 10:46:53,176] [INFO] Task succeeded: fastANI
[2023-03-16 10:46:53,177] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0a0944c-b432-4573-acea-8f0bb2d87501/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:46:53,177] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0a0944c-b432-4573-acea-8f0bb2d87501/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:46:53,177] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:46:53,177] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 10:46:53,177] [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
--------------------------------------------------------------------------------
[2023-03-16 10:46:53,177] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4842/tc_result.tsv
[2023-03-16 10:46:53,177] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:46:53,178] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:46:53,178] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0a0944c-b432-4573-acea-8f0bb2d87501/dqc_reference/checkm_data
[2023-03-16 10:46:53,181] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:46:53,184] [INFO] Task started: CheckM
[2023-03-16 10:46:53,184] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4842/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4842/checkm_input OceanDNA-b4842/checkm_result
[2023-03-16 10:47:26,865] [INFO] Task succeeded: CheckM
[2023-03-16 10:47:26,865] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:47:26,867] [INFO] ===== Completeness check finished =====
[2023-03-16 10:47:26,867] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:47:26,867] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4842/markers.fasta)
[2023-03-16 10:47:26,867] [INFO] Task started: Blastn
[2023-03-16 10:47:26,868] [INFO] Running command: blastn -query OceanDNA-b4842/markers.fasta -db /var/lib/cwl/stge0a0944c-b432-4573-acea-8f0bb2d87501/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4842/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:47:27,832] [INFO] Task succeeded: Blastn
[2023-03-16 10:47:27,833] [INFO] Selected 21 target genomes.
[2023-03-16 10:47:27,833] [INFO] Target genome list was writen to OceanDNA-b4842/target_genomes_gtdb.txt
[2023-03-16 10:47:27,842] [INFO] Task started: fastANI
[2023-03-16 10:47:27,842] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d293986-d5f4-4cc3-af89-8e3aaa3ef184/OceanDNA-b4842.fa --refList OceanDNA-b4842/target_genomes_gtdb.txt --output OceanDNA-b4842/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:47:34,574] [INFO] Task succeeded: fastANI
[2023-03-16 10:47:34,581] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 10:47:34,581] [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_018675825.1	s__GCA-002715885 sp018675825	96.1575	289	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014239655.1	s__GCA-002715885 sp014239655	78.6782	227	426	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_902579065.1	s__GCA-002715885 sp902579065	77.7246	99	426	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_002689735.1	s__GCA-002715885 sp002689735	77.6661	85	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	96.30	96.30	0.76	0.76	2	-
GCA_905181585.1	s__CAJIYG01 sp905181585	77.1687	157	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__CAJIYG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018652335.1	s__GCA-2683775 sp018652335	76.6476	61	426	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_905478765.1	s__UWMA-0277 sp905478765	76.5772	60	426	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_002696275.1	s__GCA-002697625 sp002696275	76.3772	56	426	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_002711125.1	s__GCA-2711125 sp002711125	76.37	70	426	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_002697505.1	s__GCA-2697505 sp002697505	75.6093	54	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2697505	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:47:34,582] [INFO] GTDB search result was written to OceanDNA-b4842/result_gtdb.tsv
[2023-03-16 10:47:34,582] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:47:34,584] [INFO] DFAST_QC result json was written to OceanDNA-b4842/dqc_result.json
[2023-03-16 10:47:34,584] [INFO] DFAST_QC completed!
[2023-03-16 10:47:34,584] [INFO] Total running time: 0h1m11s