[2023-03-17 02:31:12,876] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:31:12,876] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:31:12,876] [INFO] DQC Reference Directory: /var/lib/cwl/stg038a52a2-5933-4d7a-9a25-8b95f7957c4c/dqc_reference
[2023-03-17 02:31:14,379] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:31:14,379] [INFO] Task started: Prodigal
[2023-03-17 02:31:14,379] [INFO] Running command: cat /var/lib/cwl/stg575f776d-c813-4f8c-ab94-c6383200b1ac/OceanDNA-b23037.fa | prodigal -d OceanDNA-b23037/cds.fna -a OceanDNA-b23037/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:31:23,059] [INFO] Task succeeded: Prodigal
[2023-03-17 02:31:23,060] [INFO] Task started: HMMsearch
[2023-03-17 02:31:23,060] [INFO] Running command: hmmsearch --tblout OceanDNA-b23037/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg038a52a2-5933-4d7a-9a25-8b95f7957c4c/dqc_reference/reference_markers.hmm OceanDNA-b23037/protein.faa > /dev/null
[2023-03-17 02:31:23,194] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:31:23,195] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg575f776d-c813-4f8c-ab94-c6383200b1ac/OceanDNA-b23037.fa]
[2023-03-17 02:31:23,208] [INFO] Query marker FASTA was written to OceanDNA-b23037/markers.fasta
[2023-03-17 02:31:23,208] [INFO] Task started: Blastn
[2023-03-17 02:31:23,208] [INFO] Running command: blastn -query OceanDNA-b23037/markers.fasta -db /var/lib/cwl/stg038a52a2-5933-4d7a-9a25-8b95f7957c4c/dqc_reference/reference_markers.fasta -out OceanDNA-b23037/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:31:23,719] [INFO] Task succeeded: Blastn
[2023-03-17 02:31:23,720] [INFO] Selected 10 target genomes.
[2023-03-17 02:31:23,720] [INFO] Target genome list was writen to OceanDNA-b23037/target_genomes.txt
[2023-03-17 02:31:23,727] [INFO] Task started: fastANI
[2023-03-17 02:31:23,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg575f776d-c813-4f8c-ab94-c6383200b1ac/OceanDNA-b23037.fa --refList OceanDNA-b23037/target_genomes.txt --output OceanDNA-b23037/fastani_result.tsv --threads 1
[2023-03-17 02:31:30,158] [INFO] Task succeeded: fastANI
[2023-03-17 02:31:30,158] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg038a52a2-5933-4d7a-9a25-8b95f7957c4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:31:30,159] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg038a52a2-5933-4d7a-9a25-8b95f7957c4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:31:30,159] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:31:30,159] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 02:31:30,159] [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 02:31:30,159] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23037/tc_result.tsv
[2023-03-17 02:31:30,159] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:31:30,159] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:31:30,159] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg038a52a2-5933-4d7a-9a25-8b95f7957c4c/dqc_reference/checkm_data
[2023-03-17 02:31:30,162] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:31:30,165] [INFO] Task started: CheckM
[2023-03-17 02:31:30,166] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23037/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23037/checkm_input OceanDNA-b23037/checkm_result
[2023-03-17 02:31:56,347] [INFO] Task succeeded: CheckM
[2023-03-17 02:31:56,347] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.99%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 02:31:56,355] [INFO] ===== Completeness check finished =====
[2023-03-17 02:31:56,355] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:31:56,356] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23037/markers.fasta)
[2023-03-17 02:31:56,357] [INFO] Task started: Blastn
[2023-03-17 02:31:56,357] [INFO] Running command: blastn -query OceanDNA-b23037/markers.fasta -db /var/lib/cwl/stg038a52a2-5933-4d7a-9a25-8b95f7957c4c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23037/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:31:57,065] [INFO] Task succeeded: Blastn
[2023-03-17 02:31:57,066] [INFO] Selected 8 target genomes.
[2023-03-17 02:31:57,066] [INFO] Target genome list was writen to OceanDNA-b23037/target_genomes_gtdb.txt
[2023-03-17 02:31:57,370] [INFO] Task started: fastANI
[2023-03-17 02:31:57,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg575f776d-c813-4f8c-ab94-c6383200b1ac/OceanDNA-b23037.fa --refList OceanDNA-b23037/target_genomes_gtdb.txt --output OceanDNA-b23037/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:32:02,695] [INFO] Task succeeded: fastANI
[2023-03-17 02:32:02,698] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 02:32:02,698] [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_011524785.1	s__GCA-2686945 sp011524785	95.3768	73	73	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2686945	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016779225.1	s__GCA-2686945 sp016779225	84.4664	55	73	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2686945	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:32:02,698] [INFO] GTDB search result was written to OceanDNA-b23037/result_gtdb.tsv
[2023-03-17 02:32:02,698] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:32:02,699] [INFO] DFAST_QC result json was written to OceanDNA-b23037/dqc_result.json
[2023-03-17 02:32:02,699] [INFO] DFAST_QC completed!
[2023-03-17 02:32:02,699] [INFO] Total running time: 0h0m50s