[2023-03-19 00:51:14,089] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:51:14,089] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:51:14,090] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e1de601-f7c6-4063-9fc0-5883c67f7569/dqc_reference
[2023-03-19 00:51:15,251] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:51:15,252] [INFO] Task started: Prodigal
[2023-03-19 00:51:15,252] [INFO] Running command: cat /var/lib/cwl/stg63cccab8-5c5c-4ce7-99b2-4cc511df4a33/OceanDNA-b36832.fa | prodigal -d OceanDNA-b36832/cds.fna -a OceanDNA-b36832/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:51:23,561] [INFO] Task succeeded: Prodigal
[2023-03-19 00:51:23,561] [INFO] Task started: HMMsearch
[2023-03-19 00:51:23,561] [INFO] Running command: hmmsearch --tblout OceanDNA-b36832/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e1de601-f7c6-4063-9fc0-5883c67f7569/dqc_reference/reference_markers.hmm OceanDNA-b36832/protein.faa > /dev/null
[2023-03-19 00:51:23,739] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:51:23,739] [INFO] Found 6/6 markers.
[2023-03-19 00:51:23,753] [INFO] Query marker FASTA was written to OceanDNA-b36832/markers.fasta
[2023-03-19 00:51:23,753] [INFO] Task started: Blastn
[2023-03-19 00:51:23,753] [INFO] Running command: blastn -query OceanDNA-b36832/markers.fasta -db /var/lib/cwl/stg5e1de601-f7c6-4063-9fc0-5883c67f7569/dqc_reference/reference_markers.fasta -out OceanDNA-b36832/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:51:24,317] [INFO] Task succeeded: Blastn
[2023-03-19 00:51:24,318] [INFO] Selected 21 target genomes.
[2023-03-19 00:51:24,318] [INFO] Target genome list was writen to OceanDNA-b36832/target_genomes.txt
[2023-03-19 00:51:24,334] [INFO] Task started: fastANI
[2023-03-19 00:51:24,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg63cccab8-5c5c-4ce7-99b2-4cc511df4a33/OceanDNA-b36832.fa --refList OceanDNA-b36832/target_genomes.txt --output OceanDNA-b36832/fastani_result.tsv --threads 1
[2023-03-19 00:51:34,818] [INFO] Task succeeded: fastANI
[2023-03-19 00:51:34,818] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e1de601-f7c6-4063-9fc0-5883c67f7569/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:51:34,818] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e1de601-f7c6-4063-9fc0-5883c67f7569/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:51:34,818] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:51:34,818] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:51:34,819] [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
--------------------------------------------------------------------------------
[2023-03-19 00:51:34,819] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36832/tc_result.tsv
[2023-03-19 00:51:34,819] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:51:34,819] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:51:34,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e1de601-f7c6-4063-9fc0-5883c67f7569/dqc_reference/checkm_data
[2023-03-19 00:51:34,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:51:35,020] [INFO] Task started: CheckM
[2023-03-19 00:51:35,020] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36832/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36832/checkm_input OceanDNA-b36832/checkm_result
[2023-03-19 00:52:00,678] [INFO] Task succeeded: CheckM
[2023-03-19 00:52:00,679] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:52:00,681] [INFO] ===== Completeness check finished =====
[2023-03-19 00:52:00,681] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:52:00,681] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36832/markers.fasta)
[2023-03-19 00:52:00,682] [INFO] Task started: Blastn
[2023-03-19 00:52:00,682] [INFO] Running command: blastn -query OceanDNA-b36832/markers.fasta -db /var/lib/cwl/stg5e1de601-f7c6-4063-9fc0-5883c67f7569/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36832/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:52:01,580] [INFO] Task succeeded: Blastn
[2023-03-19 00:52:01,581] [INFO] Selected 20 target genomes.
[2023-03-19 00:52:01,581] [INFO] Target genome list was writen to OceanDNA-b36832/target_genomes_gtdb.txt
[2023-03-19 00:52:01,594] [INFO] Task started: fastANI
[2023-03-19 00:52:01,594] [INFO] Running command: fastANI --query /var/lib/cwl/stg63cccab8-5c5c-4ce7-99b2-4cc511df4a33/OceanDNA-b36832.fa --refList OceanDNA-b36832/target_genomes_gtdb.txt --output OceanDNA-b36832/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:52:12,156] [INFO] Task succeeded: fastANI
[2023-03-19 00:52:12,159] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:52:12,159] [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_002313255.1	s__UBA11889 sp002313255	82.609	371	443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA11889	95.0	98.77	98.77	0.86	0.86	2	-
GCA_002719135.1	s__UBA11889 sp002719135	82.1904	293	443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA11889	95.0	98.11	97.65	0.74	0.72	3	-
GCA_002715785.1	s__UBA11889 sp002715785	80.2143	269	443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA11889	95.0	99.18	99.12	0.79	0.76	3	-
--------------------------------------------------------------------------------
[2023-03-19 00:52:12,160] [INFO] GTDB search result was written to OceanDNA-b36832/result_gtdb.tsv
[2023-03-19 00:52:12,160] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:52:12,161] [INFO] DFAST_QC result json was written to OceanDNA-b36832/dqc_result.json
[2023-03-19 00:52:12,161] [INFO] DFAST_QC completed!
[2023-03-19 00:52:12,161] [INFO] Total running time: 0h0m58s