[2024-01-24 13:56:13,258] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:13,260] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:13,260] [INFO] DQC Reference Directory: /var/lib/cwl/stg05808cf3-1c83-4154-ac1c-9dad1695528e/dqc_reference
[2024-01-24 13:56:14,560] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:14,561] [INFO] Task started: Prodigal
[2024-01-24 13:56:14,561] [INFO] Running command: gunzip -c /var/lib/cwl/stg154c175e-b1da-4aab-9907-47a072514dc2/GCF_000155735.2_ASM15573v2_genomic.fna.gz | prodigal -d GCF_000155735.2_ASM15573v2_genomic.fna/cds.fna -a GCF_000155735.2_ASM15573v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:32,603] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:32,604] [INFO] Task started: HMMsearch
[2024-01-24 13:56:32,604] [INFO] Running command: hmmsearch --tblout GCF_000155735.2_ASM15573v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05808cf3-1c83-4154-ac1c-9dad1695528e/dqc_reference/reference_markers.hmm GCF_000155735.2_ASM15573v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:32,903] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:32,905] [INFO] Found 6/6 markers.
[2024-01-24 13:56:32,972] [INFO] Query marker FASTA was written to GCF_000155735.2_ASM15573v2_genomic.fna/markers.fasta
[2024-01-24 13:56:32,972] [INFO] Task started: Blastn
[2024-01-24 13:56:32,972] [INFO] Running command: blastn -query GCF_000155735.2_ASM15573v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg05808cf3-1c83-4154-ac1c-9dad1695528e/dqc_reference/reference_markers.fasta -out GCF_000155735.2_ASM15573v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:33,771] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:33,775] [INFO] Selected 16 target genomes.
[2024-01-24 13:56:33,775] [INFO] Target genome list was writen to GCF_000155735.2_ASM15573v2_genomic.fna/target_genomes.txt
[2024-01-24 13:56:33,786] [INFO] Task started: fastANI
[2024-01-24 13:56:33,786] [INFO] Running command: fastANI --query /var/lib/cwl/stg154c175e-b1da-4aab-9907-47a072514dc2/GCF_000155735.2_ASM15573v2_genomic.fna.gz --refList GCF_000155735.2_ASM15573v2_genomic.fna/target_genomes.txt --output GCF_000155735.2_ASM15573v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:56,876] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:56,877] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05808cf3-1c83-4154-ac1c-9dad1695528e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:56,878] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05808cf3-1c83-4154-ac1c-9dad1695528e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:56,889] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:56,890] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:56,890] [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 arcticus	strain=238	GCA_000155735.2	53946	53946	type	True	100.0	1824	1825	95	conclusive
Octadecabacter antarcticus	strain=307	GCA_000155675.2	1217908	1217908	type	True	84.2702	963	1825	95	below_threshold
Octadecabacter temperatus	strain=DSM 26878	GCA_900142425.1	1458307	1458307	type	True	78.4325	453	1825	95	below_threshold
Octadecabacter ascidiaceicola	strain=CECT 8868	GCA_900185015.1	1655543	1655543	type	True	78.404	475	1825	95	below_threshold
Octadecabacter temperatus	strain=SB1	GCA_001187845.1	1458307	1458307	type	True	78.4005	452	1825	95	below_threshold
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	77.1188	316	1825	95	below_threshold
Cognatiyoonia koreensis	strain=DSM 17925	GCA_900109295.1	364200	364200	type	True	77.0888	135	1825	95	below_threshold
Yoonia maritima	strain=DSM 101533	GCA_003003285.1	1435347	1435347	type	True	76.9068	133	1825	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	76.7754	138	1825	95	below_threshold
Yoonia litorea	strain=DSM 29433	GCA_900114675.1	1123755	1123755	type	True	76.5936	125	1825	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	76.3575	160	1825	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	76.2879	117	1825	95	below_threshold
Cochlodiniinecator piscidefendens	strain=M26A2M	GCA_011326755.1	2715756	2715756	type	True	76.0762	95	1825	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:56,891] [INFO] DFAST Taxonomy check result was written to GCF_000155735.2_ASM15573v2_genomic.fna/tc_result.tsv
[2024-01-24 13:56:56,892] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:56,892] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:56,892] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05808cf3-1c83-4154-ac1c-9dad1695528e/dqc_reference/checkm_data
[2024-01-24 13:56:56,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:56,943] [INFO] Task started: CheckM
[2024-01-24 13:56:56,943] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000155735.2_ASM15573v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000155735.2_ASM15573v2_genomic.fna/checkm_input GCF_000155735.2_ASM15573v2_genomic.fna/checkm_result
[2024-01-24 13:57:50,814] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:50,815] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:50,839] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:50,840] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:50,840] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000155735.2_ASM15573v2_genomic.fna/markers.fasta)
[2024-01-24 13:57:50,841] [INFO] Task started: Blastn
[2024-01-24 13:57:50,841] [INFO] Running command: blastn -query GCF_000155735.2_ASM15573v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg05808cf3-1c83-4154-ac1c-9dad1695528e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000155735.2_ASM15573v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:52,185] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:52,188] [INFO] Selected 9 target genomes.
[2024-01-24 13:57:52,189] [INFO] Target genome list was writen to GCF_000155735.2_ASM15573v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:52,197] [INFO] Task started: fastANI
[2024-01-24 13:57:52,197] [INFO] Running command: fastANI --query /var/lib/cwl/stg154c175e-b1da-4aab-9907-47a072514dc2/GCF_000155735.2_ASM15573v2_genomic.fna.gz --refList GCF_000155735.2_ASM15573v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000155735.2_ASM15573v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:11,984] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:11,998] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:11,998] [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_000155735.2	s__Octadecabacter arcticus	100.0	1821	1825	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	96.73	96.73	0.93	0.93	2	conclusive
GCA_017886375.1	s__Octadecabacter sp017886375	93.4803	823	1825	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	99.96	99.96	0.97	0.97	2	-
GCF_000155675.2	s__Octadecabacter antarcticus	84.2542	967	1825	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	78.629	408	1825	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	98.68	98.68	0.85	0.85	2	-
GCF_900185015.1	s__Octadecabacter ascidiaceicola	78.404	475	1825	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	78.4005	452	1825	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	78.3045	325	1825	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	77.9144	377	1825	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003285.1	s__Yoonia maritima	76.9255	132	1825	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 13:58:12,000] [INFO] GTDB search result was written to GCF_000155735.2_ASM15573v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:12,001] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:12,004] [INFO] DFAST_QC result json was written to GCF_000155735.2_ASM15573v2_genomic.fna/dqc_result.json
[2024-01-24 13:58:12,004] [INFO] DFAST_QC completed!
[2024-01-24 13:58:12,004] [INFO] Total running time: 0h1m59s