[2023-03-15 11:20:30,899] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:20:30,899] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:20:30,899] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f133306-5c51-4af4-9fef-058316387c35/dqc_reference
[2023-03-15 11:20:31,996] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:20:31,996] [INFO] Task started: Prodigal
[2023-03-15 11:20:31,996] [INFO] Running command: cat /var/lib/cwl/stg67c3d4dc-53c2-4584-b731-4b7763dada2c/OceanDNA-b11122.fa | prodigal -d OceanDNA-b11122/cds.fna -a OceanDNA-b11122/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:20:40,582] [INFO] Task succeeded: Prodigal
[2023-03-15 11:20:40,583] [INFO] Task started: HMMsearch
[2023-03-15 11:20:40,583] [INFO] Running command: hmmsearch --tblout OceanDNA-b11122/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f133306-5c51-4af4-9fef-058316387c35/dqc_reference/reference_markers.hmm OceanDNA-b11122/protein.faa > /dev/null
[2023-03-15 11:20:40,750] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:20:40,751] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg67c3d4dc-53c2-4584-b731-4b7763dada2c/OceanDNA-b11122.fa]
[2023-03-15 11:20:40,767] [INFO] Query marker FASTA was written to OceanDNA-b11122/markers.fasta
[2023-03-15 11:20:40,767] [INFO] Task started: Blastn
[2023-03-15 11:20:40,767] [INFO] Running command: blastn -query OceanDNA-b11122/markers.fasta -db /var/lib/cwl/stg5f133306-5c51-4af4-9fef-058316387c35/dqc_reference/reference_markers.fasta -out OceanDNA-b11122/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:20:41,299] [INFO] Task succeeded: Blastn
[2023-03-15 11:20:41,301] [INFO] Selected 24 target genomes.
[2023-03-15 11:20:41,301] [INFO] Target genome list was writen to OceanDNA-b11122/target_genomes.txt
[2023-03-15 11:20:41,319] [INFO] Task started: fastANI
[2023-03-15 11:20:41,319] [INFO] Running command: fastANI --query /var/lib/cwl/stg67c3d4dc-53c2-4584-b731-4b7763dada2c/OceanDNA-b11122.fa --refList OceanDNA-b11122/target_genomes.txt --output OceanDNA-b11122/fastani_result.tsv --threads 1
[2023-03-15 11:20:54,808] [INFO] Task succeeded: fastANI
[2023-03-15 11:20:54,808] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f133306-5c51-4af4-9fef-058316387c35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:20:54,808] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f133306-5c51-4af4-9fef-058316387c35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:20:54,809] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:20:54,809] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 11:20:54,809] [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
--------------------------------------------------------------------------------
[2023-03-15 11:20:54,810] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11122/tc_result.tsv
[2023-03-15 11:20:54,810] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:20:54,810] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:20:54,810] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f133306-5c51-4af4-9fef-058316387c35/dqc_reference/checkm_data
[2023-03-15 11:20:54,813] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:20:54,819] [INFO] Task started: CheckM
[2023-03-15 11:20:54,819] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11122/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11122/checkm_input OceanDNA-b11122/checkm_result
[2023-03-15 11:21:21,018] [INFO] Task succeeded: CheckM
[2023-03-15 11:21:21,018] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:21:21,097] [INFO] ===== Completeness check finished =====
[2023-03-15 11:21:21,097] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:21:21,097] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11122/markers.fasta)
[2023-03-15 11:21:21,098] [INFO] Task started: Blastn
[2023-03-15 11:21:21,098] [INFO] Running command: blastn -query OceanDNA-b11122/markers.fasta -db /var/lib/cwl/stg5f133306-5c51-4af4-9fef-058316387c35/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11122/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:21:21,849] [INFO] Task succeeded: Blastn
[2023-03-15 11:21:21,850] [INFO] Selected 6 target genomes.
[2023-03-15 11:21:21,850] [INFO] Target genome list was writen to OceanDNA-b11122/target_genomes_gtdb.txt
[2023-03-15 11:21:21,854] [INFO] Task started: fastANI
[2023-03-15 11:21:21,854] [INFO] Running command: fastANI --query /var/lib/cwl/stg67c3d4dc-53c2-4584-b731-4b7763dada2c/OceanDNA-b11122.fa --refList OceanDNA-b11122/target_genomes_gtdb.txt --output OceanDNA-b11122/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:21:23,802] [INFO] Task succeeded: fastANI
[2023-03-15 11:21:23,806] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:21:23,806] [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_002698745.1	s__UBA7446 sp002698745	97.6073	316	382	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009886265.1	s__UBA7446 sp009886265	86.7235	265	382	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862705.1	s__UBA7446 sp002862705	84.3602	283	382	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	99.06	98.27	0.87	0.83	14	-
GCA_002862645.1	s__UBA7446 sp002862645	83.7872	268	382	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	95.15	95.15	0.79	0.79	2	-
GCA_002313325.1	s__UBA7446 sp002313325	83.7428	213	382	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	99.90	99.90	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-15 11:21:23,808] [INFO] GTDB search result was written to OceanDNA-b11122/result_gtdb.tsv
[2023-03-15 11:21:23,809] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:21:23,811] [INFO] DFAST_QC result json was written to OceanDNA-b11122/dqc_result.json
[2023-03-15 11:21:23,812] [INFO] DFAST_QC completed!
[2023-03-15 11:21:23,812] [INFO] Total running time: 0h0m53s