[2023-03-18 08:36:16,000] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:36:16,001] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:36:16,001] [INFO] DQC Reference Directory: /var/lib/cwl/stg62f450fc-bbb2-4be9-adc6-1b6fda639bd3/dqc_reference
[2023-03-18 08:36:17,822] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:36:17,823] [INFO] Task started: Prodigal
[2023-03-18 08:36:17,823] [INFO] Running command: cat /var/lib/cwl/stgb18b4485-6a3d-4b99-b1cc-33b3c6b50c06/OceanDNA-b2563.fa | prodigal -d OceanDNA-b2563/cds.fna -a OceanDNA-b2563/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:36:24,558] [INFO] Task succeeded: Prodigal
[2023-03-18 08:36:24,558] [INFO] Task started: HMMsearch
[2023-03-18 08:36:24,558] [INFO] Running command: hmmsearch --tblout OceanDNA-b2563/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62f450fc-bbb2-4be9-adc6-1b6fda639bd3/dqc_reference/reference_markers.hmm OceanDNA-b2563/protein.faa > /dev/null
[2023-03-18 08:36:24,730] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:36:24,731] [INFO] Found 6/6 markers.
[2023-03-18 08:36:24,740] [INFO] Query marker FASTA was written to OceanDNA-b2563/markers.fasta
[2023-03-18 08:36:24,740] [INFO] Task started: Blastn
[2023-03-18 08:36:24,740] [INFO] Running command: blastn -query OceanDNA-b2563/markers.fasta -db /var/lib/cwl/stg62f450fc-bbb2-4be9-adc6-1b6fda639bd3/dqc_reference/reference_markers.fasta -out OceanDNA-b2563/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:36:25,283] [INFO] Task succeeded: Blastn
[2023-03-18 08:36:25,285] [INFO] Selected 21 target genomes.
[2023-03-18 08:36:25,285] [INFO] Target genome list was writen to OceanDNA-b2563/target_genomes.txt
[2023-03-18 08:36:25,302] [INFO] Task started: fastANI
[2023-03-18 08:36:25,302] [INFO] Running command: fastANI --query /var/lib/cwl/stgb18b4485-6a3d-4b99-b1cc-33b3c6b50c06/OceanDNA-b2563.fa --refList OceanDNA-b2563/target_genomes.txt --output OceanDNA-b2563/fastani_result.tsv --threads 1
[2023-03-18 08:36:40,818] [INFO] Task succeeded: fastANI
[2023-03-18 08:36:40,818] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62f450fc-bbb2-4be9-adc6-1b6fda639bd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:36:40,819] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62f450fc-bbb2-4be9-adc6-1b6fda639bd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:36:40,819] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:36:40,819] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 08:36:40,819] [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
--------------------------------------------------------------------------------
[2023-03-18 08:36:40,819] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2563/tc_result.tsv
[2023-03-18 08:36:40,819] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:36:40,819] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:36:40,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62f450fc-bbb2-4be9-adc6-1b6fda639bd3/dqc_reference/checkm_data
[2023-03-18 08:36:40,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:36:40,826] [INFO] Task started: CheckM
[2023-03-18 08:36:40,826] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2563/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2563/checkm_input OceanDNA-b2563/checkm_result
[2023-03-18 08:37:03,302] [INFO] Task succeeded: CheckM
[2023-03-18 08:37:03,303] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:37:03,308] [INFO] ===== Completeness check finished =====
[2023-03-18 08:37:03,308] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:37:03,309] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2563/markers.fasta)
[2023-03-18 08:37:03,309] [INFO] Task started: Blastn
[2023-03-18 08:37:03,309] [INFO] Running command: blastn -query OceanDNA-b2563/markers.fasta -db /var/lib/cwl/stg62f450fc-bbb2-4be9-adc6-1b6fda639bd3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2563/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:37:04,064] [INFO] Task succeeded: Blastn
[2023-03-18 08:37:04,073] [INFO] Selected 22 target genomes.
[2023-03-18 08:37:04,073] [INFO] Target genome list was writen to OceanDNA-b2563/target_genomes_gtdb.txt
[2023-03-18 08:37:04,122] [INFO] Task started: fastANI
[2023-03-18 08:37:04,122] [INFO] Running command: fastANI --query /var/lib/cwl/stgb18b4485-6a3d-4b99-b1cc-33b3c6b50c06/OceanDNA-b2563.fa --refList OceanDNA-b2563/target_genomes_gtdb.txt --output OceanDNA-b2563/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:37:14,202] [INFO] Task succeeded: fastANI
[2023-03-18 08:37:14,206] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:37:14,206] [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_009704945.1	s__Aquiluna sp009704945	80.1042	150	380	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aquiluna	95.0	98.46	98.46	0.89	0.89	2	-
GCA_018402685.1	s__Aquiluna sp018402685	77.338	67	380	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aquiluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002333405.1	s__Aquiluna sp002333405	76.985	51	380	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aquiluna	95.0	97.62	97.20	0.92	0.89	8	-
--------------------------------------------------------------------------------
[2023-03-18 08:37:14,208] [INFO] GTDB search result was written to OceanDNA-b2563/result_gtdb.tsv
[2023-03-18 08:37:14,212] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:37:14,214] [INFO] DFAST_QC result json was written to OceanDNA-b2563/dqc_result.json
[2023-03-18 08:37:14,214] [INFO] DFAST_QC completed!
[2023-03-18 08:37:14,214] [INFO] Total running time: 0h0m58s