[2024-01-25 18:57:35,851] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:57:35,854] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:57:35,854] [INFO] DQC Reference Directory: /var/lib/cwl/stg428866db-1c5d-4fe9-b1ad-80080f5f191c/dqc_reference
[2024-01-25 18:57:37,058] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:57:37,059] [INFO] Task started: Prodigal
[2024-01-25 18:57:37,059] [INFO] Running command: gunzip -c /var/lib/cwl/stgdfae3d83-4c61-4e00-9b75-52b5d7850102/GCF_900106965.1_IMG-taxon_2693429899_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900106965.1_IMG-taxon_2693429899_annotated_assembly_genomic.fna/cds.fna -a GCF_900106965.1_IMG-taxon_2693429899_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:57:49,023] [INFO] Task succeeded: Prodigal
[2024-01-25 18:57:49,023] [INFO] Task started: HMMsearch
[2024-01-25 18:57:49,023] [INFO] Running command: hmmsearch --tblout GCF_900106965.1_IMG-taxon_2693429899_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg428866db-1c5d-4fe9-b1ad-80080f5f191c/dqc_reference/reference_markers.hmm GCF_900106965.1_IMG-taxon_2693429899_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:57:49,302] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:57:49,303] [INFO] Found 6/6 markers.
[2024-01-25 18:57:49,347] [INFO] Query marker FASTA was written to GCF_900106965.1_IMG-taxon_2693429899_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 18:57:49,347] [INFO] Task started: Blastn
[2024-01-25 18:57:49,348] [INFO] Running command: blastn -query GCF_900106965.1_IMG-taxon_2693429899_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg428866db-1c5d-4fe9-b1ad-80080f5f191c/dqc_reference/reference_markers.fasta -out GCF_900106965.1_IMG-taxon_2693429899_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:50,232] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:50,235] [INFO] Selected 11 target genomes.
[2024-01-25 18:57:50,235] [INFO] Target genome list was writen to GCF_900106965.1_IMG-taxon_2693429899_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 18:57:50,296] [INFO] Task started: fastANI
[2024-01-25 18:57:50,297] [INFO] Running command: fastANI --query /var/lib/cwl/stgdfae3d83-4c61-4e00-9b75-52b5d7850102/GCF_900106965.1_IMG-taxon_2693429899_annotated_assembly_genomic.fna.gz --refList GCF_900106965.1_IMG-taxon_2693429899_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900106965.1_IMG-taxon_2693429899_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:58:00,308] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:00,309] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg428866db-1c5d-4fe9-b1ad-80080f5f191c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:58:00,309] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg428866db-1c5d-4fe9-b1ad-80080f5f191c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:58:00,317] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:58:00,317] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:58:00,317] [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
Celeribacter indicus	strain=P73	GCA_900106965.1	1208324	1208324	type	True	100.0	1559	1565	95	conclusive
Celeribacter indicus	strain=P73	GCA_000819565.1	1208324	1208324	type	True	99.9976	1561	1565	95	conclusive
Celeribacter persicus	strain=DSM 100434	GCA_003050785.1	1651082	1651082	type	True	81.5157	730	1565	95	below_threshold
Celeribacter ethanolicus	strain=NH195	GCA_001550095.1	1758178	1758178	type	True	81.0516	727	1565	95	below_threshold
Celeribacter neptunius	strain=DSM 26471	GCA_900113955.1	588602	588602	type	True	80.7497	683	1565	95	below_threshold
Celeribacter halophilus	strain=ZXM137	GCA_001550085.1	576117	576117	type	True	79.088	480	1565	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	78.7089	386	1565	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.4037	437	1565	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.3783	429	1565	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	78.3448	439	1565	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.645	340	1565	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:58:00,319] [INFO] DFAST Taxonomy check result was written to GCF_900106965.1_IMG-taxon_2693429899_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 18:58:00,319] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:58:00,319] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:58:00,320] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg428866db-1c5d-4fe9-b1ad-80080f5f191c/dqc_reference/checkm_data
[2024-01-25 18:58:00,321] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:58:00,367] [INFO] Task started: CheckM
[2024-01-25 18:58:00,367] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900106965.1_IMG-taxon_2693429899_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900106965.1_IMG-taxon_2693429899_annotated_assembly_genomic.fna/checkm_input GCF_900106965.1_IMG-taxon_2693429899_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 18:58:47,398] [INFO] Task succeeded: CheckM
[2024-01-25 18:58:47,399] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:58:47,419] [INFO] ===== Completeness check finished =====
[2024-01-25 18:58:47,419] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:58:47,422] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900106965.1_IMG-taxon_2693429899_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 18:58:47,422] [INFO] Task started: Blastn
[2024-01-25 18:58:47,422] [INFO] Running command: blastn -query GCF_900106965.1_IMG-taxon_2693429899_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg428866db-1c5d-4fe9-b1ad-80080f5f191c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900106965.1_IMG-taxon_2693429899_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:48,858] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:48,861] [INFO] Selected 9 target genomes.
[2024-01-25 18:58:48,861] [INFO] Target genome list was writen to GCF_900106965.1_IMG-taxon_2693429899_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:58:48,892] [INFO] Task started: fastANI
[2024-01-25 18:58:48,892] [INFO] Running command: fastANI --query /var/lib/cwl/stgdfae3d83-4c61-4e00-9b75-52b5d7850102/GCF_900106965.1_IMG-taxon_2693429899_annotated_assembly_genomic.fna.gz --refList GCF_900106965.1_IMG-taxon_2693429899_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900106965.1_IMG-taxon_2693429899_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:58:57,246] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:57,253] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:58:57,253] [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_000819565.1	s__Celeribacter indicus	99.9976	1561	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003050785.1	s__Celeribacter persicus	81.5318	728	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001550095.1	s__Celeribacter ethanolicus	81.0596	727	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	98.17	98.15	0.91	0.89	3	-
GCF_900113955.1	s__Celeribacter neptunius	80.7379	685	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011806455.1	s__Celeribacter sp011806455	79.6228	593	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	97.95	97.95	0.96	0.96	2	-
GCF_900114135.1	s__Celeribacter halophilus	78.9519	489	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	98.37	95.14	0.95	0.87	4	-
GCF_004339675.1	s__Rhodovulum steppense	78.4777	427	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640115.1	s__Muriiphilus lacisalsi	78.3933	445	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Muriiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003605175.1	s__IMCC34051 sp003605175	78.3181	448	1565	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:58:57,254] [INFO] GTDB search result was written to GCF_900106965.1_IMG-taxon_2693429899_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 18:58:57,255] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:58:57,257] [INFO] DFAST_QC result json was written to GCF_900106965.1_IMG-taxon_2693429899_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 18:58:57,257] [INFO] DFAST_QC completed!
[2024-01-25 18:58:57,257] [INFO] Total running time: 0h1m21s