[2023-03-17 06:30:49,799] [INFO] DFAST_QC pipeline started.
[2023-03-17 06:30:49,799] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 06:30:49,799] [INFO] DQC Reference Directory: /var/lib/cwl/stga1c6671f-e04f-4112-bffb-1f0ba2eb231b/dqc_reference
[2023-03-17 06:30:51,359] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 06:30:51,359] [INFO] Task started: Prodigal
[2023-03-17 06:30:51,359] [INFO] Running command: cat /var/lib/cwl/stg0da00b60-571f-445d-a29a-f0ef66e696b0/OceanDNA-b42542.fa | prodigal -d OceanDNA-b42542/cds.fna -a OceanDNA-b42542/protein.faa -g 11 -q > /dev/null
[2023-03-17 06:30:57,344] [INFO] Task succeeded: Prodigal
[2023-03-17 06:30:57,344] [INFO] Task started: HMMsearch
[2023-03-17 06:30:57,344] [INFO] Running command: hmmsearch --tblout OceanDNA-b42542/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1c6671f-e04f-4112-bffb-1f0ba2eb231b/dqc_reference/reference_markers.hmm OceanDNA-b42542/protein.faa > /dev/null
[2023-03-17 06:30:57,482] [INFO] Task succeeded: HMMsearch
[2023-03-17 06:30:57,483] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0da00b60-571f-445d-a29a-f0ef66e696b0/OceanDNA-b42542.fa]
[2023-03-17 06:30:57,493] [INFO] Query marker FASTA was written to OceanDNA-b42542/markers.fasta
[2023-03-17 06:30:57,493] [INFO] Task started: Blastn
[2023-03-17 06:30:57,493] [INFO] Running command: blastn -query OceanDNA-b42542/markers.fasta -db /var/lib/cwl/stga1c6671f-e04f-4112-bffb-1f0ba2eb231b/dqc_reference/reference_markers.fasta -out OceanDNA-b42542/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:30:57,977] [INFO] Task succeeded: Blastn
[2023-03-17 06:30:57,978] [INFO] Selected 10 target genomes.
[2023-03-17 06:30:57,978] [INFO] Target genome list was writen to OceanDNA-b42542/target_genomes.txt
[2023-03-17 06:30:57,983] [INFO] Task started: fastANI
[2023-03-17 06:30:57,983] [INFO] Running command: fastANI --query /var/lib/cwl/stg0da00b60-571f-445d-a29a-f0ef66e696b0/OceanDNA-b42542.fa --refList OceanDNA-b42542/target_genomes.txt --output OceanDNA-b42542/fastani_result.tsv --threads 1
[2023-03-17 06:31:03,241] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:03,242] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1c6671f-e04f-4112-bffb-1f0ba2eb231b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 06:31:03,242] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1c6671f-e04f-4112-bffb-1f0ba2eb231b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 06:31:03,242] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 06:31:03,242] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 06:31:03,242] [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 06:31:03,242] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42542/tc_result.tsv
[2023-03-17 06:31:03,243] [INFO] ===== Taxonomy check completed =====
[2023-03-17 06:31:03,243] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 06:31:03,243] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1c6671f-e04f-4112-bffb-1f0ba2eb231b/dqc_reference/checkm_data
[2023-03-17 06:31:03,253] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 06:31:03,312] [INFO] Task started: CheckM
[2023-03-17 06:31:03,312] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42542/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42542/checkm_input OceanDNA-b42542/checkm_result
[2023-03-17 06:31:25,163] [INFO] Task succeeded: CheckM
[2023-03-17 06:31:25,164] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 06:31:25,166] [INFO] ===== Completeness check finished =====
[2023-03-17 06:31:25,166] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:31:25,166] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42542/markers.fasta)
[2023-03-17 06:31:25,166] [INFO] Task started: Blastn
[2023-03-17 06:31:25,166] [INFO] Running command: blastn -query OceanDNA-b42542/markers.fasta -db /var/lib/cwl/stga1c6671f-e04f-4112-bffb-1f0ba2eb231b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42542/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:31:25,850] [INFO] Task succeeded: Blastn
[2023-03-17 06:31:25,851] [INFO] Selected 15 target genomes.
[2023-03-17 06:31:25,851] [INFO] Target genome list was writen to OceanDNA-b42542/target_genomes_gtdb.txt
[2023-03-17 06:31:26,144] [INFO] Task started: fastANI
[2023-03-17 06:31:26,144] [INFO] Running command: fastANI --query /var/lib/cwl/stg0da00b60-571f-445d-a29a-f0ef66e696b0/OceanDNA-b42542.fa --refList OceanDNA-b42542/target_genomes_gtdb.txt --output OceanDNA-b42542/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:31:29,520] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:29,527] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 06:31:29,528] [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_016777005.1	s__GCA-2707915 sp016777005	97.9144	284	386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004214065.1	s__GCA-2707915 sp004214065	77.9645	112	386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	97.49	97.45	0.77	0.70	3	-
GCA_902604855.1	s__GCA-2707915 sp902604855	77.9639	106	386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902542325.1	s__GCA-2707915 sp902542325	77.7726	108	386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	99.62	99.62	0.80	0.80	2	-
GCA_902517565.1	s__GCA-2707915 sp902517565	77.7721	107	386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003212335.1	s__GCA-2707915 sp003212335	77.7692	136	386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	96.12	95.05	0.82	0.77	11	-
GCA_902606175.1	s__GCA-2707915 sp902606175	77.605	116	386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	95.24	95.17	0.72	0.71	3	-
GCA_902574355.1	s__GCA-2707915 sp902574355	77.4996	123	386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902620785.1	s__GCA-2707915 sp902620785	77.4945	124	386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	95.48	95.02	0.87	0.85	6	-
GCA_902594545.1	s__GCA-2707915 sp902594545	77.2311	92	386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	99.77	99.77	0.82	0.82	2	-
GCA_902532675.1	s__GCA-2730855 sp902532675	76.7335	69	386	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2730855	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 06:31:29,528] [INFO] GTDB search result was written to OceanDNA-b42542/result_gtdb.tsv
[2023-03-17 06:31:29,528] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:31:29,529] [INFO] DFAST_QC result json was written to OceanDNA-b42542/dqc_result.json
[2023-03-17 06:31:29,529] [INFO] DFAST_QC completed!
[2023-03-17 06:31:29,529] [INFO] Total running time: 0h0m40s