[2023-03-17 04:48:54,028] [INFO] DFAST_QC pipeline started.
[2023-03-17 04:48:54,028] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 04:48:54,028] [INFO] DQC Reference Directory: /var/lib/cwl/stgf82761cb-1b91-413a-94fc-059634603202/dqc_reference
[2023-03-17 04:48:55,167] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 04:48:55,168] [INFO] Task started: Prodigal
[2023-03-17 04:48:55,168] [INFO] Running command: cat /var/lib/cwl/stg4ae27f0a-f02f-4ede-9114-204f0111aa5f/OceanDNA-b5040.fa | prodigal -d OceanDNA-b5040/cds.fna -a OceanDNA-b5040/protein.faa -g 11 -q > /dev/null
[2023-03-17 04:49:02,457] [INFO] Task succeeded: Prodigal
[2023-03-17 04:49:02,457] [INFO] Task started: HMMsearch
[2023-03-17 04:49:02,457] [INFO] Running command: hmmsearch --tblout OceanDNA-b5040/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf82761cb-1b91-413a-94fc-059634603202/dqc_reference/reference_markers.hmm OceanDNA-b5040/protein.faa > /dev/null
[2023-03-17 04:49:02,651] [INFO] Task succeeded: HMMsearch
[2023-03-17 04:49:02,651] [INFO] Found 6/6 markers.
[2023-03-17 04:49:02,662] [INFO] Query marker FASTA was written to OceanDNA-b5040/markers.fasta
[2023-03-17 04:49:02,663] [INFO] Task started: Blastn
[2023-03-17 04:49:02,663] [INFO] Running command: blastn -query OceanDNA-b5040/markers.fasta -db /var/lib/cwl/stgf82761cb-1b91-413a-94fc-059634603202/dqc_reference/reference_markers.fasta -out OceanDNA-b5040/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:49:03,177] [INFO] Task succeeded: Blastn
[2023-03-17 04:49:03,178] [INFO] Selected 32 target genomes.
[2023-03-17 04:49:03,178] [INFO] Target genome list was writen to OceanDNA-b5040/target_genomes.txt
[2023-03-17 04:49:03,193] [INFO] Task started: fastANI
[2023-03-17 04:49:03,193] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ae27f0a-f02f-4ede-9114-204f0111aa5f/OceanDNA-b5040.fa --refList OceanDNA-b5040/target_genomes.txt --output OceanDNA-b5040/fastani_result.tsv --threads 1
[2023-03-17 04:49:20,759] [INFO] Task succeeded: fastANI
[2023-03-17 04:49:20,759] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf82761cb-1b91-413a-94fc-059634603202/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 04:49:20,759] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf82761cb-1b91-413a-94fc-059634603202/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 04:49:20,760] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 04:49:20,760] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 04:49:20,760] [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
--------------------------------------------------------------------------------
[2023-03-17 04:49:20,760] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5040/tc_result.tsv
[2023-03-17 04:49:20,760] [INFO] ===== Taxonomy check completed =====
[2023-03-17 04:49:20,760] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 04:49:20,760] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf82761cb-1b91-413a-94fc-059634603202/dqc_reference/checkm_data
[2023-03-17 04:49:20,763] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 04:49:20,766] [INFO] Task started: CheckM
[2023-03-17 04:49:20,766] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5040/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5040/checkm_input OceanDNA-b5040/checkm_result
[2023-03-17 04:49:44,268] [INFO] Task succeeded: CheckM
[2023-03-17 04:49:44,269] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.66%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 04:49:44,270] [INFO] ===== Completeness check finished =====
[2023-03-17 04:49:44,271] [INFO] ===== Start GTDB Search =====
[2023-03-17 04:49:44,271] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5040/markers.fasta)
[2023-03-17 04:49:44,271] [INFO] Task started: Blastn
[2023-03-17 04:49:44,271] [INFO] Running command: blastn -query OceanDNA-b5040/markers.fasta -db /var/lib/cwl/stgf82761cb-1b91-413a-94fc-059634603202/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5040/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 04:49:44,963] [INFO] Task succeeded: Blastn
[2023-03-17 04:49:44,963] [INFO] Selected 24 target genomes.
[2023-03-17 04:49:44,964] [INFO] Target genome list was writen to OceanDNA-b5040/target_genomes_gtdb.txt
[2023-03-17 04:49:45,498] [INFO] Task started: fastANI
[2023-03-17 04:49:45,498] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ae27f0a-f02f-4ede-9114-204f0111aa5f/OceanDNA-b5040.fa --refList OceanDNA-b5040/target_genomes_gtdb.txt --output OceanDNA-b5040/fastani_result_gtdb.tsv --threads 1
[2023-03-17 04:49:52,332] [INFO] Task succeeded: fastANI
[2023-03-17 04:49:52,340] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 04:49:52,340] [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_002724895.1	s__GCA-2693335 sp002724895	97.6144	326	380	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2693335	95.0	97.78	97.48	0.81	0.76	3	conclusive
GCA_002728175.1	s__GCA-2697505 sp002728175	77.491	90	380	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2697505	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002711125.1	s__GCA-2711125 sp002711125	76.3828	81	380	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_905181585.1	s__CAJIYG01 sp905181585	76.2185	70	380	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__CAJIYG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902627575.1	s__GCA-2711125 sp902627575	76.1213	58	380	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_905479165.1	s__UWMA-0277 sp905479165	76.1018	61	380	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_905478765.1	s__UWMA-0277 sp905478765	75.9005	62	380	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_002705205.1	s__GCA-2705205 sp002705205	75.8758	50	380	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2705205	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478185.1	s__UWMA-0277 sp905478185	75.8326	66	380	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_018652335.1	s__GCA-2683775 sp018652335	75.6573	59	380	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_002697625.1	s__GCA-002697625 sp002697625	75.6387	53	380	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_018675825.1	s__GCA-002715885 sp018675825	75.6376	51	380	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-002715885	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 04:49:52,340] [INFO] GTDB search result was written to OceanDNA-b5040/result_gtdb.tsv
[2023-03-17 04:49:52,340] [INFO] ===== GTDB Search completed =====
[2023-03-17 04:49:52,341] [INFO] DFAST_QC result json was written to OceanDNA-b5040/dqc_result.json
[2023-03-17 04:49:52,341] [INFO] DFAST_QC completed!
[2023-03-17 04:49:52,341] [INFO] Total running time: 0h0m58s