[2023-03-16 10:46:24,059] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:46:24,059] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:46:24,060] [INFO] DQC Reference Directory: /var/lib/cwl/stg43d44012-7372-47da-945a-04adce0d934b/dqc_reference
[2023-03-16 10:46:25,192] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:46:25,193] [INFO] Task started: Prodigal
[2023-03-16 10:46:25,193] [INFO] Running command: cat /var/lib/cwl/stgf9c9af02-8716-4f2e-a3b7-96b2c7897605/OceanDNA-b44627.fa | prodigal -d OceanDNA-b44627/cds.fna -a OceanDNA-b44627/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:46:46,147] [INFO] Task succeeded: Prodigal
[2023-03-16 10:46:46,148] [INFO] Task started: HMMsearch
[2023-03-16 10:46:46,148] [INFO] Running command: hmmsearch --tblout OceanDNA-b44627/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43d44012-7372-47da-945a-04adce0d934b/dqc_reference/reference_markers.hmm OceanDNA-b44627/protein.faa > /dev/null
[2023-03-16 10:46:46,344] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:46:46,344] [INFO] Found 6/6 markers.
[2023-03-16 10:46:46,364] [INFO] Query marker FASTA was written to OceanDNA-b44627/markers.fasta
[2023-03-16 10:46:46,365] [INFO] Task started: Blastn
[2023-03-16 10:46:46,365] [INFO] Running command: blastn -query OceanDNA-b44627/markers.fasta -db /var/lib/cwl/stg43d44012-7372-47da-945a-04adce0d934b/dqc_reference/reference_markers.fasta -out OceanDNA-b44627/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:46:46,909] [INFO] Task succeeded: Blastn
[2023-03-16 10:46:46,910] [INFO] Selected 26 target genomes.
[2023-03-16 10:46:46,910] [INFO] Target genome list was writen to OceanDNA-b44627/target_genomes.txt
[2023-03-16 10:46:46,980] [INFO] Task started: fastANI
[2023-03-16 10:46:46,980] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9c9af02-8716-4f2e-a3b7-96b2c7897605/OceanDNA-b44627.fa --refList OceanDNA-b44627/target_genomes.txt --output OceanDNA-b44627/fastani_result.tsv --threads 1
[2023-03-16 10:47:16,633] [INFO] Task succeeded: fastANI
[2023-03-16 10:47:16,634] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43d44012-7372-47da-945a-04adce0d934b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:47:16,634] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43d44012-7372-47da-945a-04adce0d934b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:47:16,639] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:47:16,639] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:47:16,639] [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
Marinicella litoralis	strain=DSM 25488	GCA_004363335.1	644220	644220	type	True	77.8458	297	1069	95	below_threshold
Marinicella litoralis	strain=KMM 3900	GCA_002591915.1	644220	644220	type	True	77.8299	301	1069	95	below_threshold
Marinicella sediminis	strain=F2	GCA_002000055.1	1792834	1792834	type	True	77.663	330	1069	95	below_threshold
Marinicella rhabdoformis	strain=3539	GCA_009671245.1	2580566	2580566	type	True	77.3637	162	1069	95	below_threshold
Marinicella pacifica	strain=CGMCC 1.12181	GCA_014636635.1	1171543	1171543	type	True	76.7106	126	1069	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:47:16,639] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44627/tc_result.tsv
[2023-03-16 10:47:16,639] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:47:16,639] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:47:16,639] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43d44012-7372-47da-945a-04adce0d934b/dqc_reference/checkm_data
[2023-03-16 10:47:16,640] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:47:16,738] [INFO] Task started: CheckM
[2023-03-16 10:47:16,739] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44627/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44627/checkm_input OceanDNA-b44627/checkm_result
[2023-03-16 10:48:20,746] [INFO] Task succeeded: CheckM
[2023-03-16 10:48:20,747] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:48:20,750] [INFO] ===== Completeness check finished =====
[2023-03-16 10:48:20,750] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:48:20,751] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44627/markers.fasta)
[2023-03-16 10:48:20,752] [INFO] Task started: Blastn
[2023-03-16 10:48:20,752] [INFO] Running command: blastn -query OceanDNA-b44627/markers.fasta -db /var/lib/cwl/stg43d44012-7372-47da-945a-04adce0d934b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44627/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:48:21,541] [INFO] Task succeeded: Blastn
[2023-03-16 10:48:21,543] [INFO] Selected 26 target genomes.
[2023-03-16 10:48:21,543] [INFO] Target genome list was writen to OceanDNA-b44627/target_genomes_gtdb.txt
[2023-03-16 10:48:21,608] [INFO] Task started: fastANI
[2023-03-16 10:48:21,608] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9c9af02-8716-4f2e-a3b7-96b2c7897605/OceanDNA-b44627.fa --refList OceanDNA-b44627/target_genomes_gtdb.txt --output OceanDNA-b44627/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:48:36,012] [INFO] Task succeeded: fastANI
[2023-03-16 10:48:36,016] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:48:36,016] [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_002591915.1	s__Marinicella litoralis	77.8299	301	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Marinicellaceae;g__Marinicella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002000055.1	s__Marinicella sediminis	77.663	330	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Marinicellaceae;g__Marinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009671245.1	s__Marinicella rhabdoformis	77.3637	162	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Marinicellaceae;g__Marinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014636635.1	s__Marinicella pacifica	76.7106	126	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Marinicellaceae;g__Marinicella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:48:36,017] [INFO] GTDB search result was written to OceanDNA-b44627/result_gtdb.tsv
[2023-03-16 10:48:36,017] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:48:36,019] [INFO] DFAST_QC result json was written to OceanDNA-b44627/dqc_result.json
[2023-03-16 10:48:36,019] [INFO] DFAST_QC completed!
[2023-03-16 10:48:36,019] [INFO] Total running time: 0h2m12s