[2023-03-18 07:06:20,692] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:06:20,692] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:06:20,692] [INFO] DQC Reference Directory: /var/lib/cwl/stg31a11349-8aa8-4036-b880-5cbc8adb06f7/dqc_reference
[2023-03-18 07:06:22,304] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:06:22,304] [INFO] Task started: Prodigal
[2023-03-18 07:06:22,304] [INFO] Running command: cat /var/lib/cwl/stg1944e555-7541-42a6-88fa-375d045b0227/OceanDNA-b37345.fa | prodigal -d OceanDNA-b37345/cds.fna -a OceanDNA-b37345/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:06:37,040] [INFO] Task succeeded: Prodigal
[2023-03-18 07:06:37,041] [INFO] Task started: HMMsearch
[2023-03-18 07:06:37,041] [INFO] Running command: hmmsearch --tblout OceanDNA-b37345/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31a11349-8aa8-4036-b880-5cbc8adb06f7/dqc_reference/reference_markers.hmm OceanDNA-b37345/protein.faa > /dev/null
[2023-03-18 07:06:37,228] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:06:37,228] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg1944e555-7541-42a6-88fa-375d045b0227/OceanDNA-b37345.fa]
[2023-03-18 07:06:37,253] [INFO] Query marker FASTA was written to OceanDNA-b37345/markers.fasta
[2023-03-18 07:06:37,253] [INFO] Task started: Blastn
[2023-03-18 07:06:37,253] [INFO] Running command: blastn -query OceanDNA-b37345/markers.fasta -db /var/lib/cwl/stg31a11349-8aa8-4036-b880-5cbc8adb06f7/dqc_reference/reference_markers.fasta -out OceanDNA-b37345/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:06:37,679] [INFO] Task succeeded: Blastn
[2023-03-18 07:06:37,680] [INFO] Selected 13 target genomes.
[2023-03-18 07:06:37,680] [INFO] Target genome list was writen to OceanDNA-b37345/target_genomes.txt
[2023-03-18 07:06:37,685] [INFO] Task started: fastANI
[2023-03-18 07:06:37,685] [INFO] Running command: fastANI --query /var/lib/cwl/stg1944e555-7541-42a6-88fa-375d045b0227/OceanDNA-b37345.fa --refList OceanDNA-b37345/target_genomes.txt --output OceanDNA-b37345/fastani_result.tsv --threads 1
[2023-03-18 07:06:44,997] [INFO] Task succeeded: fastANI
[2023-03-18 07:06:44,998] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31a11349-8aa8-4036-b880-5cbc8adb06f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:06:44,998] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31a11349-8aa8-4036-b880-5cbc8adb06f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:06:44,998] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:06:44,998] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:06:44,998] [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 07:06:44,998] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37345/tc_result.tsv
[2023-03-18 07:06:44,999] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:06:44,999] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:06:44,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31a11349-8aa8-4036-b880-5cbc8adb06f7/dqc_reference/checkm_data
[2023-03-18 07:06:45,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:06:45,006] [INFO] Task started: CheckM
[2023-03-18 07:06:45,006] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37345/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37345/checkm_input OceanDNA-b37345/checkm_result
[2023-03-18 07:07:25,312] [INFO] Task succeeded: CheckM
[2023-03-18 07:07:25,312] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.03%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:07:25,315] [INFO] ===== Completeness check finished =====
[2023-03-18 07:07:25,315] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:07:25,315] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37345/markers.fasta)
[2023-03-18 07:07:25,315] [INFO] Task started: Blastn
[2023-03-18 07:07:25,316] [INFO] Running command: blastn -query OceanDNA-b37345/markers.fasta -db /var/lib/cwl/stg31a11349-8aa8-4036-b880-5cbc8adb06f7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37345/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:07:25,724] [INFO] Task succeeded: Blastn
[2023-03-18 07:07:25,725] [INFO] Selected 8 target genomes.
[2023-03-18 07:07:25,725] [INFO] Target genome list was writen to OceanDNA-b37345/target_genomes_gtdb.txt
[2023-03-18 07:07:25,743] [INFO] Task started: fastANI
[2023-03-18 07:07:25,743] [INFO] Running command: fastANI --query /var/lib/cwl/stg1944e555-7541-42a6-88fa-375d045b0227/OceanDNA-b37345.fa --refList OceanDNA-b37345/target_genomes_gtdb.txt --output OceanDNA-b37345/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:07:31,050] [INFO] Task succeeded: fastANI
[2023-03-18 07:07:31,054] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:07:31,054] [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_018645845.1	s__UBA9659 sp018645845	98.6629	598	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	98.73	98.60	0.77	0.73	4	conclusive
GCA_012961165.1	s__UBA9659 sp012961165	89.387	548	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	99.55	99.55	0.89	0.89	2	-
GCA_018665025.1	s__UBA9659 sp018665025	88.796	525	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	99.67	99.61	0.89	0.86	14	-
GCA_018667205.1	s__UBA9659 sp018667205	80.5817	293	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018607685.1	s__UBA9659 sp018607685	79.7006	295	719	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:07:31,054] [INFO] GTDB search result was written to OceanDNA-b37345/result_gtdb.tsv
[2023-03-18 07:07:31,054] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:07:31,055] [INFO] DFAST_QC result json was written to OceanDNA-b37345/dqc_result.json
[2023-03-18 07:07:31,055] [INFO] DFAST_QC completed!
[2023-03-18 07:07:31,055] [INFO] Total running time: 0h1m10s