[2023-03-16 05:52:41,067] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:52:41,067] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:52:41,067] [INFO] DQC Reference Directory: /var/lib/cwl/stgc12ba189-5266-4cde-9506-d3955920b3ed/dqc_reference
[2023-03-16 05:52:42,185] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:52:42,186] [INFO] Task started: Prodigal
[2023-03-16 05:52:42,186] [INFO] Running command: cat /var/lib/cwl/stg551519c2-90a5-4161-a22c-312bd6bd8b41/OceanDNA-b22260.fa | prodigal -d OceanDNA-b22260/cds.fna -a OceanDNA-b22260/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:52:56,373] [INFO] Task succeeded: Prodigal
[2023-03-16 05:52:56,374] [INFO] Task started: HMMsearch
[2023-03-16 05:52:56,374] [INFO] Running command: hmmsearch --tblout OceanDNA-b22260/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc12ba189-5266-4cde-9506-d3955920b3ed/dqc_reference/reference_markers.hmm OceanDNA-b22260/protein.faa > /dev/null
[2023-03-16 05:52:56,558] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:52:56,558] [INFO] Found 6/6 markers.
[2023-03-16 05:52:56,576] [INFO] Query marker FASTA was written to OceanDNA-b22260/markers.fasta
[2023-03-16 05:52:56,577] [INFO] Task started: Blastn
[2023-03-16 05:52:56,577] [INFO] Running command: blastn -query OceanDNA-b22260/markers.fasta -db /var/lib/cwl/stgc12ba189-5266-4cde-9506-d3955920b3ed/dqc_reference/reference_markers.fasta -out OceanDNA-b22260/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:52:57,139] [INFO] Task succeeded: Blastn
[2023-03-16 05:52:57,142] [INFO] Selected 25 target genomes.
[2023-03-16 05:52:57,142] [INFO] Target genome list was writen to OceanDNA-b22260/target_genomes.txt
[2023-03-16 05:52:57,158] [INFO] Task started: fastANI
[2023-03-16 05:52:57,158] [INFO] Running command: fastANI --query /var/lib/cwl/stg551519c2-90a5-4161-a22c-312bd6bd8b41/OceanDNA-b22260.fa --refList OceanDNA-b22260/target_genomes.txt --output OceanDNA-b22260/fastani_result.tsv --threads 1
[2023-03-16 05:53:17,332] [INFO] Task succeeded: fastANI
[2023-03-16 05:53:17,332] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc12ba189-5266-4cde-9506-d3955920b3ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:53:17,332] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc12ba189-5266-4cde-9506-d3955920b3ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:53:17,336] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:53:17,336] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 05:53:17,336] [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
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	75.9539	50	748	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.0249	56	748	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 05:53:17,337] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22260/tc_result.tsv
[2023-03-16 05:53:17,338] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:53:17,338] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:53:17,338] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc12ba189-5266-4cde-9506-d3955920b3ed/dqc_reference/checkm_data
[2023-03-16 05:53:17,339] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:53:17,514] [INFO] Task started: CheckM
[2023-03-16 05:53:17,514] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22260/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22260/checkm_input OceanDNA-b22260/checkm_result
[2023-03-16 05:54:01,771] [INFO] Task succeeded: CheckM
[2023-03-16 05:54:01,772] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 05:54:01,780] [INFO] ===== Completeness check finished =====
[2023-03-16 05:54:01,780] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:54:01,780] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22260/markers.fasta)
[2023-03-16 05:54:01,781] [INFO] Task started: Blastn
[2023-03-16 05:54:01,781] [INFO] Running command: blastn -query OceanDNA-b22260/markers.fasta -db /var/lib/cwl/stgc12ba189-5266-4cde-9506-d3955920b3ed/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22260/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:54:02,537] [INFO] Task succeeded: Blastn
[2023-03-16 05:54:02,540] [INFO] Selected 14 target genomes.
[2023-03-16 05:54:02,540] [INFO] Target genome list was writen to OceanDNA-b22260/target_genomes_gtdb.txt
[2023-03-16 05:54:02,552] [INFO] Task started: fastANI
[2023-03-16 05:54:02,553] [INFO] Running command: fastANI --query /var/lib/cwl/stg551519c2-90a5-4161-a22c-312bd6bd8b41/OceanDNA-b22260.fa --refList OceanDNA-b22260/target_genomes_gtdb.txt --output OceanDNA-b22260/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:54:09,416] [INFO] Task succeeded: fastANI
[2023-03-16 05:54:09,423] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 05:54:09,423] [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_002295885.1	s__UBA854 sp002295885	99.9148	713	748	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA854	95.0	99.78	99.78	0.94	0.94	2	conclusive
GCA_002591705.1	s__UBA854 sp002591705	85.9542	567	748	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA854	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364485.1	s__UBA854 sp002364485	79.6026	450	748	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA854	95.0	99.87	99.87	0.97	0.97	2	-
GCA_002722935.1	s__SP202 sp002722935	77.3254	139	748	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__SP202	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862305.1	s__UBA8087 sp002862305	76.6181	95	748	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA8087	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013003065.1	s__JABDLI01 sp013003065	76.5707	106	748	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__JABDLI01	95.0	99.48	99.44	0.94	0.93	3	-
GCA_002702575.1	s__UBA1668 sp002702575	76.5579	82	748	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA1668	95.0	99.83	99.83	0.97	0.97	3	-
GCA_017859745.1	s__VGXO01 sp017859745	76.4945	99	748	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__VGXO01	95.0	99.59	99.54	0.95	0.94	4	-
GCA_018883105.1	s__UBA966 sp018883105	76.2779	65	748	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA966	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009936695.1	s__UBA12014 sp009936695	76.1737	78	748	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873275.1	s__VGXO01 sp016873275	75.8721	86	748	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__VGXO01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 05:54:09,425] [INFO] GTDB search result was written to OceanDNA-b22260/result_gtdb.tsv
[2023-03-16 05:54:09,425] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:54:09,427] [INFO] DFAST_QC result json was written to OceanDNA-b22260/dqc_result.json
[2023-03-16 05:54:09,428] [INFO] DFAST_QC completed!
[2023-03-16 05:54:09,428] [INFO] Total running time: 0h1m28s