[2023-03-19 03:10:00,743] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:10:00,743] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:10:00,743] [INFO] DQC Reference Directory: /var/lib/cwl/stge03d2a44-3124-404a-b838-bf0b5a0cba4b/dqc_reference
[2023-03-19 03:10:01,837] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:10:01,837] [INFO] Task started: Prodigal
[2023-03-19 03:10:01,837] [INFO] Running command: cat /var/lib/cwl/stg95bf53ec-a00c-496c-9751-61793ff54dea/OceanDNA-b45796.fa | prodigal -d OceanDNA-b45796/cds.fna -a OceanDNA-b45796/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:10:29,093] [INFO] Task succeeded: Prodigal
[2023-03-19 03:10:29,094] [INFO] Task started: HMMsearch
[2023-03-19 03:10:29,094] [INFO] Running command: hmmsearch --tblout OceanDNA-b45796/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge03d2a44-3124-404a-b838-bf0b5a0cba4b/dqc_reference/reference_markers.hmm OceanDNA-b45796/protein.faa > /dev/null
[2023-03-19 03:10:29,286] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:10:29,287] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg95bf53ec-a00c-496c-9751-61793ff54dea/OceanDNA-b45796.fa]
[2023-03-19 03:10:29,308] [INFO] Query marker FASTA was written to OceanDNA-b45796/markers.fasta
[2023-03-19 03:10:29,308] [INFO] Task started: Blastn
[2023-03-19 03:10:29,308] [INFO] Running command: blastn -query OceanDNA-b45796/markers.fasta -db /var/lib/cwl/stge03d2a44-3124-404a-b838-bf0b5a0cba4b/dqc_reference/reference_markers.fasta -out OceanDNA-b45796/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:10:29,856] [INFO] Task succeeded: Blastn
[2023-03-19 03:10:29,857] [INFO] Selected 15 target genomes.
[2023-03-19 03:10:29,857] [INFO] Target genome list was writen to OceanDNA-b45796/target_genomes.txt
[2023-03-19 03:10:29,865] [INFO] Task started: fastANI
[2023-03-19 03:10:29,865] [INFO] Running command: fastANI --query /var/lib/cwl/stg95bf53ec-a00c-496c-9751-61793ff54dea/OceanDNA-b45796.fa --refList OceanDNA-b45796/target_genomes.txt --output OceanDNA-b45796/fastani_result.tsv --threads 1
[2023-03-19 03:10:40,092] [INFO] Task succeeded: fastANI
[2023-03-19 03:10:40,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge03d2a44-3124-404a-b838-bf0b5a0cba4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:10:40,092] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge03d2a44-3124-404a-b838-bf0b5a0cba4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:10:40,093] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:10:40,093] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:10:40,093] [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
--------------------------------------------------------------------------------
[2023-03-19 03:10:40,093] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45796/tc_result.tsv
[2023-03-19 03:10:40,093] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:10:40,093] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:10:40,093] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge03d2a44-3124-404a-b838-bf0b5a0cba4b/dqc_reference/checkm_data
[2023-03-19 03:10:40,096] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:10:40,100] [INFO] Task started: CheckM
[2023-03-19 03:10:40,101] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45796/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45796/checkm_input OceanDNA-b45796/checkm_result
[2023-03-19 03:11:48,387] [INFO] Task succeeded: CheckM
[2023-03-19 03:11:48,387] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:11:48,390] [INFO] ===== Completeness check finished =====
[2023-03-19 03:11:48,390] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:11:48,390] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45796/markers.fasta)
[2023-03-19 03:11:48,391] [INFO] Task started: Blastn
[2023-03-19 03:11:48,391] [INFO] Running command: blastn -query OceanDNA-b45796/markers.fasta -db /var/lib/cwl/stge03d2a44-3124-404a-b838-bf0b5a0cba4b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45796/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:11:49,559] [INFO] Task succeeded: Blastn
[2023-03-19 03:11:49,560] [INFO] Selected 24 target genomes.
[2023-03-19 03:11:49,560] [INFO] Target genome list was writen to OceanDNA-b45796/target_genomes_gtdb.txt
[2023-03-19 03:11:49,588] [INFO] Task started: fastANI
[2023-03-19 03:11:49,588] [INFO] Running command: fastANI --query /var/lib/cwl/stg95bf53ec-a00c-496c-9751-61793ff54dea/OceanDNA-b45796.fa --refList OceanDNA-b45796/target_genomes_gtdb.txt --output OceanDNA-b45796/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:12:01,343] [INFO] Task succeeded: fastANI
[2023-03-19 03:12:01,347] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 03:12:01,347] [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_002721705.1	s__UBA2993 sp002721705	79.61	270	912	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__UBA2993	95.0	99.38	99.15	0.85	0.79	3	-
GCA_002716045.1	s__UBA2993 sp002716045	78.2988	271	912	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__UBA2993	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382645.1	s__GCA-2730975 sp014382645	78.0161	90	912	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__GCA-2730975	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002500665.1	s__MB11C04 sp002500665	75.6165	63	912	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	98.37	95.55	0.93	0.84	7	-
--------------------------------------------------------------------------------
[2023-03-19 03:12:01,347] [INFO] GTDB search result was written to OceanDNA-b45796/result_gtdb.tsv
[2023-03-19 03:12:01,347] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:12:01,348] [INFO] DFAST_QC result json was written to OceanDNA-b45796/dqc_result.json
[2023-03-19 03:12:01,348] [INFO] DFAST_QC completed!
[2023-03-19 03:12:01,348] [INFO] Total running time: 0h2m1s