[2023-03-17 11:36:54,003] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:36:54,003] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:36:54,003] [INFO] DQC Reference Directory: /var/lib/cwl/stg60bb35d7-cf57-4b63-bc07-6daa069bd379/dqc_reference
[2023-03-17 11:36:55,106] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:36:55,106] [INFO] Task started: Prodigal
[2023-03-17 11:36:55,106] [INFO] Running command: cat /var/lib/cwl/stg8a0a7615-f62e-4cb3-9b72-63c9bd64700a/OceanDNA-b26246.fa | prodigal -d OceanDNA-b26246/cds.fna -a OceanDNA-b26246/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:37:05,982] [INFO] Task succeeded: Prodigal
[2023-03-17 11:37:05,982] [INFO] Task started: HMMsearch
[2023-03-17 11:37:05,983] [INFO] Running command: hmmsearch --tblout OceanDNA-b26246/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60bb35d7-cf57-4b63-bc07-6daa069bd379/dqc_reference/reference_markers.hmm OceanDNA-b26246/protein.faa > /dev/null
[2023-03-17 11:37:06,165] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:37:06,165] [INFO] Found 6/6 markers.
[2023-03-17 11:37:06,186] [INFO] Query marker FASTA was written to OceanDNA-b26246/markers.fasta
[2023-03-17 11:37:06,187] [INFO] Task started: Blastn
[2023-03-17 11:37:06,187] [INFO] Running command: blastn -query OceanDNA-b26246/markers.fasta -db /var/lib/cwl/stg60bb35d7-cf57-4b63-bc07-6daa069bd379/dqc_reference/reference_markers.fasta -out OceanDNA-b26246/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:37:06,799] [INFO] Task succeeded: Blastn
[2023-03-17 11:37:06,804] [INFO] Selected 35 target genomes.
[2023-03-17 11:37:06,804] [INFO] Target genome list was writen to OceanDNA-b26246/target_genomes.txt
[2023-03-17 11:37:06,830] [INFO] Task started: fastANI
[2023-03-17 11:37:06,830] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a0a7615-f62e-4cb3-9b72-63c9bd64700a/OceanDNA-b26246.fa --refList OceanDNA-b26246/target_genomes.txt --output OceanDNA-b26246/fastani_result.tsv --threads 1
[2023-03-17 11:37:27,709] [INFO] Task succeeded: fastANI
[2023-03-17 11:37:27,709] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60bb35d7-cf57-4b63-bc07-6daa069bd379/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:37:27,709] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60bb35d7-cf57-4b63-bc07-6daa069bd379/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:37:27,710] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:37:27,710] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:37:27,710] [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 11:37:27,711] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26246/tc_result.tsv
[2023-03-17 11:37:27,712] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:37:27,713] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:37:27,713] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60bb35d7-cf57-4b63-bc07-6daa069bd379/dqc_reference/checkm_data
[2023-03-17 11:37:27,716] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:37:27,793] [INFO] Task started: CheckM
[2023-03-17 11:37:27,793] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26246/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26246/checkm_input OceanDNA-b26246/checkm_result
[2023-03-17 11:37:59,309] [INFO] Task succeeded: CheckM
[2023-03-17 11:37:59,310] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.65%
Contamintation: 6.25%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 11:37:59,325] [INFO] ===== Completeness check finished =====
[2023-03-17 11:37:59,325] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:37:59,325] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26246/markers.fasta)
[2023-03-17 11:37:59,326] [INFO] Task started: Blastn
[2023-03-17 11:37:59,326] [INFO] Running command: blastn -query OceanDNA-b26246/markers.fasta -db /var/lib/cwl/stg60bb35d7-cf57-4b63-bc07-6daa069bd379/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26246/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:38:00,414] [INFO] Task succeeded: Blastn
[2023-03-17 11:38:00,418] [INFO] Selected 9 target genomes.
[2023-03-17 11:38:00,418] [INFO] Target genome list was writen to OceanDNA-b26246/target_genomes_gtdb.txt
[2023-03-17 11:38:00,427] [INFO] Task started: fastANI
[2023-03-17 11:38:00,427] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a0a7615-f62e-4cb3-9b72-63c9bd64700a/OceanDNA-b26246.fa --refList OceanDNA-b26246/target_genomes_gtdb.txt --output OceanDNA-b26246/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:38:04,363] [INFO] Task succeeded: fastANI
[2023-03-17 11:38:04,369] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:38:04,369] [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_002378605.1	s__UBA3439 sp002378605	99.2882	432	564	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	99.28	99.28	0.80	0.80	2	conclusive
GCA_905182545.1	s__UBA3439 sp905182545	90.2282	467	564	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017859295.1	s__UBA3439 sp017859295	90.0715	419	564	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	98.52	98.52	0.78	0.78	2	-
GCA_016778825.1	s__UBA3439 sp016778825	89.2131	250	564	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009919335.1	s__UBA3439 sp009919335	80.3646	317	564	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	98.81	98.81	0.76	0.76	2	-
GCA_016778895.1	s__UBA3439 sp016778895	79.701	359	564	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	99.63	99.63	0.87	0.87	2	-
GCA_902583715.1	s__UBA3439 sp902583715	77.1278	63	564	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	95.85	95.85	0.55	0.55	2	-
GCA_902559985.1	s__UBA3439 sp902559985	77.0157	105	564	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:38:04,370] [INFO] GTDB search result was written to OceanDNA-b26246/result_gtdb.tsv
[2023-03-17 11:38:04,370] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:38:04,373] [INFO] DFAST_QC result json was written to OceanDNA-b26246/dqc_result.json
[2023-03-17 11:38:04,373] [INFO] DFAST_QC completed!
[2023-03-17 11:38:04,373] [INFO] Total running time: 0h1m10s