[2023-03-15 11:36:00,599] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:36:00,601] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:36:00,601] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ab63431-f23c-4a87-ab0f-e0d44d9fa718/dqc_reference
[2023-03-15 11:36:02,577] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:36:02,577] [INFO] Task started: Prodigal
[2023-03-15 11:36:02,578] [INFO] Running command: cat /var/lib/cwl/stg1bfd9334-11ef-4362-a2e2-d583220164f8/OceanDNA-b38175.fa | prodigal -d OceanDNA-b38175/cds.fna -a OceanDNA-b38175/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:36:11,742] [INFO] Task succeeded: Prodigal
[2023-03-15 11:36:11,742] [INFO] Task started: HMMsearch
[2023-03-15 11:36:11,742] [INFO] Running command: hmmsearch --tblout OceanDNA-b38175/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ab63431-f23c-4a87-ab0f-e0d44d9fa718/dqc_reference/reference_markers.hmm OceanDNA-b38175/protein.faa > /dev/null
[2023-03-15 11:36:11,910] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:36:11,911] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1bfd9334-11ef-4362-a2e2-d583220164f8/OceanDNA-b38175.fa]
[2023-03-15 11:36:11,955] [INFO] Query marker FASTA was written to OceanDNA-b38175/markers.fasta
[2023-03-15 11:36:11,956] [INFO] Task started: Blastn
[2023-03-15 11:36:11,956] [INFO] Running command: blastn -query OceanDNA-b38175/markers.fasta -db /var/lib/cwl/stg9ab63431-f23c-4a87-ab0f-e0d44d9fa718/dqc_reference/reference_markers.fasta -out OceanDNA-b38175/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:36:14,700] [INFO] Task succeeded: Blastn
[2023-03-15 11:36:14,709] [INFO] Selected 23 target genomes.
[2023-03-15 11:36:14,709] [INFO] Target genome list was writen to OceanDNA-b38175/target_genomes.txt
[2023-03-15 11:36:14,723] [INFO] Task started: fastANI
[2023-03-15 11:36:14,724] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bfd9334-11ef-4362-a2e2-d583220164f8/OceanDNA-b38175.fa --refList OceanDNA-b38175/target_genomes.txt --output OceanDNA-b38175/fastani_result.tsv --threads 1
[2023-03-15 11:36:29,126] [INFO] Task succeeded: fastANI
[2023-03-15 11:36:29,126] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ab63431-f23c-4a87-ab0f-e0d44d9fa718/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:36:29,126] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ab63431-f23c-4a87-ab0f-e0d44d9fa718/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:36:29,127] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:36:29,127] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 11:36:29,127] [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
--------------------------------------------------------------------------------
[2023-03-15 11:36:29,130] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38175/tc_result.tsv
[2023-03-15 11:36:29,134] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:36:29,135] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:36:29,135] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ab63431-f23c-4a87-ab0f-e0d44d9fa718/dqc_reference/checkm_data
[2023-03-15 11:36:29,139] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:36:29,151] [INFO] Task started: CheckM
[2023-03-15 11:36:29,151] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38175/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38175/checkm_input OceanDNA-b38175/checkm_result
[2023-03-15 11:36:57,030] [INFO] Task succeeded: CheckM
[2023-03-15 11:36:57,030] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.22%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:36:57,163] [INFO] ===== Completeness check finished =====
[2023-03-15 11:36:57,163] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:36:57,163] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38175/markers.fasta)
[2023-03-15 11:36:57,164] [INFO] Task started: Blastn
[2023-03-15 11:36:57,164] [INFO] Running command: blastn -query OceanDNA-b38175/markers.fasta -db /var/lib/cwl/stg9ab63431-f23c-4a87-ab0f-e0d44d9fa718/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38175/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:36:58,135] [INFO] Task succeeded: Blastn
[2023-03-15 11:36:58,146] [INFO] Selected 8 target genomes.
[2023-03-15 11:36:58,146] [INFO] Target genome list was writen to OceanDNA-b38175/target_genomes_gtdb.txt
[2023-03-15 11:36:58,179] [INFO] Task started: fastANI
[2023-03-15 11:36:58,179] [INFO] Running command: fastANI --query /var/lib/cwl/stg1bfd9334-11ef-4362-a2e2-d583220164f8/OceanDNA-b38175.fa --refList OceanDNA-b38175/target_genomes_gtdb.txt --output OceanDNA-b38175/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:37:01,849] [INFO] Task succeeded: fastANI
[2023-03-15 11:37:01,854] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:37:01,854] [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_003523185.1	s__Luminiphilus sp003523185	95.327	456	506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902613175.1	s__Luminiphilus sp902613175	94.5138	293	506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902547755.1	s__Luminiphilus sp902547755	93.9701	362	506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011524755.1	s__Luminiphilus sp011524755	92.4144	356	506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	95.11	95.11	0.58	0.58	2	-
GCA_002862405.1	s__Luminiphilus sp002862405	90.8498	412	506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	95.70	95.58	0.78	0.76	4	-
GCA_002469785.1	s__Luminiphilus sp002469785	86.2461	328	506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691565.1	s__Luminiphilus sp002691565	82.1158	300	506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.50	98.99	0.85	0.71	3	-
GCA_009937065.1	s__Luminiphilus sp009937065	81.4923	365	506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:37:01,857] [INFO] GTDB search result was written to OceanDNA-b38175/result_gtdb.tsv
[2023-03-15 11:37:01,867] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:37:01,876] [INFO] DFAST_QC result json was written to OceanDNA-b38175/dqc_result.json
[2023-03-15 11:37:01,877] [INFO] DFAST_QC completed!
[2023-03-15 11:37:01,877] [INFO] Total running time: 0h1m1s