[2023-03-18 23:11:06,964] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:11:06,964] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:11:06,964] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c13e4ec-d798-4118-8a45-e49cd8df5f1f/dqc_reference
[2023-03-18 23:11:08,149] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:11:08,149] [INFO] Task started: Prodigal
[2023-03-18 23:11:08,149] [INFO] Running command: cat /var/lib/cwl/stgdcf06586-4a11-4b74-9c4d-6f4955dab7b4/OceanDNA-b33331.fa | prodigal -d OceanDNA-b33331/cds.fna -a OceanDNA-b33331/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:11:25,829] [INFO] Task succeeded: Prodigal
[2023-03-18 23:11:25,830] [INFO] Task started: HMMsearch
[2023-03-18 23:11:25,830] [INFO] Running command: hmmsearch --tblout OceanDNA-b33331/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c13e4ec-d798-4118-8a45-e49cd8df5f1f/dqc_reference/reference_markers.hmm OceanDNA-b33331/protein.faa > /dev/null
[2023-03-18 23:11:26,076] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:11:26,076] [INFO] Found 6/6 markers.
[2023-03-18 23:11:26,097] [INFO] Query marker FASTA was written to OceanDNA-b33331/markers.fasta
[2023-03-18 23:11:26,097] [INFO] Task started: Blastn
[2023-03-18 23:11:26,097] [INFO] Running command: blastn -query OceanDNA-b33331/markers.fasta -db /var/lib/cwl/stg2c13e4ec-d798-4118-8a45-e49cd8df5f1f/dqc_reference/reference_markers.fasta -out OceanDNA-b33331/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:11:26,749] [INFO] Task succeeded: Blastn
[2023-03-18 23:11:26,749] [INFO] Selected 30 target genomes.
[2023-03-18 23:11:26,750] [INFO] Target genome list was writen to OceanDNA-b33331/target_genomes.txt
[2023-03-18 23:11:26,763] [INFO] Task started: fastANI
[2023-03-18 23:11:26,763] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcf06586-4a11-4b74-9c4d-6f4955dab7b4/OceanDNA-b33331.fa --refList OceanDNA-b33331/target_genomes.txt --output OceanDNA-b33331/fastani_result.tsv --threads 1
[2023-03-18 23:11:47,272] [INFO] Task succeeded: fastANI
[2023-03-18 23:11:47,272] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c13e4ec-d798-4118-8a45-e49cd8df5f1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:11:47,272] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c13e4ec-d798-4118-8a45-e49cd8df5f1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:11:47,275] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:11:47,275] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:11:47,276] [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	84.6956	761	877	95	below_threshold
Limnobacter humi	strain=NBRC 111650	GCA_024518835.1	1778671	1778671	type	True	78.254	279	877	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:11:47,276] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33331/tc_result.tsv
[2023-03-18 23:11:47,276] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:11:47,276] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:11:47,276] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c13e4ec-d798-4118-8a45-e49cd8df5f1f/dqc_reference/checkm_data
[2023-03-18 23:11:47,277] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:11:47,288] [INFO] Task started: CheckM
[2023-03-18 23:11:47,289] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33331/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33331/checkm_input OceanDNA-b33331/checkm_result
[2023-03-18 23:12:34,933] [INFO] Task succeeded: CheckM
[2023-03-18 23:12:34,933] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 23:12:34,936] [INFO] ===== Completeness check finished =====
[2023-03-18 23:12:34,936] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:12:34,936] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33331/markers.fasta)
[2023-03-18 23:12:34,936] [INFO] Task started: Blastn
[2023-03-18 23:12:34,936] [INFO] Running command: blastn -query OceanDNA-b33331/markers.fasta -db /var/lib/cwl/stg2c13e4ec-d798-4118-8a45-e49cd8df5f1f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33331/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:12:35,974] [INFO] Task succeeded: Blastn
[2023-03-18 23:12:35,975] [INFO] Selected 9 target genomes.
[2023-03-18 23:12:35,975] [INFO] Target genome list was writen to OceanDNA-b33331/target_genomes_gtdb.txt
[2023-03-18 23:12:35,985] [INFO] Task started: fastANI
[2023-03-18 23:12:35,985] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcf06586-4a11-4b74-9c4d-6f4955dab7b4/OceanDNA-b33331.fa --refList OceanDNA-b33331/target_genomes_gtdb.txt --output OceanDNA-b33331/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:12:42,406] [INFO] Task succeeded: fastANI
[2023-03-18 23:12:42,412] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:12:42,412] [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_001601825.1	s__Limnobacter sp001601825	98.361	775	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018812945.1	s__Limnobacter sp018812945	90.1574	689	877	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	89.608	796	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	97.67	96.02	0.92	0.87	19	-
GCF_000170915.1	s__Limnobacter sp000170915	85.9348	766	877	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	84.6956	761	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506325.1	s__Limnobacter sp902506325	83.5648	732	877	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	81.772	614	877	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	80.7487	541	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:12:42,412] [INFO] GTDB search result was written to OceanDNA-b33331/result_gtdb.tsv
[2023-03-18 23:12:42,412] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:12:42,413] [INFO] DFAST_QC result json was written to OceanDNA-b33331/dqc_result.json
[2023-03-18 23:12:42,413] [INFO] DFAST_QC completed!
[2023-03-18 23:12:42,413] [INFO] Total running time: 0h1m35s