[2023-03-14 13:40:21,109] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:40:21,109] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:40:21,109] [INFO] DQC Reference Directory: /var/lib/cwl/stg84a7f10a-6fd2-4d23-bc4c-293ff1e9f41a/dqc_reference
[2023-03-14 13:40:22,259] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:40:22,260] [INFO] Task started: Prodigal
[2023-03-14 13:40:22,261] [INFO] Running command: cat /var/lib/cwl/stgbf9bde16-47c7-4417-b351-8d4dd0e7c21c/OceanDNA-b46656.fa | prodigal -d OceanDNA-b46656/cds.fna -a OceanDNA-b46656/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:40:55,329] [INFO] Task succeeded: Prodigal
[2023-03-14 13:40:55,330] [INFO] Task started: HMMsearch
[2023-03-14 13:40:55,330] [INFO] Running command: hmmsearch --tblout OceanDNA-b46656/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84a7f10a-6fd2-4d23-bc4c-293ff1e9f41a/dqc_reference/reference_markers.hmm OceanDNA-b46656/protein.faa > /dev/null
[2023-03-14 13:40:55,631] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:40:55,632] [INFO] Found 6/6 markers.
[2023-03-14 13:40:55,666] [INFO] Query marker FASTA was written to OceanDNA-b46656/markers.fasta
[2023-03-14 13:40:55,668] [INFO] Task started: Blastn
[2023-03-14 13:40:55,668] [INFO] Running command: blastn -query OceanDNA-b46656/markers.fasta -db /var/lib/cwl/stg84a7f10a-6fd2-4d23-bc4c-293ff1e9f41a/dqc_reference/reference_markers.fasta -out OceanDNA-b46656/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:40:56,358] [INFO] Task succeeded: Blastn
[2023-03-14 13:40:56,359] [INFO] Selected 22 target genomes.
[2023-03-14 13:40:56,360] [INFO] Target genome list was writen to OceanDNA-b46656/target_genomes.txt
[2023-03-14 13:40:56,373] [INFO] Task started: fastANI
[2023-03-14 13:40:56,373] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf9bde16-47c7-4417-b351-8d4dd0e7c21c/OceanDNA-b46656.fa --refList OceanDNA-b46656/target_genomes.txt --output OceanDNA-b46656/fastani_result.tsv --threads 1
[2023-03-14 13:41:23,281] [INFO] Task succeeded: fastANI
[2023-03-14 13:41:23,282] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84a7f10a-6fd2-4d23-bc4c-293ff1e9f41a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:41:23,282] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84a7f10a-6fd2-4d23-bc4c-293ff1e9f41a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:41:23,282] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:41:23,282] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:41:23,282] [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
--------------------------------------------------------------------------------
[2023-03-14 13:41:23,506] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46656/tc_result.tsv
[2023-03-14 13:41:23,510] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:41:23,510] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:41:23,510] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84a7f10a-6fd2-4d23-bc4c-293ff1e9f41a/dqc_reference/checkm_data
[2023-03-14 13:41:23,515] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:41:23,579] [INFO] Task started: CheckM
[2023-03-14 13:41:23,579] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46656/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46656/checkm_input OceanDNA-b46656/checkm_result
[2023-03-14 13:42:54,450] [INFO] Task succeeded: CheckM
[2023-03-14 13:42:54,450] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.15%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:42:54,460] [INFO] ===== Completeness check finished =====
[2023-03-14 13:42:54,460] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:42:54,461] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46656/markers.fasta)
[2023-03-14 13:42:54,462] [INFO] Task started: Blastn
[2023-03-14 13:42:54,462] [INFO] Running command: blastn -query OceanDNA-b46656/markers.fasta -db /var/lib/cwl/stg84a7f10a-6fd2-4d23-bc4c-293ff1e9f41a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46656/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:42:55,374] [INFO] Task succeeded: Blastn
[2023-03-14 13:42:55,379] [INFO] Selected 25 target genomes.
[2023-03-14 13:42:55,379] [INFO] Target genome list was writen to OceanDNA-b46656/target_genomes_gtdb.txt
[2023-03-14 13:42:55,403] [INFO] Task started: fastANI
[2023-03-14 13:42:55,403] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf9bde16-47c7-4417-b351-8d4dd0e7c21c/OceanDNA-b46656.fa --refList OceanDNA-b46656/target_genomes_gtdb.txt --output OceanDNA-b46656/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:43:10,380] [INFO] Task succeeded: fastANI
[2023-03-14 13:43:10,384] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 13:43:10,385] [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_002501065.1	s__Roseibacillus_B sp002501065	77.9678	234	951	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	99.61	99.55	0.90	0.89	3	-
GCA_014240355.1	s__Roseibacillus_B sp014240355	77.6073	132	951	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003483645.1	s__Roseibacillus_B sp003483645	77.3369	128	951	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001695.1	s__Roseibacillus_B sp013001695	76.618	108	951	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721695.1	s__Roseibacillus_B sp002721695	76.448	127	951	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:43:10,386] [INFO] GTDB search result was written to OceanDNA-b46656/result_gtdb.tsv
[2023-03-14 13:43:10,388] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:43:10,390] [INFO] DFAST_QC result json was written to OceanDNA-b46656/dqc_result.json
[2023-03-14 13:43:10,390] [INFO] DFAST_QC completed!
[2023-03-14 13:43:10,390] [INFO] Total running time: 0h2m49s