[2023-03-16 15:45:05,960] [INFO] DFAST_QC pipeline started.
[2023-03-16 15:45:05,960] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 15:45:05,960] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc463598-b013-4993-85b7-82b4990690bb/dqc_reference
[2023-03-16 15:45:07,299] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 15:45:07,299] [INFO] Task started: Prodigal
[2023-03-16 15:45:07,299] [INFO] Running command: cat /var/lib/cwl/stgccff8814-5fe6-4708-82ca-d69e027bf997/OceanDNA-b29574.fa | prodigal -d OceanDNA-b29574/cds.fna -a OceanDNA-b29574/protein.faa -g 11 -q > /dev/null
[2023-03-16 15:45:27,003] [INFO] Task succeeded: Prodigal
[2023-03-16 15:45:27,003] [INFO] Task started: HMMsearch
[2023-03-16 15:45:27,003] [INFO] Running command: hmmsearch --tblout OceanDNA-b29574/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc463598-b013-4993-85b7-82b4990690bb/dqc_reference/reference_markers.hmm OceanDNA-b29574/protein.faa > /dev/null
[2023-03-16 15:45:27,319] [INFO] Task succeeded: HMMsearch
[2023-03-16 15:45:27,319] [INFO] Found 6/6 markers.
[2023-03-16 15:45:27,336] [INFO] Query marker FASTA was written to OceanDNA-b29574/markers.fasta
[2023-03-16 15:45:27,339] [INFO] Task started: Blastn
[2023-03-16 15:45:27,339] [INFO] Running command: blastn -query OceanDNA-b29574/markers.fasta -db /var/lib/cwl/stgdc463598-b013-4993-85b7-82b4990690bb/dqc_reference/reference_markers.fasta -out OceanDNA-b29574/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:45:29,124] [INFO] Task succeeded: Blastn
[2023-03-16 15:45:29,125] [INFO] Selected 22 target genomes.
[2023-03-16 15:45:29,125] [INFO] Target genome list was writen to OceanDNA-b29574/target_genomes.txt
[2023-03-16 15:45:29,139] [INFO] Task started: fastANI
[2023-03-16 15:45:29,139] [INFO] Running command: fastANI --query /var/lib/cwl/stgccff8814-5fe6-4708-82ca-d69e027bf997/OceanDNA-b29574.fa --refList OceanDNA-b29574/target_genomes.txt --output OceanDNA-b29574/fastani_result.tsv --threads 1
[2023-03-16 15:45:48,661] [INFO] Task succeeded: fastANI
[2023-03-16 15:45:48,661] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc463598-b013-4993-85b7-82b4990690bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 15:45:48,661] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc463598-b013-4993-85b7-82b4990690bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 15:45:48,666] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 15:45:48,666] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 15:45:48,666] [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
Octadecabacter antarcticus	strain=307	GCA_000155675.2	1217908	1217908	type	True	79.4441	555	892	95	below_threshold
Octadecabacter arcticus	strain=238	GCA_000155735.2	53946	53946	type	True	79.0567	489	892	95	below_threshold
Octadecabacter temperatus	strain=DSM 26878	GCA_900142425.1	1458307	1458307	type	True	76.6787	143	892	95	below_threshold
Octadecabacter temperatus	strain=SB1	GCA_001187845.1	1458307	1458307	type	True	76.6744	141	892	95	below_threshold
Octadecabacter ascidiaceicola	strain=CECT 8868	GCA_900185015.1	1655543	1655543	type	True	76.3922	150	892	95	below_threshold
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	76.0952	70	892	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 15:45:48,666] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29574/tc_result.tsv
[2023-03-16 15:45:48,667] [INFO] ===== Taxonomy check completed =====
[2023-03-16 15:45:48,667] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 15:45:48,667] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc463598-b013-4993-85b7-82b4990690bb/dqc_reference/checkm_data
[2023-03-16 15:45:48,667] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 15:45:48,672] [INFO] Task started: CheckM
[2023-03-16 15:45:48,672] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29574/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29574/checkm_input OceanDNA-b29574/checkm_result
[2023-03-16 15:46:30,621] [INFO] Task succeeded: CheckM
[2023-03-16 15:46:30,621] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.68%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 15:46:30,624] [INFO] ===== Completeness check finished =====
[2023-03-16 15:46:30,624] [INFO] ===== Start GTDB Search =====
[2023-03-16 15:46:30,624] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29574/markers.fasta)
[2023-03-16 15:46:30,625] [INFO] Task started: Blastn
[2023-03-16 15:46:30,625] [INFO] Running command: blastn -query OceanDNA-b29574/markers.fasta -db /var/lib/cwl/stgdc463598-b013-4993-85b7-82b4990690bb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29574/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:46:31,598] [INFO] Task succeeded: Blastn
[2023-03-16 15:46:31,598] [INFO] Selected 19 target genomes.
[2023-03-16 15:46:31,599] [INFO] Target genome list was writen to OceanDNA-b29574/target_genomes_gtdb.txt
[2023-03-16 15:46:31,968] [INFO] Task started: fastANI
[2023-03-16 15:46:31,968] [INFO] Running command: fastANI --query /var/lib/cwl/stgccff8814-5fe6-4708-82ca-d69e027bf997/OceanDNA-b29574.fa --refList OceanDNA-b29574/target_genomes_gtdb.txt --output OceanDNA-b29574/fastani_result_gtdb.tsv --threads 1
[2023-03-16 15:46:43,587] [INFO] Task succeeded: fastANI
[2023-03-16 15:46:43,591] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 15:46:43,592] [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_000155675.2	s__Octadecabacter antarcticus	79.4353	556	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017886375.1	s__Octadecabacter sp017886375	79.2399	425	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	99.96	99.96	0.97	0.97	2	-
GCF_000155735.2	s__Octadecabacter arcticus	79.0606	488	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	96.73	96.73	0.93	0.93	2	-
GCF_018861045.1	s__Octadecabacter sp018861045	76.8137	127	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187845.1	s__Octadecabacter temperatus	76.6906	140	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900185015.1	s__Octadecabacter ascidiaceicola	76.3922	150	892	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 15:46:43,592] [INFO] GTDB search result was written to OceanDNA-b29574/result_gtdb.tsv
[2023-03-16 15:46:43,592] [INFO] ===== GTDB Search completed =====
[2023-03-16 15:46:43,593] [INFO] DFAST_QC result json was written to OceanDNA-b29574/dqc_result.json
[2023-03-16 15:46:43,593] [INFO] DFAST_QC completed!
[2023-03-16 15:46:43,593] [INFO] Total running time: 0h1m38s