[2023-03-19 04:46:19,984] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:46:19,984] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:46:19,985] [INFO] DQC Reference Directory: /var/lib/cwl/stgc79edfc9-6258-4494-80d3-be5b009e0ffa/dqc_reference
[2023-03-19 04:46:21,080] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:46:21,080] [INFO] Task started: Prodigal
[2023-03-19 04:46:21,080] [INFO] Running command: cat /var/lib/cwl/stg644994e4-7c10-4c28-9ab2-13efccc8fd36/OceanDNA-b26187.fa | prodigal -d OceanDNA-b26187/cds.fna -a OceanDNA-b26187/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:46:29,898] [INFO] Task succeeded: Prodigal
[2023-03-19 04:46:29,898] [INFO] Task started: HMMsearch
[2023-03-19 04:46:29,898] [INFO] Running command: hmmsearch --tblout OceanDNA-b26187/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc79edfc9-6258-4494-80d3-be5b009e0ffa/dqc_reference/reference_markers.hmm OceanDNA-b26187/protein.faa > /dev/null
[2023-03-19 04:46:30,055] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:46:30,055] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg644994e4-7c10-4c28-9ab2-13efccc8fd36/OceanDNA-b26187.fa]
[2023-03-19 04:46:30,068] [INFO] Query marker FASTA was written to OceanDNA-b26187/markers.fasta
[2023-03-19 04:46:30,068] [INFO] Task started: Blastn
[2023-03-19 04:46:30,068] [INFO] Running command: blastn -query OceanDNA-b26187/markers.fasta -db /var/lib/cwl/stgc79edfc9-6258-4494-80d3-be5b009e0ffa/dqc_reference/reference_markers.fasta -out OceanDNA-b26187/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:46:30,626] [INFO] Task succeeded: Blastn
[2023-03-19 04:46:30,627] [INFO] Selected 20 target genomes.
[2023-03-19 04:46:30,627] [INFO] Target genome list was writen to OceanDNA-b26187/target_genomes.txt
[2023-03-19 04:46:30,637] [INFO] Task started: fastANI
[2023-03-19 04:46:30,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg644994e4-7c10-4c28-9ab2-13efccc8fd36/OceanDNA-b26187.fa --refList OceanDNA-b26187/target_genomes.txt --output OceanDNA-b26187/fastani_result.tsv --threads 1
[2023-03-19 04:46:41,496] [INFO] Task succeeded: fastANI
[2023-03-19 04:46:41,496] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc79edfc9-6258-4494-80d3-be5b009e0ffa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:46:41,496] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc79edfc9-6258-4494-80d3-be5b009e0ffa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:46:41,497] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:46:41,497] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:46:41,497] [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 04:46:41,573] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26187/tc_result.tsv
[2023-03-19 04:46:41,574] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:46:41,574] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:46:41,574] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc79edfc9-6258-4494-80d3-be5b009e0ffa/dqc_reference/checkm_data
[2023-03-19 04:46:41,576] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:46:41,592] [INFO] Task started: CheckM
[2023-03-19 04:46:41,592] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26187/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26187/checkm_input OceanDNA-b26187/checkm_result
[2023-03-19 04:47:08,478] [INFO] Task succeeded: CheckM
[2023-03-19 04:47:08,478] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 04:47:08,480] [INFO] ===== Completeness check finished =====
[2023-03-19 04:47:08,480] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:47:08,480] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26187/markers.fasta)
[2023-03-19 04:47:08,480] [INFO] Task started: Blastn
[2023-03-19 04:47:08,480] [INFO] Running command: blastn -query OceanDNA-b26187/markers.fasta -db /var/lib/cwl/stgc79edfc9-6258-4494-80d3-be5b009e0ffa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26187/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:47:09,357] [INFO] Task succeeded: Blastn
[2023-03-19 04:47:09,357] [INFO] Selected 17 target genomes.
[2023-03-19 04:47:09,358] [INFO] Target genome list was writen to OceanDNA-b26187/target_genomes_gtdb.txt
[2023-03-19 04:47:09,376] [INFO] Task started: fastANI
[2023-03-19 04:47:09,376] [INFO] Running command: fastANI --query /var/lib/cwl/stg644994e4-7c10-4c28-9ab2-13efccc8fd36/OceanDNA-b26187.fa --refList OceanDNA-b26187/target_genomes_gtdb.txt --output OceanDNA-b26187/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:47:15,295] [INFO] Task succeeded: fastANI
[2023-03-19 04:47:15,302] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 04:47:15,302] [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_016780525.1	s__UBA3439 sp016780525	98.6122	297	455	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	99.22	99.22	0.71	0.71	2	conclusive
GCA_902583715.1	s__UBA3439 sp902583715	78.9979	139	455	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	95.85	95.85	0.55	0.55	2	-
GCA_017859295.1	s__UBA3439 sp017859295	77.2561	127	455	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	98.52	98.52	0.78	0.78	2	-
GCA_009919335.1	s__UBA3439 sp009919335	77.1574	111	455	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	98.81	98.81	0.76	0.76	2	-
GCA_016778895.1	s__UBA3439 sp016778895	77.0609	119	455	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	99.63	99.63	0.87	0.87	2	-
GCA_002378605.1	s__UBA3439 sp002378605	76.8872	127	455	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	99.28	99.28	0.80	0.80	2	-
GCA_016778825.1	s__UBA3439 sp016778825	76.8116	83	455	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024465.1	s__Puniceispirillum marinum	76.7817	96	455	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__Puniceispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018624035.1	s__UBA8309 sp018624035	76.2935	60	455	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004212735.1	s__MED-G116 sp004212735	76.2402	75	455	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__MED-G116	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018668795.1	s__Puniceispirillum sp018668795	76.1092	69	455	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__Puniceispirillum	95.0	99.26	99.26	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-03-19 04:47:15,302] [INFO] GTDB search result was written to OceanDNA-b26187/result_gtdb.tsv
[2023-03-19 04:47:15,302] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:47:15,303] [INFO] DFAST_QC result json was written to OceanDNA-b26187/dqc_result.json
[2023-03-19 04:47:15,303] [INFO] DFAST_QC completed!
[2023-03-19 04:47:15,303] [INFO] Total running time: 0h0m55s