[2023-03-15 13:20:53,636] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:20:53,636] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:20:53,636] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1e43369-d827-4493-9260-58327cb60cbe/dqc_reference
[2023-03-15 13:20:54,993] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:20:54,993] [INFO] Task started: Prodigal
[2023-03-15 13:20:54,993] [INFO] Running command: cat /var/lib/cwl/stg5e4bd945-d455-48a4-91fa-75c24109d542/OceanDNA-b29493.fa | prodigal -d OceanDNA-b29493/cds.fna -a OceanDNA-b29493/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:21:05,027] [INFO] Task succeeded: Prodigal
[2023-03-15 13:21:05,027] [INFO] Task started: HMMsearch
[2023-03-15 13:21:05,027] [INFO] Running command: hmmsearch --tblout OceanDNA-b29493/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1e43369-d827-4493-9260-58327cb60cbe/dqc_reference/reference_markers.hmm OceanDNA-b29493/protein.faa > /dev/null
[2023-03-15 13:21:05,227] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:21:05,228] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg5e4bd945-d455-48a4-91fa-75c24109d542/OceanDNA-b29493.fa]
[2023-03-15 13:21:05,248] [INFO] Query marker FASTA was written to OceanDNA-b29493/markers.fasta
[2023-03-15 13:21:05,250] [INFO] Task started: Blastn
[2023-03-15 13:21:05,250] [INFO] Running command: blastn -query OceanDNA-b29493/markers.fasta -db /var/lib/cwl/stgc1e43369-d827-4493-9260-58327cb60cbe/dqc_reference/reference_markers.fasta -out OceanDNA-b29493/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:21:05,711] [INFO] Task succeeded: Blastn
[2023-03-15 13:21:05,712] [INFO] Selected 5 target genomes.
[2023-03-15 13:21:05,712] [INFO] Target genome list was writen to OceanDNA-b29493/target_genomes.txt
[2023-03-15 13:21:05,716] [INFO] Task started: fastANI
[2023-03-15 13:21:05,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e4bd945-d455-48a4-91fa-75c24109d542/OceanDNA-b29493.fa --refList OceanDNA-b29493/target_genomes.txt --output OceanDNA-b29493/fastani_result.tsv --threads 1
[2023-03-15 13:21:08,676] [INFO] Task succeeded: fastANI
[2023-03-15 13:21:08,676] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1e43369-d827-4493-9260-58327cb60cbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:21:08,676] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1e43369-d827-4493-9260-58327cb60cbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:21:08,683] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:21:08,683] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 13:21:08,684] [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
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	85.3172	365	464	95	below_threshold
Loktanella fryxellensis	strain=DSM 16213	GCA_900110065.1	245187	245187	type	True	80.8366	259	464	95	below_threshold
Loktanella salsilacus	strain=DSM 16199	GCA_900114485.1	195913	195913	type	True	79.2447	227	464	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	76.7957	68	464	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	76.7609	75	464	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:21:08,684] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29493/tc_result.tsv
[2023-03-15 13:21:08,684] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:21:08,685] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:21:08,685] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1e43369-d827-4493-9260-58327cb60cbe/dqc_reference/checkm_data
[2023-03-15 13:21:08,686] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:21:08,691] [INFO] Task started: CheckM
[2023-03-15 13:21:08,691] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29493/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29493/checkm_input OceanDNA-b29493/checkm_result
[2023-03-15 13:21:38,919] [INFO] Task succeeded: CheckM
[2023-03-15 13:21:38,919] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 21.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:21:38,923] [INFO] ===== Completeness check finished =====
[2023-03-15 13:21:38,923] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:21:38,923] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29493/markers.fasta)
[2023-03-15 13:21:38,924] [INFO] Task started: Blastn
[2023-03-15 13:21:38,924] [INFO] Running command: blastn -query OceanDNA-b29493/markers.fasta -db /var/lib/cwl/stgc1e43369-d827-4493-9260-58327cb60cbe/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29493/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:21:39,391] [INFO] Task succeeded: Blastn
[2023-03-15 13:21:39,392] [INFO] Selected 5 target genomes.
[2023-03-15 13:21:39,392] [INFO] Target genome list was writen to OceanDNA-b29493/target_genomes_gtdb.txt
[2023-03-15 13:21:39,400] [INFO] Task started: fastANI
[2023-03-15 13:21:39,400] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e4bd945-d455-48a4-91fa-75c24109d542/OceanDNA-b29493.fa --refList OceanDNA-b29493/target_genomes_gtdb.txt --output OceanDNA-b29493/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:21:42,533] [INFO] Task succeeded: fastANI
[2023-03-15 13:21:42,538] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:21:42,538] [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_900128995.1	s__Loktanella atrilutea	85.3172	365	464	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110065.1	s__Loktanella fryxellensis	80.8366	259	464	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114485.1	s__Loktanella salsilacus	79.2447	227	464	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	97.76	97.75	0.91	0.90	3	-
GCF_004145405.1	s__Loktanella sp004145405	78.649	183	464	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420005.1	s__Loktanella sp001420005	78.2185	175	464	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Loktanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:21:42,540] [INFO] GTDB search result was written to OceanDNA-b29493/result_gtdb.tsv
[2023-03-15 13:21:42,540] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:21:42,542] [INFO] DFAST_QC result json was written to OceanDNA-b29493/dqc_result.json
[2023-03-15 13:21:42,542] [INFO] DFAST_QC completed!
[2023-03-15 13:21:42,542] [INFO] Total running time: 0h0m49s