[2023-03-17 23:39:58,822] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:39:58,822] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:39:58,823] [INFO] DQC Reference Directory: /var/lib/cwl/stg95619386-35b7-4385-b287-00198b02a5e6/dqc_reference
[2023-03-17 23:39:59,972] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:39:59,972] [INFO] Task started: Prodigal
[2023-03-17 23:39:59,973] [INFO] Running command: cat /var/lib/cwl/stg588cb102-c8ea-49ff-8ca3-5792f57ff6a4/OceanDNA-b40449.fa | prodigal -d OceanDNA-b40449/cds.fna -a OceanDNA-b40449/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:40:16,831] [INFO] Task succeeded: Prodigal
[2023-03-17 23:40:16,831] [INFO] Task started: HMMsearch
[2023-03-17 23:40:16,831] [INFO] Running command: hmmsearch --tblout OceanDNA-b40449/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95619386-35b7-4385-b287-00198b02a5e6/dqc_reference/reference_markers.hmm OceanDNA-b40449/protein.faa > /dev/null
[2023-03-17 23:40:17,019] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:40:17,019] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg588cb102-c8ea-49ff-8ca3-5792f57ff6a4/OceanDNA-b40449.fa]
[2023-03-17 23:40:17,035] [INFO] Query marker FASTA was written to OceanDNA-b40449/markers.fasta
[2023-03-17 23:40:17,036] [INFO] Task started: Blastn
[2023-03-17 23:40:17,036] [INFO] Running command: blastn -query OceanDNA-b40449/markers.fasta -db /var/lib/cwl/stg95619386-35b7-4385-b287-00198b02a5e6/dqc_reference/reference_markers.fasta -out OceanDNA-b40449/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:40:17,682] [INFO] Task succeeded: Blastn
[2023-03-17 23:40:17,683] [INFO] Selected 25 target genomes.
[2023-03-17 23:40:17,683] [INFO] Target genome list was writen to OceanDNA-b40449/target_genomes.txt
[2023-03-17 23:40:17,806] [INFO] Task started: fastANI
[2023-03-17 23:40:17,806] [INFO] Running command: fastANI --query /var/lib/cwl/stg588cb102-c8ea-49ff-8ca3-5792f57ff6a4/OceanDNA-b40449.fa --refList OceanDNA-b40449/target_genomes.txt --output OceanDNA-b40449/fastani_result.tsv --threads 1
[2023-03-17 23:40:34,964] [INFO] Task succeeded: fastANI
[2023-03-17 23:40:34,964] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95619386-35b7-4385-b287-00198b02a5e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:40:34,964] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95619386-35b7-4385-b287-00198b02a5e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:40:34,969] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:40:34,969] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 23:40:34,969] [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
Pseudohongiella nitratireducens	strain=SCS-49	GCA_001642735.1	1768907	1768907	type	True	85.4457	713	920	95	below_threshold
Pseudohongiella nitratireducens	strain=CGMCC 1.15425	GCA_014642795.1	1768907	1768907	type	True	85.3397	716	920	95	below_threshold
Pseudohongiella spirulinae	strain=KCTC 32221	GCA_001444425.1	1249552	1249552	type	True	77.3415	126	920	95	below_threshold
Pseudohongiella acticola	strain=KCTC 42131	GCA_001758195.1	1524254	1524254	type	True	76.7896	125	920	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 23:40:34,969] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40449/tc_result.tsv
[2023-03-17 23:40:34,970] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:40:34,970] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:40:34,970] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95619386-35b7-4385-b287-00198b02a5e6/dqc_reference/checkm_data
[2023-03-17 23:40:34,970] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:40:34,975] [INFO] Task started: CheckM
[2023-03-17 23:40:34,975] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40449/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40449/checkm_input OceanDNA-b40449/checkm_result
[2023-03-17 23:41:19,492] [INFO] Task succeeded: CheckM
[2023-03-17 23:41:19,492] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:41:19,517] [INFO] ===== Completeness check finished =====
[2023-03-17 23:41:19,517] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:41:19,517] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40449/markers.fasta)
[2023-03-17 23:41:19,519] [INFO] Task started: Blastn
[2023-03-17 23:41:19,519] [INFO] Running command: blastn -query OceanDNA-b40449/markers.fasta -db /var/lib/cwl/stg95619386-35b7-4385-b287-00198b02a5e6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40449/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:41:20,567] [INFO] Task succeeded: Blastn
[2023-03-17 23:41:20,583] [INFO] Selected 24 target genomes.
[2023-03-17 23:41:20,583] [INFO] Target genome list was writen to OceanDNA-b40449/target_genomes_gtdb.txt
[2023-03-17 23:41:20,815] [INFO] Task started: fastANI
[2023-03-17 23:41:20,815] [INFO] Running command: fastANI --query /var/lib/cwl/stg588cb102-c8ea-49ff-8ca3-5792f57ff6a4/OceanDNA-b40449.fa --refList OceanDNA-b40449/target_genomes_gtdb.txt --output OceanDNA-b40449/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:41:35,881] [INFO] Task succeeded: fastANI
[2023-03-17 23:41:35,888] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:41:35,888] [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
GCF_001642735.1	s__Pseudohongiella nitratireducens	85.4424	711	920	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	99.60	98.82	0.97	0.93	4	-
GCA_001802565.1	s__UBA5078 sp001802565	77.7336	53	920	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA5078	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001444425.1	s__Pseudohongiella spirulinae	77.3415	126	920	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706685.1	s__Pseudohongiella sp002706685	77.1305	149	920	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	99.93	99.90	0.98	0.96	5	-
GCA_011050365.1	s__Pseudohongiella sp011050365	76.9152	132	920	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_004535785.1	s__Pseudohongiella sp004535785	76.881	89	920	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002711845.1	s__Pseudohongiella sp002711845	76.4427	125	920	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__Pseudohongiella	95.0	99.97	99.97	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-03-17 23:41:35,889] [INFO] GTDB search result was written to OceanDNA-b40449/result_gtdb.tsv
[2023-03-17 23:41:35,889] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:41:35,891] [INFO] DFAST_QC result json was written to OceanDNA-b40449/dqc_result.json
[2023-03-17 23:41:35,891] [INFO] DFAST_QC completed!
[2023-03-17 23:41:35,891] [INFO] Total running time: 0h1m37s