[2023-03-18 00:24:19,472] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:24:19,472] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:24:19,472] [INFO] DQC Reference Directory: /var/lib/cwl/stg9fc58c09-04cb-4e82-808f-2f52c3d8b861/dqc_reference
[2023-03-18 00:24:20,558] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:24:20,558] [INFO] Task started: Prodigal
[2023-03-18 00:24:20,559] [INFO] Running command: cat /var/lib/cwl/stgf76b2887-81cb-4b2f-87bc-aec56d6bdc99/OceanDNA-b4786.fa | prodigal -d OceanDNA-b4786/cds.fna -a OceanDNA-b4786/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:24:25,197] [INFO] Task succeeded: Prodigal
[2023-03-18 00:24:25,197] [INFO] Task started: HMMsearch
[2023-03-18 00:24:25,197] [INFO] Running command: hmmsearch --tblout OceanDNA-b4786/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9fc58c09-04cb-4e82-808f-2f52c3d8b861/dqc_reference/reference_markers.hmm OceanDNA-b4786/protein.faa > /dev/null
[2023-03-18 00:24:25,334] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:24:25,334] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf76b2887-81cb-4b2f-87bc-aec56d6bdc99/OceanDNA-b4786.fa]
[2023-03-18 00:24:25,346] [INFO] Query marker FASTA was written to OceanDNA-b4786/markers.fasta
[2023-03-18 00:24:25,346] [INFO] Task started: Blastn
[2023-03-18 00:24:25,346] [INFO] Running command: blastn -query OceanDNA-b4786/markers.fasta -db /var/lib/cwl/stg9fc58c09-04cb-4e82-808f-2f52c3d8b861/dqc_reference/reference_markers.fasta -out OceanDNA-b4786/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:24:25,839] [INFO] Task succeeded: Blastn
[2023-03-18 00:24:25,840] [INFO] Selected 13 target genomes.
[2023-03-18 00:24:25,840] [INFO] Target genome list was writen to OceanDNA-b4786/target_genomes.txt
[2023-03-18 00:24:25,877] [INFO] Task started: fastANI
[2023-03-18 00:24:25,877] [INFO] Running command: fastANI --query /var/lib/cwl/stgf76b2887-81cb-4b2f-87bc-aec56d6bdc99/OceanDNA-b4786.fa --refList OceanDNA-b4786/target_genomes.txt --output OceanDNA-b4786/fastani_result.tsv --threads 1
[2023-03-18 00:24:32,684] [INFO] Task succeeded: fastANI
[2023-03-18 00:24:32,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9fc58c09-04cb-4e82-808f-2f52c3d8b861/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:24:32,684] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9fc58c09-04cb-4e82-808f-2f52c3d8b861/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:24:32,685] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:24:32,685] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:24:32,685] [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
--------------------------------------------------------------------------------
[2023-03-18 00:24:32,685] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4786/tc_result.tsv
[2023-03-18 00:24:32,685] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:24:32,685] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:24:32,685] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9fc58c09-04cb-4e82-808f-2f52c3d8b861/dqc_reference/checkm_data
[2023-03-18 00:24:32,688] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:24:32,699] [INFO] Task started: CheckM
[2023-03-18 00:24:32,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4786/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4786/checkm_input OceanDNA-b4786/checkm_result
[2023-03-18 00:24:51,997] [INFO] Task succeeded: CheckM
[2023-03-18 00:24:51,998] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:24:52,000] [INFO] ===== Completeness check finished =====
[2023-03-18 00:24:52,000] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:24:52,000] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4786/markers.fasta)
[2023-03-18 00:24:52,001] [INFO] Task started: Blastn
[2023-03-18 00:24:52,001] [INFO] Running command: blastn -query OceanDNA-b4786/markers.fasta -db /var/lib/cwl/stg9fc58c09-04cb-4e82-808f-2f52c3d8b861/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4786/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:24:52,636] [INFO] Task succeeded: Blastn
[2023-03-18 00:24:52,637] [INFO] Selected 32 target genomes.
[2023-03-18 00:24:52,637] [INFO] Target genome list was writen to OceanDNA-b4786/target_genomes_gtdb.txt
[2023-03-18 00:24:52,699] [INFO] Task started: fastANI
[2023-03-18 00:24:52,699] [INFO] Running command: fastANI --query /var/lib/cwl/stgf76b2887-81cb-4b2f-87bc-aec56d6bdc99/OceanDNA-b4786.fa --refList OceanDNA-b4786/target_genomes_gtdb.txt --output OceanDNA-b4786/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:25:03,524] [INFO] Task succeeded: fastANI
[2023-03-18 00:25:03,527] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:25:03,527] [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_002693745.1	s__BACL11 sp002693745	77.5405	65	190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__BACL11	95.0	98.58	98.58	0.90	0.90	2	-
GCA_002730985.1	s__BACL11 sp002730985	77.1027	65	190	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	76.3153	52	190	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:25:03,528] [INFO] GTDB search result was written to OceanDNA-b4786/result_gtdb.tsv
[2023-03-18 00:25:03,528] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:25:03,528] [INFO] DFAST_QC result json was written to OceanDNA-b4786/dqc_result.json
[2023-03-18 00:25:03,529] [INFO] DFAST_QC completed!
[2023-03-18 00:25:03,529] [INFO] Total running time: 0h0m44s