[2023-03-19 01:50:01,538] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:50:01,538] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:50:01,539] [INFO] DQC Reference Directory: /var/lib/cwl/stg8fc0096e-4f2e-4cd3-975c-c73a93d966eb/dqc_reference
[2023-03-19 01:50:02,653] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:50:02,654] [INFO] Task started: Prodigal
[2023-03-19 01:50:02,654] [INFO] Running command: cat /var/lib/cwl/stga6263ae5-154c-4932-98fc-28e0d59dc108/OceanDNA-b17059.fa | prodigal -d OceanDNA-b17059/cds.fna -a OceanDNA-b17059/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:50:08,503] [INFO] Task succeeded: Prodigal
[2023-03-19 01:50:08,503] [INFO] Task started: HMMsearch
[2023-03-19 01:50:08,503] [INFO] Running command: hmmsearch --tblout OceanDNA-b17059/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8fc0096e-4f2e-4cd3-975c-c73a93d966eb/dqc_reference/reference_markers.hmm OceanDNA-b17059/protein.faa > /dev/null
[2023-03-19 01:50:08,671] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:50:08,672] [INFO] Found 6/6 markers.
[2023-03-19 01:50:08,679] [INFO] Query marker FASTA was written to OceanDNA-b17059/markers.fasta
[2023-03-19 01:50:08,680] [INFO] Task started: Blastn
[2023-03-19 01:50:08,680] [INFO] Running command: blastn -query OceanDNA-b17059/markers.fasta -db /var/lib/cwl/stg8fc0096e-4f2e-4cd3-975c-c73a93d966eb/dqc_reference/reference_markers.fasta -out OceanDNA-b17059/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:50:09,190] [INFO] Task succeeded: Blastn
[2023-03-19 01:50:09,191] [INFO] Selected 16 target genomes.
[2023-03-19 01:50:09,191] [INFO] Target genome list was writen to OceanDNA-b17059/target_genomes.txt
[2023-03-19 01:50:09,202] [INFO] Task started: fastANI
[2023-03-19 01:50:09,202] [INFO] Running command: fastANI --query /var/lib/cwl/stga6263ae5-154c-4932-98fc-28e0d59dc108/OceanDNA-b17059.fa --refList OceanDNA-b17059/target_genomes.txt --output OceanDNA-b17059/fastani_result.tsv --threads 1
[2023-03-19 01:50:17,287] [INFO] Task succeeded: fastANI
[2023-03-19 01:50:17,288] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8fc0096e-4f2e-4cd3-975c-c73a93d966eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:50:17,288] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8fc0096e-4f2e-4cd3-975c-c73a93d966eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:50:17,288] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:50:17,288] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 01:50:17,288] [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 01:50:17,289] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17059/tc_result.tsv
[2023-03-19 01:50:17,289] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:50:17,289] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:50:17,289] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8fc0096e-4f2e-4cd3-975c-c73a93d966eb/dqc_reference/checkm_data
[2023-03-19 01:50:17,291] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:50:17,294] [INFO] Task started: CheckM
[2023-03-19 01:50:17,294] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17059/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17059/checkm_input OceanDNA-b17059/checkm_result
[2023-03-19 01:50:37,241] [INFO] Task succeeded: CheckM
[2023-03-19 01:50:37,241] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:50:37,242] [INFO] ===== Completeness check finished =====
[2023-03-19 01:50:37,243] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:50:37,243] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17059/markers.fasta)
[2023-03-19 01:50:37,243] [INFO] Task started: Blastn
[2023-03-19 01:50:37,243] [INFO] Running command: blastn -query OceanDNA-b17059/markers.fasta -db /var/lib/cwl/stg8fc0096e-4f2e-4cd3-975c-c73a93d966eb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17059/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:50:37,953] [INFO] Task succeeded: Blastn
[2023-03-19 01:50:37,954] [INFO] Selected 20 target genomes.
[2023-03-19 01:50:37,954] [INFO] Target genome list was writen to OceanDNA-b17059/target_genomes_gtdb.txt
[2023-03-19 01:50:37,971] [INFO] Task started: fastANI
[2023-03-19 01:50:37,971] [INFO] Running command: fastANI --query /var/lib/cwl/stga6263ae5-154c-4932-98fc-28e0d59dc108/OceanDNA-b17059.fa --refList OceanDNA-b17059/target_genomes_gtdb.txt --output OceanDNA-b17059/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:50:44,218] [INFO] Task succeeded: fastANI
[2023-03-19 01:50:44,220] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 01:50:44,221] [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_018660415.1	s__2-12-FULL-36-22 sp018660415	99.9827	341	344	d__Bacteria;p__Dependentiae;c__Babeliae;o__Babeliales;f__UBA12409;g__2-12-FULL-36-22	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCA_001771315.1	s__2-12-FULL-36-22 sp001771315	77.5551	88	344	d__Bacteria;p__Dependentiae;c__Babeliae;o__Babeliales;f__UBA12409;g__2-12-FULL-36-22	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:50:44,221] [INFO] GTDB search result was written to OceanDNA-b17059/result_gtdb.tsv
[2023-03-19 01:50:44,221] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:50:44,221] [INFO] DFAST_QC result json was written to OceanDNA-b17059/dqc_result.json
[2023-03-19 01:50:44,221] [INFO] DFAST_QC completed!
[2023-03-19 01:50:44,221] [INFO] Total running time: 0h0m43s