[2023-03-16 02:38:04,970] [INFO] DFAST_QC pipeline started.
[2023-03-16 02:38:04,971] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 02:38:04,971] [INFO] DQC Reference Directory: /var/lib/cwl/stgdace8633-158d-4005-994c-1aecc9c859d7/dqc_reference
[2023-03-16 02:38:06,281] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 02:38:06,282] [INFO] Task started: Prodigal
[2023-03-16 02:38:06,282] [INFO] Running command: cat /var/lib/cwl/stg9ddd944d-1276-4b02-b7f6-d7ee05bd6e8e/OceanDNA-b37716.fa | prodigal -d OceanDNA-b37716/cds.fna -a OceanDNA-b37716/protein.faa -g 11 -q > /dev/null
[2023-03-16 02:38:13,285] [INFO] Task succeeded: Prodigal
[2023-03-16 02:38:13,285] [INFO] Task started: HMMsearch
[2023-03-16 02:38:13,285] [INFO] Running command: hmmsearch --tblout OceanDNA-b37716/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdace8633-158d-4005-994c-1aecc9c859d7/dqc_reference/reference_markers.hmm OceanDNA-b37716/protein.faa > /dev/null
[2023-03-16 02:38:13,463] [INFO] Task succeeded: HMMsearch
[2023-03-16 02:38:13,463] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9ddd944d-1276-4b02-b7f6-d7ee05bd6e8e/OceanDNA-b37716.fa]
[2023-03-16 02:38:13,480] [INFO] Query marker FASTA was written to OceanDNA-b37716/markers.fasta
[2023-03-16 02:38:13,480] [INFO] Task started: Blastn
[2023-03-16 02:38:13,480] [INFO] Running command: blastn -query OceanDNA-b37716/markers.fasta -db /var/lib/cwl/stgdace8633-158d-4005-994c-1aecc9c859d7/dqc_reference/reference_markers.fasta -out OceanDNA-b37716/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:38:14,082] [INFO] Task succeeded: Blastn
[2023-03-16 02:38:14,083] [INFO] Selected 30 target genomes.
[2023-03-16 02:38:14,083] [INFO] Target genome list was writen to OceanDNA-b37716/target_genomes.txt
[2023-03-16 02:38:14,104] [INFO] Task started: fastANI
[2023-03-16 02:38:14,104] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ddd944d-1276-4b02-b7f6-d7ee05bd6e8e/OceanDNA-b37716.fa --refList OceanDNA-b37716/target_genomes.txt --output OceanDNA-b37716/fastani_result.tsv --threads 1
[2023-03-16 02:38:33,952] [INFO] Task succeeded: fastANI
[2023-03-16 02:38:33,953] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdace8633-158d-4005-994c-1aecc9c859d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 02:38:33,953] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdace8633-158d-4005-994c-1aecc9c859d7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 02:38:33,953] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 02:38:33,953] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 02:38:33,953] [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
--------------------------------------------------------------------------------
[2023-03-16 02:38:33,953] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37716/tc_result.tsv
[2023-03-16 02:38:33,954] [INFO] ===== Taxonomy check completed =====
[2023-03-16 02:38:33,954] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 02:38:33,954] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdace8633-158d-4005-994c-1aecc9c859d7/dqc_reference/checkm_data
[2023-03-16 02:38:33,956] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 02:38:33,959] [INFO] Task started: CheckM
[2023-03-16 02:38:33,959] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37716/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37716/checkm_input OceanDNA-b37716/checkm_result
[2023-03-16 02:38:56,930] [INFO] Task succeeded: CheckM
[2023-03-16 02:38:56,930] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 40.28%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 02:38:56,932] [INFO] ===== Completeness check finished =====
[2023-03-16 02:38:56,933] [INFO] ===== Start GTDB Search =====
[2023-03-16 02:38:56,933] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37716/markers.fasta)
[2023-03-16 02:38:56,933] [INFO] Task started: Blastn
[2023-03-16 02:38:56,933] [INFO] Running command: blastn -query OceanDNA-b37716/markers.fasta -db /var/lib/cwl/stgdace8633-158d-4005-994c-1aecc9c859d7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37716/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 02:38:57,911] [INFO] Task succeeded: Blastn
[2023-03-16 02:38:57,912] [INFO] Selected 18 target genomes.
[2023-03-16 02:38:57,912] [INFO] Target genome list was writen to OceanDNA-b37716/target_genomes_gtdb.txt
[2023-03-16 02:38:58,272] [INFO] Task started: fastANI
[2023-03-16 02:38:58,272] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ddd944d-1276-4b02-b7f6-d7ee05bd6e8e/OceanDNA-b37716.fa --refList OceanDNA-b37716/target_genomes_gtdb.txt --output OceanDNA-b37716/fastani_result_gtdb.tsv --threads 1
[2023-03-16 02:39:06,535] [INFO] Task succeeded: fastANI
[2023-03-16 02:39:06,541] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 02:39:06,541] [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_011523115.1	s__Luminiphilus sp011523115	97.3347	251	303	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_002705465.1	s__Luminiphilus sp002705465	93.6724	166	303	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902520195.1	s__Luminiphilus sp902520195	78.4352	68	303	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	96.03	95.89	0.61	0.58	3	-
GCA_902623175.1	s__Luminiphilus sp902623175	77.7781	66	303	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222695.1	s__Luminiphilus sp018222695	77.4616	69	303	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016778085.1	s__Luminiphilus sp016778085	77.4589	61	303	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016778045.1	s__Luminiphilus sp016778045	77.2907	66	303	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721785.1	s__Luminiphilus sp002721785	77.0972	70	303	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	99.68	99.68	0.89	0.89	2	-
GCA_002683395.1	s__Luminiphilus sp002683395	76.6246	56	303	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Luminiphilus	95.0	98.62	98.62	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-03-16 02:39:06,541] [INFO] GTDB search result was written to OceanDNA-b37716/result_gtdb.tsv
[2023-03-16 02:39:06,541] [INFO] ===== GTDB Search completed =====
[2023-03-16 02:39:06,542] [INFO] DFAST_QC result json was written to OceanDNA-b37716/dqc_result.json
[2023-03-16 02:39:06,542] [INFO] DFAST_QC completed!
[2023-03-16 02:39:06,542] [INFO] Total running time: 0h1m2s