[2023-03-18 08:17:20,536] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:17:20,537] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:17:20,537] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7308f77-91fd-4d17-b94d-6b856965785c/dqc_reference
[2023-03-18 08:17:21,633] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:17:21,634] [INFO] Task started: Prodigal
[2023-03-18 08:17:21,634] [INFO] Running command: cat /var/lib/cwl/stgdeac56bd-0e6b-4ab6-8889-561bafd5a07d/OceanDNA-b44609.fa | prodigal -d OceanDNA-b44609/cds.fna -a OceanDNA-b44609/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:17:42,788] [INFO] Task succeeded: Prodigal
[2023-03-18 08:17:42,788] [INFO] Task started: HMMsearch
[2023-03-18 08:17:42,788] [INFO] Running command: hmmsearch --tblout OceanDNA-b44609/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7308f77-91fd-4d17-b94d-6b856965785c/dqc_reference/reference_markers.hmm OceanDNA-b44609/protein.faa > /dev/null
[2023-03-18 08:17:43,111] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:17:43,111] [INFO] Found 6/6 markers.
[2023-03-18 08:17:43,139] [INFO] Query marker FASTA was written to OceanDNA-b44609/markers.fasta
[2023-03-18 08:17:43,139] [INFO] Task started: Blastn
[2023-03-18 08:17:43,140] [INFO] Running command: blastn -query OceanDNA-b44609/markers.fasta -db /var/lib/cwl/stgb7308f77-91fd-4d17-b94d-6b856965785c/dqc_reference/reference_markers.fasta -out OceanDNA-b44609/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:17:43,814] [INFO] Task succeeded: Blastn
[2023-03-18 08:17:43,815] [INFO] Selected 32 target genomes.
[2023-03-18 08:17:43,815] [INFO] Target genome list was writen to OceanDNA-b44609/target_genomes.txt
[2023-03-18 08:17:43,831] [INFO] Task started: fastANI
[2023-03-18 08:17:43,831] [INFO] Running command: fastANI --query /var/lib/cwl/stgdeac56bd-0e6b-4ab6-8889-561bafd5a07d/OceanDNA-b44609.fa --refList OceanDNA-b44609/target_genomes.txt --output OceanDNA-b44609/fastani_result.tsv --threads 1
[2023-03-18 08:18:05,117] [INFO] Task succeeded: fastANI
[2023-03-18 08:18:05,118] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7308f77-91fd-4d17-b94d-6b856965785c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:18:05,118] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7308f77-91fd-4d17-b94d-6b856965785c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:18:05,121] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:18:05,121] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:18:05,121] [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
Woeseia oceani	strain=XK5	GCA_001677435.1	1548547	1548547	type	True	76.6342	106	1115	95	below_threshold
Steroidobacter agariperforans	strain=KA5-B	GCA_004138335.1	268404	268404	type	True	75.028	52	1115	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:18:05,122] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44609/tc_result.tsv
[2023-03-18 08:18:05,122] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:18:05,122] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:18:05,122] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7308f77-91fd-4d17-b94d-6b856965785c/dqc_reference/checkm_data
[2023-03-18 08:18:05,123] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:18:05,127] [INFO] Task started: CheckM
[2023-03-18 08:18:05,128] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44609/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44609/checkm_input OceanDNA-b44609/checkm_result
[2023-03-18 08:18:57,890] [INFO] Task succeeded: CheckM
[2023-03-18 08:18:57,890] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:18:57,892] [INFO] ===== Completeness check finished =====
[2023-03-18 08:18:57,892] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:18:57,892] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44609/markers.fasta)
[2023-03-18 08:18:57,893] [INFO] Task started: Blastn
[2023-03-18 08:18:57,893] [INFO] Running command: blastn -query OceanDNA-b44609/markers.fasta -db /var/lib/cwl/stgb7308f77-91fd-4d17-b94d-6b856965785c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44609/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:18:59,030] [INFO] Task succeeded: Blastn
[2023-03-18 08:18:59,031] [INFO] Selected 30 target genomes.
[2023-03-18 08:18:59,031] [INFO] Target genome list was writen to OceanDNA-b44609/target_genomes_gtdb.txt
[2023-03-18 08:18:59,237] [INFO] Task started: fastANI
[2023-03-18 08:18:59,238] [INFO] Running command: fastANI --query /var/lib/cwl/stgdeac56bd-0e6b-4ab6-8889-561bafd5a07d/OceanDNA-b44609.fa --refList OceanDNA-b44609/target_genomes_gtdb.txt --output OceanDNA-b44609/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:19:16,707] [INFO] Task succeeded: fastANI
[2023-03-18 08:19:16,715] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:19:16,715] [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_002338605.1	s__UBA1847 sp002338605	79.3073	119	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002338615.1	s__UBA1844 sp002338615	77.1939	217	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1844	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001045.1	s__UBA1847 sp013001045	76.8279	94	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	99.51	99.51	0.75	0.75	2	-
GCF_001677435.1	s__Woeseia oceani	76.6342	106	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__Woeseia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013043165.1	s__UBA1847 sp013043165	76.5177	127	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	99.92	99.83	0.96	0.93	3	-
GCA_009937525.1	s__JAACFE01 sp009937525	76.4038	109	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004282875.1	s__UBA1847 sp004282875	76.347	116	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042375.1	s__UBA1847 sp013042375	76.2794	132	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	99.79	99.73	0.92	0.88	6	-
GCA_009937615.1	s__JAACFB01 sp009937615	76.2085	101	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937605.1	s__UBA1847 sp009937605	76.2	89	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937505.1	s__JAACFE01 sp009937505	76.1629	100	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018677555.1	s__IDS-8 sp018677555	75.7067	89	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__IDS-8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004138335.1	s__Steroidobacter_A agariperforans	75.028	52	1115	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__Steroidobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:19:16,715] [INFO] GTDB search result was written to OceanDNA-b44609/result_gtdb.tsv
[2023-03-18 08:19:16,715] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:19:16,716] [INFO] DFAST_QC result json was written to OceanDNA-b44609/dqc_result.json
[2023-03-18 08:19:16,716] [INFO] DFAST_QC completed!
[2023-03-18 08:19:16,716] [INFO] Total running time: 0h1m56s