[2023-03-17 10:48:45,548] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:48:45,548] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:48:45,548] [INFO] DQC Reference Directory: /var/lib/cwl/stge8a2ec5a-0307-41fb-8367-dac4ffef749c/dqc_reference
[2023-03-17 10:48:46,694] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:48:46,694] [INFO] Task started: Prodigal
[2023-03-17 10:48:46,694] [INFO] Running command: cat /var/lib/cwl/stg1c50a3ee-19f0-4f28-ae48-b32236d66ae0/OceanDNA-b40912.fa | prodigal -d OceanDNA-b40912/cds.fna -a OceanDNA-b40912/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:48:57,171] [INFO] Task succeeded: Prodigal
[2023-03-17 10:48:57,171] [INFO] Task started: HMMsearch
[2023-03-17 10:48:57,171] [INFO] Running command: hmmsearch --tblout OceanDNA-b40912/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8a2ec5a-0307-41fb-8367-dac4ffef749c/dqc_reference/reference_markers.hmm OceanDNA-b40912/protein.faa > /dev/null
[2023-03-17 10:48:57,433] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:48:57,434] [INFO] Found 6/6 markers.
[2023-03-17 10:48:57,449] [INFO] Query marker FASTA was written to OceanDNA-b40912/markers.fasta
[2023-03-17 10:48:57,449] [INFO] Task started: Blastn
[2023-03-17 10:48:57,449] [INFO] Running command: blastn -query OceanDNA-b40912/markers.fasta -db /var/lib/cwl/stge8a2ec5a-0307-41fb-8367-dac4ffef749c/dqc_reference/reference_markers.fasta -out OceanDNA-b40912/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:48:58,068] [INFO] Task succeeded: Blastn
[2023-03-17 10:48:58,069] [INFO] Selected 32 target genomes.
[2023-03-17 10:48:58,069] [INFO] Target genome list was writen to OceanDNA-b40912/target_genomes.txt
[2023-03-17 10:48:58,126] [INFO] Task started: fastANI
[2023-03-17 10:48:58,126] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c50a3ee-19f0-4f28-ae48-b32236d66ae0/OceanDNA-b40912.fa --refList OceanDNA-b40912/target_genomes.txt --output OceanDNA-b40912/fastani_result.tsv --threads 1
[2023-03-17 10:49:16,466] [INFO] Task succeeded: fastANI
[2023-03-17 10:49:16,467] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8a2ec5a-0307-41fb-8367-dac4ffef749c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:49:16,467] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8a2ec5a-0307-41fb-8367-dac4ffef749c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:49:16,467] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:49:16,467] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 10:49:16,467] [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 10:49:16,468] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40912/tc_result.tsv
[2023-03-17 10:49:16,468] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:49:16,468] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:49:16,468] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8a2ec5a-0307-41fb-8367-dac4ffef749c/dqc_reference/checkm_data
[2023-03-17 10:49:16,471] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:49:16,476] [INFO] Task started: CheckM
[2023-03-17 10:49:16,476] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40912/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40912/checkm_input OceanDNA-b40912/checkm_result
[2023-03-17 10:49:47,107] [INFO] Task succeeded: CheckM
[2023-03-17 10:49:47,108] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.76%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 10:49:47,111] [INFO] ===== Completeness check finished =====
[2023-03-17 10:49:47,111] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:49:47,111] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40912/markers.fasta)
[2023-03-17 10:49:47,112] [INFO] Task started: Blastn
[2023-03-17 10:49:47,112] [INFO] Running command: blastn -query OceanDNA-b40912/markers.fasta -db /var/lib/cwl/stge8a2ec5a-0307-41fb-8367-dac4ffef749c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40912/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:49:48,114] [INFO] Task succeeded: Blastn
[2023-03-17 10:49:48,114] [INFO] Selected 9 target genomes.
[2023-03-17 10:49:48,114] [INFO] Target genome list was writen to OceanDNA-b40912/target_genomes_gtdb.txt
[2023-03-17 10:49:48,148] [INFO] Task started: fastANI
[2023-03-17 10:49:48,148] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c50a3ee-19f0-4f28-ae48-b32236d66ae0/OceanDNA-b40912.fa --refList OceanDNA-b40912/target_genomes_gtdb.txt --output OceanDNA-b40912/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:49:52,659] [INFO] Task succeeded: fastANI
[2023-03-17 10:49:52,664] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 10:49:52,664] [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_002729315.1	s__UBA9145 sp002729315	99.0301	476	542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002691885.1	s__UBA9145 sp002691885	90.9773	430	542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	100.00	100.00	0.99	0.99	2	-
GCA_008081045.1	s__UBA9145 sp008081045	86.4152	452	542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.92	98.40	0.89	0.82	4	-
GCA_902537815.1	s__UBA9145 sp902537815	85.8304	336	542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902597095.1	s__UBA9145 sp902597095	85.5978	368	542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002719575.1	s__UBA9145 sp002719575	78.8436	269	542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002477465.1	s__UBA9145 sp002477465	76.6562	71	542	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__UBA9145	95.0	98.95	97.46	0.90	0.76	11	-
--------------------------------------------------------------------------------
[2023-03-17 10:49:52,665] [INFO] GTDB search result was written to OceanDNA-b40912/result_gtdb.tsv
[2023-03-17 10:49:52,665] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:49:52,665] [INFO] DFAST_QC result json was written to OceanDNA-b40912/dqc_result.json
[2023-03-17 10:49:52,666] [INFO] DFAST_QC completed!
[2023-03-17 10:49:52,666] [INFO] Total running time: 0h1m7s