[2024-01-24 13:30:11,270] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:30:11,272] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:30:11,272] [INFO] DQC Reference Directory: /var/lib/cwl/stgb947a371-56a7-4ef3-a05f-8dba3afb7016/dqc_reference
[2024-01-24 13:30:12,496] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:30:12,497] [INFO] Task started: Prodigal
[2024-01-24 13:30:12,498] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2d7e9f4-0b87-4a9e-810a-0bd8a8816394/GCF_900113875.1_IMG-taxon_2622736536_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113875.1_IMG-taxon_2622736536_annotated_assembly_genomic.fna/cds.fna -a GCF_900113875.1_IMG-taxon_2622736536_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:30:23,712] [INFO] Task succeeded: Prodigal
[2024-01-24 13:30:23,713] [INFO] Task started: HMMsearch
[2024-01-24 13:30:23,713] [INFO] Running command: hmmsearch --tblout GCF_900113875.1_IMG-taxon_2622736536_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb947a371-56a7-4ef3-a05f-8dba3afb7016/dqc_reference/reference_markers.hmm GCF_900113875.1_IMG-taxon_2622736536_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:30:23,981] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:30:23,982] [INFO] Found 6/6 markers.
[2024-01-24 13:30:24,018] [INFO] Query marker FASTA was written to GCF_900113875.1_IMG-taxon_2622736536_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:30:24,018] [INFO] Task started: Blastn
[2024-01-24 13:30:24,018] [INFO] Running command: blastn -query GCF_900113875.1_IMG-taxon_2622736536_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgb947a371-56a7-4ef3-a05f-8dba3afb7016/dqc_reference/reference_markers.fasta -out GCF_900113875.1_IMG-taxon_2622736536_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:25,049] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:25,052] [INFO] Selected 16 target genomes.
[2024-01-24 13:30:25,052] [INFO] Target genome list was writen to GCF_900113875.1_IMG-taxon_2622736536_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:30:25,063] [INFO] Task started: fastANI
[2024-01-24 13:30:25,064] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2d7e9f4-0b87-4a9e-810a-0bd8a8816394/GCF_900113875.1_IMG-taxon_2622736536_annotated_assembly_genomic.fna.gz --refList GCF_900113875.1_IMG-taxon_2622736536_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113875.1_IMG-taxon_2622736536_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:30:37,226] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:37,226] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb947a371-56a7-4ef3-a05f-8dba3afb7016/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:30:37,227] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb947a371-56a7-4ef3-a05f-8dba3afb7016/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:30:37,240] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:30:37,241] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:30:37,241] [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
Jannaschia pohangensis	strain=DSM 19073	GCA_900113875.1	390807	390807	type	True	100.0	1236	1236	95	conclusive
Jannaschia rubra	strain=CECT 5088	GCA_001403735.1	282197	282197	type	True	80.0133	631	1236	95	below_threshold
Jannaschia rubra	strain=DSM 16279	GCA_900113265.1	282197	282197	type	True	79.978	623	1236	95	below_threshold
Jannaschia marina	strain=SHC163	GCA_013404595.1	2741674	2741674	type	True	79.8645	701	1236	95	below_threshold
Jannaschia helgolandensis	strain=DSM 14858	GCA_900109285.1	188906	188906	type	True	79.3826	593	1236	95	below_threshold
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	79.3571	648	1236	95	below_threshold
Jannaschia faecimaris	strain=DSM 100420	GCA_900107415.1	1244108	1244108	type	True	79.1901	576	1236	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_003149265.1	475081	475081	type	True	79.1085	569	1236	95	below_threshold
Jannaschia seohaensis	strain=DSM 25227	GCA_900116765.1	475081	475081	type	True	79.1085	569	1236	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.8228	300	1236	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.6715	323	1236	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	77.5015	330	1236	95	below_threshold
Pseudoroseicyclus tamaricis	strain=CLL3-39	GCA_010435925.1	2705421	2705421	type	True	77.4049	284	1236	95	below_threshold
Hasllibacter halocynthiae	strain=DSM 29318	GCA_003003095.1	595589	595589	type	True	77.3569	258	1236	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	77.317	278	1236	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	77.0009	267	1236	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:30:37,243] [INFO] DFAST Taxonomy check result was written to GCF_900113875.1_IMG-taxon_2622736536_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:30:37,243] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:30:37,244] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:30:37,244] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb947a371-56a7-4ef3-a05f-8dba3afb7016/dqc_reference/checkm_data
[2024-01-24 13:30:37,245] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:30:37,283] [INFO] Task started: CheckM
[2024-01-24 13:30:37,284] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113875.1_IMG-taxon_2622736536_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113875.1_IMG-taxon_2622736536_annotated_assembly_genomic.fna/checkm_input GCF_900113875.1_IMG-taxon_2622736536_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:31:18,322] [INFO] Task succeeded: CheckM
[2024-01-24 13:31:18,323] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:31:18,345] [INFO] ===== Completeness check finished =====
[2024-01-24 13:31:18,346] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:31:18,346] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113875.1_IMG-taxon_2622736536_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:31:18,346] [INFO] Task started: Blastn
[2024-01-24 13:31:18,347] [INFO] Running command: blastn -query GCF_900113875.1_IMG-taxon_2622736536_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgb947a371-56a7-4ef3-a05f-8dba3afb7016/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113875.1_IMG-taxon_2622736536_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:20,025] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:20,028] [INFO] Selected 11 target genomes.
[2024-01-24 13:31:20,028] [INFO] Target genome list was writen to GCF_900113875.1_IMG-taxon_2622736536_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:31:20,051] [INFO] Task started: fastANI
[2024-01-24 13:31:20,051] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2d7e9f4-0b87-4a9e-810a-0bd8a8816394/GCF_900113875.1_IMG-taxon_2622736536_annotated_assembly_genomic.fna.gz --refList GCF_900113875.1_IMG-taxon_2622736536_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113875.1_IMG-taxon_2622736536_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:31:28,679] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:28,692] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:31:28,692] [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_900113875.1	s__Jannaschia pohangensis	100.0	1236	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001403735.1	s__Jannaschia rubra	80.0318	629	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001403795.1	s__Jannaschia donghaensis	79.9677	681	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013404595.1	s__Jannaschia marina	79.8587	701	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109285.1	s__Jannaschia helgolandensis	79.3792	594	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340555.1	s__Jannaschia formosa	79.3576	648	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107415.1	s__Jannaschia faecimaris	79.1822	577	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116765.1	s__Jannaschia seohaensis	79.1004	570	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018139985.1	s__JAGSOU01 sp018139985	77.9934	386	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004005435.1	s__CCMM004 sp004005435	77.7763	373	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CCMM004	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003095.1	s__Hasllibacter halocynthiae	77.3569	258	1236	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Hasllibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:31:28,694] [INFO] GTDB search result was written to GCF_900113875.1_IMG-taxon_2622736536_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:31:28,694] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:31:28,698] [INFO] DFAST_QC result json was written to GCF_900113875.1_IMG-taxon_2622736536_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:31:28,698] [INFO] DFAST_QC completed!
[2024-01-24 13:31:28,698] [INFO] Total running time: 0h1m17s