[2023-03-16 13:03:55,321] [INFO] DFAST_QC pipeline started.
[2023-03-16 13:03:55,321] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 13:03:55,321] [INFO] DQC Reference Directory: /var/lib/cwl/stge3af46b0-b6b2-4422-b312-617e1491d2f3/dqc_reference
[2023-03-16 13:03:57,163] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 13:03:57,163] [INFO] Task started: Prodigal
[2023-03-16 13:03:57,164] [INFO] Running command: cat /var/lib/cwl/stgc6d8fa96-fa43-4d31-b769-f2d16c3ffa08/OceanDNA-b29407.fa | prodigal -d OceanDNA-b29407/cds.fna -a OceanDNA-b29407/protein.faa -g 11 -q > /dev/null
[2023-03-16 13:04:09,751] [INFO] Task succeeded: Prodigal
[2023-03-16 13:04:09,751] [INFO] Task started: HMMsearch
[2023-03-16 13:04:09,751] [INFO] Running command: hmmsearch --tblout OceanDNA-b29407/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3af46b0-b6b2-4422-b312-617e1491d2f3/dqc_reference/reference_markers.hmm OceanDNA-b29407/protein.faa > /dev/null
[2023-03-16 13:04:09,882] [INFO] Task succeeded: HMMsearch
[2023-03-16 13:04:09,882] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgc6d8fa96-fa43-4d31-b769-f2d16c3ffa08/OceanDNA-b29407.fa]
[2023-03-16 13:04:09,899] [INFO] Query marker FASTA was written to OceanDNA-b29407/markers.fasta
[2023-03-16 13:04:09,900] [INFO] Task started: Blastn
[2023-03-16 13:04:09,900] [INFO] Running command: blastn -query OceanDNA-b29407/markers.fasta -db /var/lib/cwl/stge3af46b0-b6b2-4422-b312-617e1491d2f3/dqc_reference/reference_markers.fasta -out OceanDNA-b29407/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 13:04:10,353] [INFO] Task succeeded: Blastn
[2023-03-16 13:04:10,353] [INFO] Selected 5 target genomes.
[2023-03-16 13:04:10,354] [INFO] Target genome list was writen to OceanDNA-b29407/target_genomes.txt
[2023-03-16 13:04:10,359] [INFO] Task started: fastANI
[2023-03-16 13:04:10,359] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6d8fa96-fa43-4d31-b769-f2d16c3ffa08/OceanDNA-b29407.fa --refList OceanDNA-b29407/target_genomes.txt --output OceanDNA-b29407/fastani_result.tsv --threads 1
[2023-03-16 13:04:15,494] [INFO] Task succeeded: fastANI
[2023-03-16 13:04:15,494] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3af46b0-b6b2-4422-b312-617e1491d2f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 13:04:15,494] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3af46b0-b6b2-4422-b312-617e1491d2f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 13:04:15,499] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 13:04:15,499] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 13:04:15,499] [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
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	89.8934	415	457	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	89.5299	418	457	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	88.9662	410	457	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	85.13	392	457	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	84.6402	368	457	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 13:04:15,499] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29407/tc_result.tsv
[2023-03-16 13:04:15,499] [INFO] ===== Taxonomy check completed =====
[2023-03-16 13:04:15,499] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 13:04:15,499] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3af46b0-b6b2-4422-b312-617e1491d2f3/dqc_reference/checkm_data
[2023-03-16 13:04:15,500] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 13:04:15,503] [INFO] Task started: CheckM
[2023-03-16 13:04:15,504] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29407/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29407/checkm_input OceanDNA-b29407/checkm_result
[2023-03-16 13:04:41,851] [INFO] Task succeeded: CheckM
[2023-03-16 13:04:41,851] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 29.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 13:04:41,853] [INFO] ===== Completeness check finished =====
[2023-03-16 13:04:41,854] [INFO] ===== Start GTDB Search =====
[2023-03-16 13:04:41,854] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29407/markers.fasta)
[2023-03-16 13:04:41,854] [INFO] Task started: Blastn
[2023-03-16 13:04:41,854] [INFO] Running command: blastn -query OceanDNA-b29407/markers.fasta -db /var/lib/cwl/stge3af46b0-b6b2-4422-b312-617e1491d2f3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29407/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 13:04:42,336] [INFO] Task succeeded: Blastn
[2023-03-16 13:04:42,337] [INFO] Selected 7 target genomes.
[2023-03-16 13:04:42,337] [INFO] Target genome list was writen to OceanDNA-b29407/target_genomes_gtdb.txt
[2023-03-16 13:04:42,360] [INFO] Task started: fastANI
[2023-03-16 13:04:42,360] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6d8fa96-fa43-4d31-b769-f2d16c3ffa08/OceanDNA-b29407.fa --refList OceanDNA-b29407/target_genomes_gtdb.txt --output OceanDNA-b29407/fastani_result_gtdb.tsv --threads 1
[2023-03-16 13:04:47,923] [INFO] Task succeeded: fastANI
[2023-03-16 13:04:47,928] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 13:04:47,928] [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
GCF_000473325.1	s__Leisingera caerulea	89.8934	415	457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458395.1	s__Leisingera aquaemixtae	89.5299	418	457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	97.55	97.51	0.94	0.92	3	-
GCF_000473145.1	s__Leisingera daeponensis	88.9662	410	457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.26	98.26	0.94	0.94	2	-
GCF_013317235.1	s__Leisingera sp013317235	86.7541	378	457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000203975.2	s__Leisingera sp000203975	85.9766	374	457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.92	98.17	0.96	0.94	6	-
GCF_001679925.1	s__Leisingera sp001679925	85.5191	379	457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000511355.1	s__Leisingera methylohalidivorans	84.6402	368	457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 13:04:47,928] [INFO] GTDB search result was written to OceanDNA-b29407/result_gtdb.tsv
[2023-03-16 13:04:47,928] [INFO] ===== GTDB Search completed =====
[2023-03-16 13:04:47,929] [INFO] DFAST_QC result json was written to OceanDNA-b29407/dqc_result.json
[2023-03-16 13:04:47,929] [INFO] DFAST_QC completed!
[2023-03-16 13:04:47,929] [INFO] Total running time: 0h0m53s