[2023-03-16 03:23:47,623] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:23:47,623] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:23:47,623] [INFO] DQC Reference Directory: /var/lib/cwl/stg84ae448a-113b-4ee6-96d4-e172df1ec114/dqc_reference
[2023-03-16 03:23:49,402] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:23:49,415] [INFO] Task started: Prodigal
[2023-03-16 03:23:49,415] [INFO] Running command: cat /var/lib/cwl/stg85691b41-1b1e-40f4-9fa2-0925c961e68b/OceanDNA-b33328.fa | prodigal -d OceanDNA-b33328/cds.fna -a OceanDNA-b33328/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:23:56,741] [INFO] Task succeeded: Prodigal
[2023-03-16 03:23:56,741] [INFO] Task started: HMMsearch
[2023-03-16 03:23:56,741] [INFO] Running command: hmmsearch --tblout OceanDNA-b33328/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84ae448a-113b-4ee6-96d4-e172df1ec114/dqc_reference/reference_markers.hmm OceanDNA-b33328/protein.faa > /dev/null
[2023-03-16 03:23:56,913] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:23:56,914] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg85691b41-1b1e-40f4-9fa2-0925c961e68b/OceanDNA-b33328.fa]
[2023-03-16 03:23:56,929] [INFO] Query marker FASTA was written to OceanDNA-b33328/markers.fasta
[2023-03-16 03:23:56,929] [INFO] Task started: Blastn
[2023-03-16 03:23:56,929] [INFO] Running command: blastn -query OceanDNA-b33328/markers.fasta -db /var/lib/cwl/stg84ae448a-113b-4ee6-96d4-e172df1ec114/dqc_reference/reference_markers.fasta -out OceanDNA-b33328/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:23:57,534] [INFO] Task succeeded: Blastn
[2023-03-16 03:23:57,535] [INFO] Selected 21 target genomes.
[2023-03-16 03:23:57,535] [INFO] Target genome list was writen to OceanDNA-b33328/target_genomes.txt
[2023-03-16 03:23:57,545] [INFO] Task started: fastANI
[2023-03-16 03:23:57,545] [INFO] Running command: fastANI --query /var/lib/cwl/stg85691b41-1b1e-40f4-9fa2-0925c961e68b/OceanDNA-b33328.fa --refList OceanDNA-b33328/target_genomes.txt --output OceanDNA-b33328/fastani_result.tsv --threads 1
[2023-03-16 03:24:11,930] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:11,931] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84ae448a-113b-4ee6-96d4-e172df1ec114/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:24:11,931] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84ae448a-113b-4ee6-96d4-e172df1ec114/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:24:11,934] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:24:11,934] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 03:24:11,934] [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
Limnobacter alexandrii	strain=LZ-4	GCA_005871185.1	2570352	2570352	type	True	79.8048	96	166	95	below_threshold
Limnobacter humi	strain=NBRC 111650	GCA_024518835.1	1778671	1778671	type	True	77.8132	54	166	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 03:24:11,935] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33328/tc_result.tsv
[2023-03-16 03:24:11,935] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:24:11,935] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:24:11,935] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84ae448a-113b-4ee6-96d4-e172df1ec114/dqc_reference/checkm_data
[2023-03-16 03:24:11,936] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:24:11,939] [INFO] Task started: CheckM
[2023-03-16 03:24:11,940] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33328/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33328/checkm_input OceanDNA-b33328/checkm_result
[2023-03-16 03:24:36,458] [INFO] Task succeeded: CheckM
[2023-03-16 03:24:36,458] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.74%
Contamintation: 5.73%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 03:24:36,460] [INFO] ===== Completeness check finished =====
[2023-03-16 03:24:36,460] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:24:36,461] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33328/markers.fasta)
[2023-03-16 03:24:36,461] [INFO] Task started: Blastn
[2023-03-16 03:24:36,461] [INFO] Running command: blastn -query OceanDNA-b33328/markers.fasta -db /var/lib/cwl/stg84ae448a-113b-4ee6-96d4-e172df1ec114/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33328/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:24:37,420] [INFO] Task succeeded: Blastn
[2023-03-16 03:24:37,420] [INFO] Selected 19 target genomes.
[2023-03-16 03:24:37,421] [INFO] Target genome list was writen to OceanDNA-b33328/target_genomes_gtdb.txt
[2023-03-16 03:24:37,915] [INFO] Task started: fastANI
[2023-03-16 03:24:37,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg85691b41-1b1e-40f4-9fa2-0925c961e68b/OceanDNA-b33328.fa --refList OceanDNA-b33328/target_genomes_gtdb.txt --output OceanDNA-b33328/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:24:48,276] [INFO] Task succeeded: fastANI
[2023-03-16 03:24:48,281] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 03:24:48,282] [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
GCF_000170915.1	s__Limnobacter sp000170915	80.3214	89	166	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	98.10	98.01	0.88	0.86	5	-
GCF_005871185.1	s__Limnobacter alexandrii	79.8048	96	166	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013004065.1	s__Limnobacter sp002954425	79.6899	93	166	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	97.67	96.02	0.92	0.87	19	-
GCF_902506325.1	s__Limnobacter sp902506325	79.5784	87	166	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001601825.1	s__Limnobacter sp001601825	79.3236	81	166	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018815245.1	s__Limnobacter sp018815245	79.0592	94	166	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	99.98	99.93	0.99	0.98	9	-
GCA_004291335.1	s__Limnobacter thiooxidans	78.9809	75	166	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018812945.1	s__Limnobacter sp018812945	78.7351	83	166	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 03:24:48,282] [INFO] GTDB search result was written to OceanDNA-b33328/result_gtdb.tsv
[2023-03-16 03:24:48,282] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:24:48,283] [INFO] DFAST_QC result json was written to OceanDNA-b33328/dqc_result.json
[2023-03-16 03:24:48,283] [INFO] DFAST_QC completed!
[2023-03-16 03:24:48,283] [INFO] Total running time: 0h1m1s