[2023-03-16 11:12:54,344] [INFO] DFAST_QC pipeline started.
[2023-03-16 11:12:54,345] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 11:12:54,345] [INFO] DQC Reference Directory: /var/lib/cwl/stge78b0ffd-b8cd-4537-9911-dd43d780cb5e/dqc_reference
[2023-03-16 11:12:55,445] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 11:12:55,446] [INFO] Task started: Prodigal
[2023-03-16 11:12:55,446] [INFO] Running command: cat /var/lib/cwl/stg8c3a4a2d-f730-4702-90cb-13ffdc4a995e/OceanDNA-b32717.fa | prodigal -d OceanDNA-b32717/cds.fna -a OceanDNA-b32717/protein.faa -g 11 -q > /dev/null
[2023-03-16 11:13:12,477] [INFO] Task succeeded: Prodigal
[2023-03-16 11:13:12,477] [INFO] Task started: HMMsearch
[2023-03-16 11:13:12,477] [INFO] Running command: hmmsearch --tblout OceanDNA-b32717/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge78b0ffd-b8cd-4537-9911-dd43d780cb5e/dqc_reference/reference_markers.hmm OceanDNA-b32717/protein.faa > /dev/null
[2023-03-16 11:13:12,663] [INFO] Task succeeded: HMMsearch
[2023-03-16 11:13:12,663] [INFO] Found 6/6 markers.
[2023-03-16 11:13:12,684] [INFO] Query marker FASTA was written to OceanDNA-b32717/markers.fasta
[2023-03-16 11:13:12,685] [INFO] Task started: Blastn
[2023-03-16 11:13:12,685] [INFO] Running command: blastn -query OceanDNA-b32717/markers.fasta -db /var/lib/cwl/stge78b0ffd-b8cd-4537-9911-dd43d780cb5e/dqc_reference/reference_markers.fasta -out OceanDNA-b32717/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:13:13,367] [INFO] Task succeeded: Blastn
[2023-03-16 11:13:13,368] [INFO] Selected 28 target genomes.
[2023-03-16 11:13:13,368] [INFO] Target genome list was writen to OceanDNA-b32717/target_genomes.txt
[2023-03-16 11:13:13,399] [INFO] Task started: fastANI
[2023-03-16 11:13:13,400] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c3a4a2d-f730-4702-90cb-13ffdc4a995e/OceanDNA-b32717.fa --refList OceanDNA-b32717/target_genomes.txt --output OceanDNA-b32717/fastani_result.tsv --threads 1
[2023-03-16 11:13:47,195] [INFO] Task succeeded: fastANI
[2023-03-16 11:13:47,195] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge78b0ffd-b8cd-4537-9911-dd43d780cb5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 11:13:47,195] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge78b0ffd-b8cd-4537-9911-dd43d780cb5e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 11:13:47,246] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 11:13:47,246] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 11:13:47,246] [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
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	75.6076	50	889	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	75.5466	51	889	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 11:13:47,247] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32717/tc_result.tsv
[2023-03-16 11:13:47,247] [INFO] ===== Taxonomy check completed =====
[2023-03-16 11:13:47,247] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 11:13:47,248] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge78b0ffd-b8cd-4537-9911-dd43d780cb5e/dqc_reference/checkm_data
[2023-03-16 11:13:47,248] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 11:13:47,325] [INFO] Task started: CheckM
[2023-03-16 11:13:47,325] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32717/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32717/checkm_input OceanDNA-b32717/checkm_result
[2023-03-16 11:14:44,532] [INFO] Task succeeded: CheckM
[2023-03-16 11:14:44,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 11:14:44,537] [INFO] ===== Completeness check finished =====
[2023-03-16 11:14:44,537] [INFO] ===== Start GTDB Search =====
[2023-03-16 11:14:44,538] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32717/markers.fasta)
[2023-03-16 11:14:44,557] [INFO] Task started: Blastn
[2023-03-16 11:14:44,557] [INFO] Running command: blastn -query OceanDNA-b32717/markers.fasta -db /var/lib/cwl/stge78b0ffd-b8cd-4537-9911-dd43d780cb5e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32717/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 11:14:45,843] [INFO] Task succeeded: Blastn
[2023-03-16 11:14:45,844] [INFO] Selected 23 target genomes.
[2023-03-16 11:14:45,844] [INFO] Target genome list was writen to OceanDNA-b32717/target_genomes_gtdb.txt
[2023-03-16 11:14:45,965] [INFO] Task started: fastANI
[2023-03-16 11:14:45,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c3a4a2d-f730-4702-90cb-13ffdc4a995e/OceanDNA-b32717.fa --refList OceanDNA-b32717/target_genomes_gtdb.txt --output OceanDNA-b32717/fastani_result_gtdb.tsv --threads 1
[2023-03-16 11:14:59,622] [INFO] Task succeeded: fastANI
[2023-03-16 11:14:59,628] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 11:14:59,628] [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_018666195.1	s__JABJAG01 sp018666195	78.7277	409	889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABJAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018667335.1	s__UBA8079 sp018667335	77.7025	299	889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.89	99.79	0.96	0.96	6	-
GCA_018702955.1	s__UBA8079 sp018702955	77.6771	288	889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.54	99.39	0.93	0.91	5	-
GCA_002727315.1	s__UBA8079 sp002727315	77.442	210	889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643325.1	s__JABJAG01 sp017643325	77.3826	242	889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABJAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724635.1	s__UBA8079 sp002724635	76.7649	159	889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011087645.1	s__JABDJY01 sp011087645	76.3241	124	889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABDJY01	95.0	99.97	99.97	0.97	0.97	2	-
GCA_013003285.1	s__JABDJY01 sp013003285	76.2241	98	889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABDJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722515.1	s__UBA8079 sp002722515	76.0742	85	889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840595.1	s__Bin65 sp009840595	75.6174	54	889	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Bin65;f__Bin65;g__Bin65	95.0	98.91	96.90	0.94	0.92	4	-
--------------------------------------------------------------------------------
[2023-03-16 11:14:59,628] [INFO] GTDB search result was written to OceanDNA-b32717/result_gtdb.tsv
[2023-03-16 11:14:59,629] [INFO] ===== GTDB Search completed =====
[2023-03-16 11:14:59,629] [INFO] DFAST_QC result json was written to OceanDNA-b32717/dqc_result.json
[2023-03-16 11:14:59,630] [INFO] DFAST_QC completed!
[2023-03-16 11:14:59,630] [INFO] Total running time: 0h2m5s