[2023-03-18 03:28:30,812] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:28:30,812] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:28:30,812] [INFO] DQC Reference Directory: /var/lib/cwl/stgae514a2f-ec1a-460f-9d10-cfd02e67a9d9/dqc_reference
[2023-03-18 03:28:31,894] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:28:31,895] [INFO] Task started: Prodigal
[2023-03-18 03:28:31,895] [INFO] Running command: cat /var/lib/cwl/stg88248597-356c-45fd-801e-674310e75ff3/OceanDNA-b26143.fa | prodigal -d OceanDNA-b26143/cds.fna -a OceanDNA-b26143/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:28:46,020] [INFO] Task succeeded: Prodigal
[2023-03-18 03:28:46,020] [INFO] Task started: HMMsearch
[2023-03-18 03:28:46,020] [INFO] Running command: hmmsearch --tblout OceanDNA-b26143/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae514a2f-ec1a-460f-9d10-cfd02e67a9d9/dqc_reference/reference_markers.hmm OceanDNA-b26143/protein.faa > /dev/null
[2023-03-18 03:28:46,188] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:28:46,188] [INFO] Found 6/6 markers.
[2023-03-18 03:28:46,203] [INFO] Query marker FASTA was written to OceanDNA-b26143/markers.fasta
[2023-03-18 03:28:46,204] [INFO] Task started: Blastn
[2023-03-18 03:28:46,204] [INFO] Running command: blastn -query OceanDNA-b26143/markers.fasta -db /var/lib/cwl/stgae514a2f-ec1a-460f-9d10-cfd02e67a9d9/dqc_reference/reference_markers.fasta -out OceanDNA-b26143/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:28:46,797] [INFO] Task succeeded: Blastn
[2023-03-18 03:28:46,798] [INFO] Selected 32 target genomes.
[2023-03-18 03:28:46,798] [INFO] Target genome list was writen to OceanDNA-b26143/target_genomes.txt
[2023-03-18 03:28:46,812] [INFO] Task started: fastANI
[2023-03-18 03:28:46,846] [INFO] Running command: fastANI --query /var/lib/cwl/stg88248597-356c-45fd-801e-674310e75ff3/OceanDNA-b26143.fa --refList OceanDNA-b26143/target_genomes.txt --output OceanDNA-b26143/fastani_result.tsv --threads 1
[2023-03-18 03:29:07,890] [INFO] Task succeeded: fastANI
[2023-03-18 03:29:07,890] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae514a2f-ec1a-460f-9d10-cfd02e67a9d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:29:07,890] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae514a2f-ec1a-460f-9d10-cfd02e67a9d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:29:07,891] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:29:07,891] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 03:29:07,891] [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 03:29:07,891] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26143/tc_result.tsv
[2023-03-18 03:29:07,891] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:29:07,891] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:29:07,891] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae514a2f-ec1a-460f-9d10-cfd02e67a9d9/dqc_reference/checkm_data
[2023-03-18 03:29:07,894] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:29:07,897] [INFO] Task started: CheckM
[2023-03-18 03:29:07,897] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26143/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26143/checkm_input OceanDNA-b26143/checkm_result
[2023-03-18 03:29:46,776] [INFO] Task succeeded: CheckM
[2023-03-18 03:29:46,776] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 03:29:46,778] [INFO] ===== Completeness check finished =====
[2023-03-18 03:29:46,778] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:29:46,779] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26143/markers.fasta)
[2023-03-18 03:29:46,779] [INFO] Task started: Blastn
[2023-03-18 03:29:46,779] [INFO] Running command: blastn -query OceanDNA-b26143/markers.fasta -db /var/lib/cwl/stgae514a2f-ec1a-460f-9d10-cfd02e67a9d9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26143/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:29:47,789] [INFO] Task succeeded: Blastn
[2023-03-18 03:29:47,790] [INFO] Selected 18 target genomes.
[2023-03-18 03:29:47,790] [INFO] Target genome list was writen to OceanDNA-b26143/target_genomes_gtdb.txt
[2023-03-18 03:29:47,808] [INFO] Task started: fastANI
[2023-03-18 03:29:47,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg88248597-356c-45fd-801e-674310e75ff3/OceanDNA-b26143.fa --refList OceanDNA-b26143/target_genomes_gtdb.txt --output OceanDNA-b26143/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:29:54,876] [INFO] Task succeeded: fastANI
[2023-03-18 03:29:54,884] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:29:54,884] [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_004212735.1	s__MED-G116 sp004212735	99.5516	667	732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__MED-G116	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902547925.1	s__MED-G116 sp902547925	93.2265	326	732	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_902596655.1	s__MED-G116 sp902596655	81.1129	340	732	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_902578815.1	s__MED-G116 sp902578815	81.0446	311	732	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_902623185.1	s__MED-G116 sp902623185	79.0538	205	732	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_009920665.1	s__UBA8309 sp009920665	77.0818	129	732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780765.1	s__UBA8309 sp016780765	77.0566	122	732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	98.39	97.46	0.74	0.59	14	-
GCA_002457745.1	s__UBA8309 sp002457745	76.8051	99	732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018624035.1	s__UBA8309 sp018624035	76.7443	129	732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686685.1	s__UBA8309 sp002686685	76.7438	76	732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	97.96	97.78	0.70	0.66	5	-
GCA_018668795.1	s__Puniceispirillum sp018668795	76.5967	86	732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__Puniceispirillum	95.0	99.26	99.26	0.87	0.87	2	-
GCA_002683535.1	s__UBA8309 sp002683535	76.5946	63	732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011524735.1	s__UBA8309 sp011524735	76.3175	74	732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA8309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017859295.1	s__UBA3439 sp017859295	76.0385	79	732	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	98.52	98.52	0.78	0.78	2	-
--------------------------------------------------------------------------------
[2023-03-18 03:29:54,884] [INFO] GTDB search result was written to OceanDNA-b26143/result_gtdb.tsv
[2023-03-18 03:29:54,885] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:29:54,886] [INFO] DFAST_QC result json was written to OceanDNA-b26143/dqc_result.json
[2023-03-18 03:29:54,886] [INFO] DFAST_QC completed!
[2023-03-18 03:29:54,886] [INFO] Total running time: 0h1m24s