[2023-03-15 17:50:47,194] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:50:47,195] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:50:47,195] [INFO] DQC Reference Directory: /var/lib/cwl/stgd54b92cc-fd4a-4c98-b22d-8c9864abd713/dqc_reference
[2023-03-15 17:50:48,292] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:50:48,293] [INFO] Task started: Prodigal
[2023-03-15 17:50:48,293] [INFO] Running command: cat /var/lib/cwl/stg7cc029ea-6074-4151-8306-a47ec85dac97/OceanDNA-b38157.fa | prodigal -d OceanDNA-b38157/cds.fna -a OceanDNA-b38157/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:50:58,809] [INFO] Task succeeded: Prodigal
[2023-03-15 17:50:58,809] [INFO] Task started: HMMsearch
[2023-03-15 17:50:58,810] [INFO] Running command: hmmsearch --tblout OceanDNA-b38157/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd54b92cc-fd4a-4c98-b22d-8c9864abd713/dqc_reference/reference_markers.hmm OceanDNA-b38157/protein.faa > /dev/null
[2023-03-15 17:50:58,986] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:50:58,986] [INFO] Found 6/6 markers.
[2023-03-15 17:50:59,001] [INFO] Query marker FASTA was written to OceanDNA-b38157/markers.fasta
[2023-03-15 17:50:59,002] [INFO] Task started: Blastn
[2023-03-15 17:50:59,002] [INFO] Running command: blastn -query OceanDNA-b38157/markers.fasta -db /var/lib/cwl/stgd54b92cc-fd4a-4c98-b22d-8c9864abd713/dqc_reference/reference_markers.fasta -out OceanDNA-b38157/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:50:59,609] [INFO] Task succeeded: Blastn
[2023-03-15 17:50:59,610] [INFO] Selected 24 target genomes.
[2023-03-15 17:50:59,610] [INFO] Target genome list was writen to OceanDNA-b38157/target_genomes.txt
[2023-03-15 17:50:59,624] [INFO] Task started: fastANI
[2023-03-15 17:50:59,624] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cc029ea-6074-4151-8306-a47ec85dac97/OceanDNA-b38157.fa --refList OceanDNA-b38157/target_genomes.txt --output OceanDNA-b38157/fastani_result.tsv --threads 1
[2023-03-15 17:51:13,671] [INFO] Task succeeded: fastANI
[2023-03-15 17:51:13,671] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd54b92cc-fd4a-4c98-b22d-8c9864abd713/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:51:13,672] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd54b92cc-fd4a-4c98-b22d-8c9864abd713/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:51:13,672] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:51:13,672] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 17:51:13,672] [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 17:51:13,672] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38157/tc_result.tsv
[2023-03-15 17:51:13,672] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:51:13,672] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:51:13,672] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd54b92cc-fd4a-4c98-b22d-8c9864abd713/dqc_reference/checkm_data
[2023-03-15 17:51:13,675] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:51:13,680] [INFO] Task started: CheckM
[2023-03-15 17:51:13,680] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38157/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38157/checkm_input OceanDNA-b38157/checkm_result
[2023-03-15 17:51:44,096] [INFO] Task succeeded: CheckM
[2023-03-15 17:51:44,096] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 17:51:44,099] [INFO] ===== Completeness check finished =====
[2023-03-15 17:51:44,099] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:51:44,099] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38157/markers.fasta)
[2023-03-15 17:51:44,101] [INFO] Task started: Blastn
[2023-03-15 17:51:44,101] [INFO] Running command: blastn -query OceanDNA-b38157/markers.fasta -db /var/lib/cwl/stgd54b92cc-fd4a-4c98-b22d-8c9864abd713/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38157/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:51:45,110] [INFO] Task succeeded: Blastn
[2023-03-15 17:51:45,110] [INFO] Selected 8 target genomes.
[2023-03-15 17:51:45,111] [INFO] Target genome list was writen to OceanDNA-b38157/target_genomes_gtdb.txt
[2023-03-15 17:51:45,115] [INFO] Task started: fastANI
[2023-03-15 17:51:45,115] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cc029ea-6074-4151-8306-a47ec85dac97/OceanDNA-b38157.fa --refList OceanDNA-b38157/target_genomes_gtdb.txt --output OceanDNA-b38157/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:51:48,661] [INFO] Task succeeded: fastANI
[2023-03-15 17:51:48,667] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 17:51:48,667] [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_002862405.1	s__Luminiphilus sp002862405	95.9979	491	574	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	95.70	95.58	0.78	0.76	4	conclusive
GCA_011524755.1	s__Luminiphilus sp011524755	92.7166	368	574	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	95.11	95.11	0.58	0.58	2	-
GCA_902547755.1	s__Luminiphilus sp902547755	90.6998	421	574	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003523185.1	s__Luminiphilus sp003523185	90.0189	490	574	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902613175.1	s__Luminiphilus sp902613175	89.7928	362	574	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002469785.1	s__Luminiphilus sp002469785	85.0705	363	574	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937065.1	s__Luminiphilus sp009937065	81.7258	407	574	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	81.3835	299	574	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.50	98.99	0.85	0.71	3	-
--------------------------------------------------------------------------------
[2023-03-15 17:51:48,668] [INFO] GTDB search result was written to OceanDNA-b38157/result_gtdb.tsv
[2023-03-15 17:51:48,668] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:51:48,669] [INFO] DFAST_QC result json was written to OceanDNA-b38157/dqc_result.json
[2023-03-15 17:51:48,669] [INFO] DFAST_QC completed!
[2023-03-15 17:51:48,669] [INFO] Total running time: 0h1m1s