[2023-03-14 10:55:58,907] [INFO] DFAST_QC pipeline started.
[2023-03-14 10:55:58,907] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 10:55:58,907] [INFO] DQC Reference Directory: /var/lib/cwl/stgeec7b13b-0de1-4e9e-a18d-514b56c5c9ec/dqc_reference
[2023-03-14 10:56:00,753] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 10:56:00,753] [INFO] Task started: Prodigal
[2023-03-14 10:56:00,753] [INFO] Running command: cat /var/lib/cwl/stg5236a77f-776b-486f-90ef-b6dc0c26d166/OceanDNA-b26239.fa | prodigal -d OceanDNA-b26239/cds.fna -a OceanDNA-b26239/protein.faa -g 11 -q > /dev/null
[2023-03-14 10:56:08,962] [INFO] Task succeeded: Prodigal
[2023-03-14 10:56:08,962] [INFO] Task started: HMMsearch
[2023-03-14 10:56:08,962] [INFO] Running command: hmmsearch --tblout OceanDNA-b26239/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeec7b13b-0de1-4e9e-a18d-514b56c5c9ec/dqc_reference/reference_markers.hmm OceanDNA-b26239/protein.faa > /dev/null
[2023-03-14 10:56:09,200] [INFO] Task succeeded: HMMsearch
[2023-03-14 10:56:09,201] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg5236a77f-776b-486f-90ef-b6dc0c26d166/OceanDNA-b26239.fa]
[2023-03-14 10:56:09,228] [INFO] Query marker FASTA was written to OceanDNA-b26239/markers.fasta
[2023-03-14 10:56:09,228] [INFO] Task started: Blastn
[2023-03-14 10:56:09,228] [INFO] Running command: blastn -query OceanDNA-b26239/markers.fasta -db /var/lib/cwl/stgeec7b13b-0de1-4e9e-a18d-514b56c5c9ec/dqc_reference/reference_markers.fasta -out OceanDNA-b26239/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:09,760] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:09,761] [INFO] Selected 19 target genomes.
[2023-03-14 10:56:09,761] [INFO] Target genome list was writen to OceanDNA-b26239/target_genomes.txt
[2023-03-14 10:56:09,773] [INFO] Task started: fastANI
[2023-03-14 10:56:09,773] [INFO] Running command: fastANI --query /var/lib/cwl/stg5236a77f-776b-486f-90ef-b6dc0c26d166/OceanDNA-b26239.fa --refList OceanDNA-b26239/target_genomes.txt --output OceanDNA-b26239/fastani_result.tsv --threads 1
[2023-03-14 10:56:22,751] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:22,751] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeec7b13b-0de1-4e9e-a18d-514b56c5c9ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 10:56:22,752] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeec7b13b-0de1-4e9e-a18d-514b56c5c9ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 10:56:22,752] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 10:56:22,752] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 10:56:22,752] [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
--------------------------------------------------------------------------------
[2023-03-14 10:56:22,752] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26239/tc_result.tsv
[2023-03-14 10:56:22,752] [INFO] ===== Taxonomy check completed =====
[2023-03-14 10:56:22,752] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 10:56:22,752] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeec7b13b-0de1-4e9e-a18d-514b56c5c9ec/dqc_reference/checkm_data
[2023-03-14 10:56:22,755] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 10:56:22,761] [INFO] Task started: CheckM
[2023-03-14 10:56:22,761] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26239/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26239/checkm_input OceanDNA-b26239/checkm_result
[2023-03-14 10:56:48,698] [INFO] Task succeeded: CheckM
[2023-03-14 10:56:48,699] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.95%
Contamintation: 1.39%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-14 10:56:48,701] [INFO] ===== Completeness check finished =====
[2023-03-14 10:56:48,701] [INFO] ===== Start GTDB Search =====
[2023-03-14 10:56:48,701] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26239/markers.fasta)
[2023-03-14 10:56:48,701] [INFO] Task started: Blastn
[2023-03-14 10:56:48,701] [INFO] Running command: blastn -query OceanDNA-b26239/markers.fasta -db /var/lib/cwl/stgeec7b13b-0de1-4e9e-a18d-514b56c5c9ec/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26239/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 10:56:49,384] [INFO] Task succeeded: Blastn
[2023-03-14 10:56:49,385] [INFO] Selected 13 target genomes.
[2023-03-14 10:56:49,385] [INFO] Target genome list was writen to OceanDNA-b26239/target_genomes_gtdb.txt
[2023-03-14 10:56:49,399] [INFO] Task started: fastANI
[2023-03-14 10:56:49,399] [INFO] Running command: fastANI --query /var/lib/cwl/stg5236a77f-776b-486f-90ef-b6dc0c26d166/OceanDNA-b26239.fa --refList OceanDNA-b26239/target_genomes_gtdb.txt --output OceanDNA-b26239/fastani_result_gtdb.tsv --threads 1
[2023-03-14 10:56:53,765] [INFO] Task succeeded: fastANI
[2023-03-14 10:56:53,770] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 10:56:53,771] [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_905182545.1	s__UBA3439 sp905182545	77.5744	125	390	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002378605.1	s__UBA3439 sp002378605	77.4854	92	390	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	99.28	99.28	0.80	0.80	2	-
GCA_009919335.1	s__UBA3439 sp009919335	77.4513	84	390	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	98.81	98.81	0.76	0.76	2	-
GCA_017859295.1	s__UBA3439 sp017859295	77.1906	110	390	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	98.52	98.52	0.78	0.78	2	-
GCA_016778895.1	s__UBA3439 sp016778895	77.051	100	390	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	99.63	99.63	0.87	0.87	2	-
GCF_000024465.1	s__Puniceispirillum marinum	76.2754	51	390	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__Puniceispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780525.1	s__UBA3439 sp016780525	76.2636	59	390	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	99.22	99.22	0.71	0.71	2	-
--------------------------------------------------------------------------------
[2023-03-14 10:56:53,771] [INFO] GTDB search result was written to OceanDNA-b26239/result_gtdb.tsv
[2023-03-14 10:56:53,771] [INFO] ===== GTDB Search completed =====
[2023-03-14 10:56:53,772] [INFO] DFAST_QC result json was written to OceanDNA-b26239/dqc_result.json
[2023-03-14 10:56:53,772] [INFO] DFAST_QC completed!
[2023-03-14 10:56:53,772] [INFO] Total running time: 0h0m55s