[2023-03-18 01:26:26,355] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:26:26,355] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:26:26,355] [INFO] DQC Reference Directory: /var/lib/cwl/stg06585b58-8643-428f-8eaf-bcbb943c605a/dqc_reference
[2023-03-18 01:26:27,583] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:26:27,583] [INFO] Task started: Prodigal
[2023-03-18 01:26:27,583] [INFO] Running command: cat /var/lib/cwl/stgc1b12814-4c40-4602-b947-409e1ceca8aa/OceanDNA-b36831.fa | prodigal -d OceanDNA-b36831/cds.fna -a OceanDNA-b36831/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:26:39,805] [INFO] Task succeeded: Prodigal
[2023-03-18 01:26:39,806] [INFO] Task started: HMMsearch
[2023-03-18 01:26:39,806] [INFO] Running command: hmmsearch --tblout OceanDNA-b36831/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06585b58-8643-428f-8eaf-bcbb943c605a/dqc_reference/reference_markers.hmm OceanDNA-b36831/protein.faa > /dev/null
[2023-03-18 01:26:40,064] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:26:40,064] [INFO] Found 6/6 markers.
[2023-03-18 01:26:40,083] [INFO] Query marker FASTA was written to OceanDNA-b36831/markers.fasta
[2023-03-18 01:26:40,086] [INFO] Task started: Blastn
[2023-03-18 01:26:40,086] [INFO] Running command: blastn -query OceanDNA-b36831/markers.fasta -db /var/lib/cwl/stg06585b58-8643-428f-8eaf-bcbb943c605a/dqc_reference/reference_markers.fasta -out OceanDNA-b36831/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:26:40,665] [INFO] Task succeeded: Blastn
[2023-03-18 01:26:40,666] [INFO] Selected 22 target genomes.
[2023-03-18 01:26:40,666] [INFO] Target genome list was writen to OceanDNA-b36831/target_genomes.txt
[2023-03-18 01:26:40,735] [INFO] Task started: fastANI
[2023-03-18 01:26:40,735] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1b12814-4c40-4602-b947-409e1ceca8aa/OceanDNA-b36831.fa --refList OceanDNA-b36831/target_genomes.txt --output OceanDNA-b36831/fastani_result.tsv --threads 1
[2023-03-18 01:26:54,468] [INFO] Task succeeded: fastANI
[2023-03-18 01:26:54,469] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06585b58-8643-428f-8eaf-bcbb943c605a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:26:54,469] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06585b58-8643-428f-8eaf-bcbb943c605a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:26:54,469] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:26:54,469] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:26:54,469] [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
--------------------------------------------------------------------------------
[2023-03-18 01:26:54,469] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36831/tc_result.tsv
[2023-03-18 01:26:54,470] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:26:54,470] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:26:54,470] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06585b58-8643-428f-8eaf-bcbb943c605a/dqc_reference/checkm_data
[2023-03-18 01:26:54,474] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:26:54,478] [INFO] Task started: CheckM
[2023-03-18 01:26:54,478] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36831/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36831/checkm_input OceanDNA-b36831/checkm_result
[2023-03-18 01:27:29,346] [INFO] Task succeeded: CheckM
[2023-03-18 01:27:29,346] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.09%
Contamintation: 6.71%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 01:27:29,348] [INFO] ===== Completeness check finished =====
[2023-03-18 01:27:29,349] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:27:29,349] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36831/markers.fasta)
[2023-03-18 01:27:29,350] [INFO] Task started: Blastn
[2023-03-18 01:27:29,350] [INFO] Running command: blastn -query OceanDNA-b36831/markers.fasta -db /var/lib/cwl/stg06585b58-8643-428f-8eaf-bcbb943c605a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36831/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:27:30,327] [INFO] Task succeeded: Blastn
[2023-03-18 01:27:30,328] [INFO] Selected 20 target genomes.
[2023-03-18 01:27:30,328] [INFO] Target genome list was writen to OceanDNA-b36831/target_genomes_gtdb.txt
[2023-03-18 01:27:30,355] [INFO] Task started: fastANI
[2023-03-18 01:27:30,355] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1b12814-4c40-4602-b947-409e1ceca8aa/OceanDNA-b36831.fa --refList OceanDNA-b36831/target_genomes_gtdb.txt --output OceanDNA-b36831/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:27:40,063] [INFO] Task succeeded: fastANI
[2023-03-18 01:27:40,066] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:27:40,066] [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_002719135.1	s__UBA11889 sp002719135	91.4417	451	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA11889	95.0	98.11	97.65	0.74	0.72	3	-
GCA_002313255.1	s__UBA11889 sp002313255	91.3784	592	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA11889	95.0	98.77	98.77	0.86	0.86	2	-
GCA_002715785.1	s__UBA11889 sp002715785	83.5688	465	671	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA11889	95.0	99.18	99.12	0.79	0.76	3	-
--------------------------------------------------------------------------------
[2023-03-18 01:27:40,067] [INFO] GTDB search result was written to OceanDNA-b36831/result_gtdb.tsv
[2023-03-18 01:27:40,067] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:27:40,067] [INFO] DFAST_QC result json was written to OceanDNA-b36831/dqc_result.json
[2023-03-18 01:27:40,067] [INFO] DFAST_QC completed!
[2023-03-18 01:27:40,068] [INFO] Total running time: 0h1m14s