[2023-03-16 00:43:05,190] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:43:05,190] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:43:05,190] [INFO] DQC Reference Directory: /var/lib/cwl/stg88ab1198-a7c3-4d81-9d5e-c2ab5a59382e/dqc_reference
[2023-03-16 00:43:06,283] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:43:06,283] [INFO] Task started: Prodigal
[2023-03-16 00:43:06,284] [INFO] Running command: cat /var/lib/cwl/stg2067a6d5-7fc6-43cf-b490-858e1c00fd5b/OceanDNA-b39489.fa | prodigal -d OceanDNA-b39489/cds.fna -a OceanDNA-b39489/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:43:20,094] [INFO] Task succeeded: Prodigal
[2023-03-16 00:43:20,094] [INFO] Task started: HMMsearch
[2023-03-16 00:43:20,094] [INFO] Running command: hmmsearch --tblout OceanDNA-b39489/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88ab1198-a7c3-4d81-9d5e-c2ab5a59382e/dqc_reference/reference_markers.hmm OceanDNA-b39489/protein.faa > /dev/null
[2023-03-16 00:43:20,280] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:43:20,281] [INFO] Found 6/6 markers.
[2023-03-16 00:43:20,296] [INFO] Query marker FASTA was written to OceanDNA-b39489/markers.fasta
[2023-03-16 00:43:20,297] [INFO] Task started: Blastn
[2023-03-16 00:43:20,297] [INFO] Running command: blastn -query OceanDNA-b39489/markers.fasta -db /var/lib/cwl/stg88ab1198-a7c3-4d81-9d5e-c2ab5a59382e/dqc_reference/reference_markers.fasta -out OceanDNA-b39489/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:43:20,894] [INFO] Task succeeded: Blastn
[2023-03-16 00:43:20,895] [INFO] Selected 34 target genomes.
[2023-03-16 00:43:20,895] [INFO] Target genome list was writen to OceanDNA-b39489/target_genomes.txt
[2023-03-16 00:43:21,161] [INFO] Task started: fastANI
[2023-03-16 00:43:21,161] [INFO] Running command: fastANI --query /var/lib/cwl/stg2067a6d5-7fc6-43cf-b490-858e1c00fd5b/OceanDNA-b39489.fa --refList OceanDNA-b39489/target_genomes.txt --output OceanDNA-b39489/fastani_result.tsv --threads 1
[2023-03-16 00:43:43,612] [INFO] Task succeeded: fastANI
[2023-03-16 00:43:43,612] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88ab1198-a7c3-4d81-9d5e-c2ab5a59382e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:43:43,612] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88ab1198-a7c3-4d81-9d5e-c2ab5a59382e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:43:43,612] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:43:43,613] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 00:43:43,613] [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
--------------------------------------------------------------------------------
[2023-03-16 00:43:43,614] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39489/tc_result.tsv
[2023-03-16 00:43:43,615] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:43:43,615] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:43:43,615] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88ab1198-a7c3-4d81-9d5e-c2ab5a59382e/dqc_reference/checkm_data
[2023-03-16 00:43:43,618] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:43:43,651] [INFO] Task started: CheckM
[2023-03-16 00:43:43,651] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39489/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39489/checkm_input OceanDNA-b39489/checkm_result
[2023-03-16 00:44:19,807] [INFO] Task succeeded: CheckM
[2023-03-16 00:44:19,808] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 00:44:19,868] [INFO] ===== Completeness check finished =====
[2023-03-16 00:44:19,868] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:44:19,868] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39489/markers.fasta)
[2023-03-16 00:44:19,869] [INFO] Task started: Blastn
[2023-03-16 00:44:19,869] [INFO] Running command: blastn -query OceanDNA-b39489/markers.fasta -db /var/lib/cwl/stg88ab1198-a7c3-4d81-9d5e-c2ab5a59382e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39489/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:44:20,872] [INFO] Task succeeded: Blastn
[2023-03-16 00:44:20,874] [INFO] Selected 15 target genomes.
[2023-03-16 00:44:20,874] [INFO] Target genome list was writen to OceanDNA-b39489/target_genomes_gtdb.txt
[2023-03-16 00:44:20,926] [INFO] Task started: fastANI
[2023-03-16 00:44:20,926] [INFO] Running command: fastANI --query /var/lib/cwl/stg2067a6d5-7fc6-43cf-b490-858e1c00fd5b/OceanDNA-b39489.fa --refList OceanDNA-b39489/target_genomes_gtdb.txt --output OceanDNA-b39489/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:44:27,953] [INFO] Task succeeded: fastANI
[2023-03-16 00:44:27,961] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 00:44:27,962] [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_018664075.1	s__HTCC2207 sp018664075	90.8177	522	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.59	99.59	0.81	0.81	2	-
GCA_002334915.1	s__HTCC2207 sp002334915	81.3651	317	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.52	99.52	0.87	0.87	2	-
GCA_002378645.1	s__HTCC2207 sp002378645	79.577	324	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.56	99.15	0.89	0.85	12	-
GCA_002685715.1	s__HTCC2207 sp002685715	78.8355	219	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018663035.1	s__HTCC2207 sp018663035	78.4257	210	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.88	99.88	0.90	0.90	2	-
GCA_905182265.1	s__HTCC2207 sp905182265	78.3421	250	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002335945.1	s__HTCC2207 sp002335945	78.0692	229	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	99.61	99.20	0.84	0.78	6	-
GCA_905182245.1	s__HTCC2207 sp905182245	77.9068	127	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017858135.1	s__HTCC2207 sp017858135	77.6373	147	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	98.96	98.94	0.87	0.86	3	-
GCA_017858295.1	s__HTCC2207 sp017858295	77.3915	125	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	97.83	97.83	0.77	0.77	2	-
GCA_000511875.1	s__HTCC2207 sp000511875	77.3235	161	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182855.1	s__HTCC2207 sp905182855	77.2595	95	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000153445.1	s__HTCC2207 sp000153445	77.1036	205	745	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	98.85	98.71	0.89	0.85	4	-
--------------------------------------------------------------------------------
[2023-03-16 00:44:27,963] [INFO] GTDB search result was written to OceanDNA-b39489/result_gtdb.tsv
[2023-03-16 00:44:27,964] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:44:27,966] [INFO] DFAST_QC result json was written to OceanDNA-b39489/dqc_result.json
[2023-03-16 00:44:27,966] [INFO] DFAST_QC completed!
[2023-03-16 00:44:27,966] [INFO] Total running time: 0h1m23s