[2024-01-24 15:10:41,093] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:41,094] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:41,095] [INFO] DQC Reference Directory: /var/lib/cwl/stg61d2f93d-ec57-446d-989f-601f375bbafd/dqc_reference
[2024-01-24 15:10:42,551] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:42,551] [INFO] Task started: Prodigal
[2024-01-24 15:10:42,552] [INFO] Running command: gunzip -c /var/lib/cwl/stgd08fe1ae-c1c0-470b-bd33-2abf3d3eadf5/GCF_900185015.1_O.ascidiaceicola_CECT8868_Spades_Prokka_genomic.fna.gz | prodigal -d GCF_900185015.1_O.ascidiaceicola_CECT8868_Spades_Prokka_genomic.fna/cds.fna -a GCF_900185015.1_O.ascidiaceicola_CECT8868_Spades_Prokka_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:53,511] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:53,511] [INFO] Task started: HMMsearch
[2024-01-24 15:10:53,511] [INFO] Running command: hmmsearch --tblout GCF_900185015.1_O.ascidiaceicola_CECT8868_Spades_Prokka_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61d2f93d-ec57-446d-989f-601f375bbafd/dqc_reference/reference_markers.hmm GCF_900185015.1_O.ascidiaceicola_CECT8868_Spades_Prokka_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:53,785] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:53,786] [INFO] Found 6/6 markers.
[2024-01-24 15:10:53,820] [INFO] Query marker FASTA was written to GCF_900185015.1_O.ascidiaceicola_CECT8868_Spades_Prokka_genomic.fna/markers.fasta
[2024-01-24 15:10:53,821] [INFO] Task started: Blastn
[2024-01-24 15:10:53,821] [INFO] Running command: blastn -query GCF_900185015.1_O.ascidiaceicola_CECT8868_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg61d2f93d-ec57-446d-989f-601f375bbafd/dqc_reference/reference_markers.fasta -out GCF_900185015.1_O.ascidiaceicola_CECT8868_Spades_Prokka_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:54,583] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:54,586] [INFO] Selected 13 target genomes.
[2024-01-24 15:10:54,587] [INFO] Target genome list was writen to GCF_900185015.1_O.ascidiaceicola_CECT8868_Spades_Prokka_genomic.fna/target_genomes.txt
[2024-01-24 15:10:54,595] [INFO] Task started: fastANI
[2024-01-24 15:10:54,595] [INFO] Running command: fastANI --query /var/lib/cwl/stgd08fe1ae-c1c0-470b-bd33-2abf3d3eadf5/GCF_900185015.1_O.ascidiaceicola_CECT8868_Spades_Prokka_genomic.fna.gz --refList GCF_900185015.1_O.ascidiaceicola_CECT8868_Spades_Prokka_genomic.fna/target_genomes.txt --output GCF_900185015.1_O.ascidiaceicola_CECT8868_Spades_Prokka_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:06,545] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:06,546] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61d2f93d-ec57-446d-989f-601f375bbafd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:06,546] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61d2f93d-ec57-446d-989f-601f375bbafd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:06,559] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:06,559] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:06,560] [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 ascidiaceicola	strain=CECT 8868	GCA_900185015.1	1655543	1655543	type	True	100.0	1069	1072	95	conclusive
Octadecabacter temperatus	strain=SB1	GCA_001187845.1	1458307	1458307	type	True	83.6382	771	1072	95	below_threshold
Octadecabacter temperatus	strain=DSM 26878	GCA_900142425.1	1458307	1458307	type	True	83.6223	769	1072	95	below_threshold
Octadecabacter arcticus	strain=238	GCA_000155735.2	53946	53946	type	True	78.4141	471	1072	95	below_threshold
Octadecabacter antarcticus	strain=307	GCA_000155675.2	1217908	1217908	type	True	78.2054	453	1072	95	below_threshold
Cochlodiniinecator piscidefendens	strain=M26A2M	GCA_011326755.1	2715756	2715756	type	True	77.7193	91	1072	95	below_threshold
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	77.4009	280	1072	95	below_threshold
Cognatiyoonia sediminum	strain=DSM 28715	GCA_900129845.1	1508389	1508389	type	True	76.983	144	1072	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	76.8702	108	1072	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	76.4538	58	1072	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.2883	102	1072	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	76.2525	75	1072	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:06,563] [INFO] DFAST Taxonomy check result was written to GCF_900185015.1_O.ascidiaceicola_CECT8868_Spades_Prokka_genomic.fna/tc_result.tsv
[2024-01-24 15:11:06,564] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:06,564] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:06,565] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61d2f93d-ec57-446d-989f-601f375bbafd/dqc_reference/checkm_data
[2024-01-24 15:11:06,567] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:06,604] [INFO] Task started: CheckM
[2024-01-24 15:11:06,604] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900185015.1_O.ascidiaceicola_CECT8868_Spades_Prokka_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900185015.1_O.ascidiaceicola_CECT8868_Spades_Prokka_genomic.fna/checkm_input GCF_900185015.1_O.ascidiaceicola_CECT8868_Spades_Prokka_genomic.fna/checkm_result
[2024-01-24 15:11:42,612] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:42,614] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:42,638] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:42,638] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:42,639] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900185015.1_O.ascidiaceicola_CECT8868_Spades_Prokka_genomic.fna/markers.fasta)
[2024-01-24 15:11:42,639] [INFO] Task started: Blastn
[2024-01-24 15:11:42,639] [INFO] Running command: blastn -query GCF_900185015.1_O.ascidiaceicola_CECT8868_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg61d2f93d-ec57-446d-989f-601f375bbafd/dqc_reference/reference_markers_gtdb.fasta -out GCF_900185015.1_O.ascidiaceicola_CECT8868_Spades_Prokka_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:43,907] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:43,910] [INFO] Selected 10 target genomes.
[2024-01-24 15:11:43,910] [INFO] Target genome list was writen to GCF_900185015.1_O.ascidiaceicola_CECT8868_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:43,918] [INFO] Task started: fastANI
[2024-01-24 15:11:43,918] [INFO] Running command: fastANI --query /var/lib/cwl/stgd08fe1ae-c1c0-470b-bd33-2abf3d3eadf5/GCF_900185015.1_O.ascidiaceicola_CECT8868_Spades_Prokka_genomic.fna.gz --refList GCF_900185015.1_O.ascidiaceicola_CECT8868_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt --output GCF_900185015.1_O.ascidiaceicola_CECT8868_Spades_Prokka_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:50,961] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:50,970] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:50,970] [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_900185015.1	s__Octadecabacter ascidiaceicola	100.0	1069	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003533975.1	s__Octadecabacter sp003533975	84.0687	518	1072	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	83.6382	771	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018500005.1	s__Octadecabacter sp018500005	82.6857	477	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861045.1	s__Octadecabacter sp018861045	79.4414	462	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608045.1	s__Octadecabacter sp018608045	78.7142	371	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	98.68	98.68	0.85	0.85	2	-
GCA_017886375.1	s__Octadecabacter sp017886375	78.6559	414	1072	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	78.4226	470	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	96.73	96.73	0.93	0.93	2	-
GCF_000155675.2	s__Octadecabacter antarcticus	78.2001	452	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182645.1	s__Yoonia sp905182645	77.1747	156	1072	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:50,973] [INFO] GTDB search result was written to GCF_900185015.1_O.ascidiaceicola_CECT8868_Spades_Prokka_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:50,974] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:50,977] [INFO] DFAST_QC result json was written to GCF_900185015.1_O.ascidiaceicola_CECT8868_Spades_Prokka_genomic.fna/dqc_result.json
[2024-01-24 15:11:50,977] [INFO] DFAST_QC completed!
[2024-01-24 15:11:50,977] [INFO] Total running time: 0h1m10s