[2023-03-17 23:20:45,988] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:20:45,989] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:20:45,989] [INFO] DQC Reference Directory: /var/lib/cwl/stg856e0301-2f6b-4acc-9f5a-0bca12998086/dqc_reference
[2023-03-17 23:20:47,116] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:20:47,117] [INFO] Task started: Prodigal
[2023-03-17 23:20:47,117] [INFO] Running command: cat /var/lib/cwl/stg59922686-ce00-4949-ab23-c3d0624b72b1/OceanDNA-b37156.fa | prodigal -d OceanDNA-b37156/cds.fna -a OceanDNA-b37156/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:21:01,277] [INFO] Task succeeded: Prodigal
[2023-03-17 23:21:01,277] [INFO] Task started: HMMsearch
[2023-03-17 23:21:01,277] [INFO] Running command: hmmsearch --tblout OceanDNA-b37156/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg856e0301-2f6b-4acc-9f5a-0bca12998086/dqc_reference/reference_markers.hmm OceanDNA-b37156/protein.faa > /dev/null
[2023-03-17 23:21:01,482] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:21:01,482] [INFO] Found 6/6 markers.
[2023-03-17 23:21:01,501] [INFO] Query marker FASTA was written to OceanDNA-b37156/markers.fasta
[2023-03-17 23:21:01,503] [INFO] Task started: Blastn
[2023-03-17 23:21:01,503] [INFO] Running command: blastn -query OceanDNA-b37156/markers.fasta -db /var/lib/cwl/stg856e0301-2f6b-4acc-9f5a-0bca12998086/dqc_reference/reference_markers.fasta -out OceanDNA-b37156/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:21:02,105] [INFO] Task succeeded: Blastn
[2023-03-17 23:21:02,107] [INFO] Selected 35 target genomes.
[2023-03-17 23:21:02,107] [INFO] Target genome list was writen to OceanDNA-b37156/target_genomes.txt
[2023-03-17 23:21:02,144] [INFO] Task started: fastANI
[2023-03-17 23:21:02,144] [INFO] Running command: fastANI --query /var/lib/cwl/stg59922686-ce00-4949-ab23-c3d0624b72b1/OceanDNA-b37156.fa --refList OceanDNA-b37156/target_genomes.txt --output OceanDNA-b37156/fastani_result.tsv --threads 1
[2023-03-17 23:21:21,399] [INFO] Task succeeded: fastANI
[2023-03-17 23:21:21,399] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg856e0301-2f6b-4acc-9f5a-0bca12998086/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:21:21,399] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg856e0301-2f6b-4acc-9f5a-0bca12998086/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:21:21,400] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:21:21,400] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:21:21,400] [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
--------------------------------------------------------------------------------
[2023-03-17 23:21:21,402] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37156/tc_result.tsv
[2023-03-17 23:21:21,403] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:21:21,403] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:21:21,403] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg856e0301-2f6b-4acc-9f5a-0bca12998086/dqc_reference/checkm_data
[2023-03-17 23:21:21,406] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:21:21,409] [INFO] Task started: CheckM
[2023-03-17 23:21:21,409] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37156/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37156/checkm_input OceanDNA-b37156/checkm_result
[2023-03-17 23:21:59,711] [INFO] Task succeeded: CheckM
[2023-03-17 23:21:59,712] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:21:59,714] [INFO] ===== Completeness check finished =====
[2023-03-17 23:21:59,714] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:21:59,714] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37156/markers.fasta)
[2023-03-17 23:21:59,715] [INFO] Task started: Blastn
[2023-03-17 23:21:59,715] [INFO] Running command: blastn -query OceanDNA-b37156/markers.fasta -db /var/lib/cwl/stg856e0301-2f6b-4acc-9f5a-0bca12998086/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37156/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:22:00,733] [INFO] Task succeeded: Blastn
[2023-03-17 23:22:00,734] [INFO] Selected 14 target genomes.
[2023-03-17 23:22:00,734] [INFO] Target genome list was writen to OceanDNA-b37156/target_genomes_gtdb.txt
[2023-03-17 23:22:00,795] [INFO] Task started: fastANI
[2023-03-17 23:22:00,795] [INFO] Running command: fastANI --query /var/lib/cwl/stg59922686-ce00-4949-ab23-c3d0624b72b1/OceanDNA-b37156.fa --refList OceanDNA-b37156/target_genomes_gtdb.txt --output OceanDNA-b37156/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:22:07,575] [INFO] Task succeeded: fastANI
[2023-03-17 23:22:07,580] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 23:22:07,580] [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_002726925.1	s__UBA4421 sp002726925	98.172	515	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	98.34	98.19	0.75	0.72	3	conclusive
GCA_004213835.1	s__UBA4421 sp004213835	87.6384	401	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	97.72	97.72	0.50	0.50	2	-
GCA_902613475.1	s__UBA4421 sp902613475	80.0198	273	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779425.1	s__UBA4421 sp016779425	79.5955	264	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	97.24	97.24	0.58	0.58	2	-
GCA_902528515.1	s__UBA4421 sp902528515	78.7477	265	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002704225.1	s__UBA4421 sp002704225	77.2353	166	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	99.56	99.05	0.92	0.86	4	-
GCA_009936775.1	s__UBA4421 sp009936775	76.8045	162	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009936895.1	s__UBA4421 sp009936895	76.7803	124	757	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA4421	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:22:07,580] [INFO] GTDB search result was written to OceanDNA-b37156/result_gtdb.tsv
[2023-03-17 23:22:07,581] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:22:07,582] [INFO] DFAST_QC result json was written to OceanDNA-b37156/dqc_result.json
[2023-03-17 23:22:07,582] [INFO] DFAST_QC completed!
[2023-03-17 23:22:07,582] [INFO] Total running time: 0h1m22s