[2024-01-24 11:51:19,616] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:19,617] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:19,618] [INFO] DQC Reference Directory: /var/lib/cwl/stg66379315-aafa-431a-9b09-461e6c58cab7/dqc_reference
[2024-01-24 11:51:20,844] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:20,845] [INFO] Task started: Prodigal
[2024-01-24 11:51:20,845] [INFO] Running command: gunzip -c /var/lib/cwl/stga9a5c67b-ff16-440c-b57b-1572799cc24f/GCF_900113955.1_IMG-taxon_2617270870_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113955.1_IMG-taxon_2617270870_annotated_assembly_genomic.fna/cds.fna -a GCF_900113955.1_IMG-taxon_2617270870_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:34,270] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:34,271] [INFO] Task started: HMMsearch
[2024-01-24 11:51:34,271] [INFO] Running command: hmmsearch --tblout GCF_900113955.1_IMG-taxon_2617270870_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66379315-aafa-431a-9b09-461e6c58cab7/dqc_reference/reference_markers.hmm GCF_900113955.1_IMG-taxon_2617270870_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:34,554] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:34,556] [INFO] Found 6/6 markers.
[2024-01-24 11:51:34,596] [INFO] Query marker FASTA was written to GCF_900113955.1_IMG-taxon_2617270870_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 11:51:34,596] [INFO] Task started: Blastn
[2024-01-24 11:51:34,596] [INFO] Running command: blastn -query GCF_900113955.1_IMG-taxon_2617270870_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg66379315-aafa-431a-9b09-461e6c58cab7/dqc_reference/reference_markers.fasta -out GCF_900113955.1_IMG-taxon_2617270870_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:35,415] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:35,423] [INFO] Selected 13 target genomes.
[2024-01-24 11:51:35,424] [INFO] Target genome list was writen to GCF_900113955.1_IMG-taxon_2617270870_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 11:51:35,429] [INFO] Task started: fastANI
[2024-01-24 11:51:35,430] [INFO] Running command: fastANI --query /var/lib/cwl/stga9a5c67b-ff16-440c-b57b-1572799cc24f/GCF_900113955.1_IMG-taxon_2617270870_annotated_assembly_genomic.fna.gz --refList GCF_900113955.1_IMG-taxon_2617270870_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113955.1_IMG-taxon_2617270870_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:46,471] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:46,472] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66379315-aafa-431a-9b09-461e6c58cab7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:46,472] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66379315-aafa-431a-9b09-461e6c58cab7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:46,487] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:46,488] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:46,488] [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 neptunius	strain=DSM 26471	GCA_900113955.1	588602	588602	type	True	100.0	1455	1457	95	conclusive
Celeribacter ethanolicus	strain=NH195	GCA_001550095.1	1758178	1758178	type	True	83.152	923	1457	95	below_threshold
Celeribacter persicus	strain=DSM 100434	GCA_003050785.1	1651082	1651082	type	True	82.3873	849	1457	95	below_threshold
Celeribacter halophilus	strain=ZXM137	GCA_001550085.1	576117	576117	type	True	80.8876	680	1457	95	below_threshold
Celeribacter halophilus	strain=CGMCC 1.8891	GCA_900114135.1	576117	576117	type	True	80.807	687	1457	95	below_threshold
Celeribacter indicus	strain=P73	GCA_000819565.1	1208324	1208324	type	True	80.8007	693	1457	95	below_threshold
Celeribacter halophilus	strain=DSM 26270	GCA_003254175.1	576117	576117	type	True	80.7744	691	1457	95	below_threshold
Celeribacter indicus	strain=P73	GCA_900106965.1	1208324	1208324	type	True	80.7146	688	1457	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	79.6237	589	1457	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	77.6122	328	1457	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.4124	312	1457	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.0454	241	1457	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.0121	301	1457	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:46,491] [INFO] DFAST Taxonomy check result was written to GCF_900113955.1_IMG-taxon_2617270870_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 11:51:46,492] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:46,492] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:46,493] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66379315-aafa-431a-9b09-461e6c58cab7/dqc_reference/checkm_data
[2024-01-24 11:51:46,494] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:46,539] [INFO] Task started: CheckM
[2024-01-24 11:51:46,539] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113955.1_IMG-taxon_2617270870_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113955.1_IMG-taxon_2617270870_annotated_assembly_genomic.fna/checkm_input GCF_900113955.1_IMG-taxon_2617270870_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 11:52:31,358] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:31,360] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:31,385] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:31,385] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:31,386] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113955.1_IMG-taxon_2617270870_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 11:52:31,386] [INFO] Task started: Blastn
[2024-01-24 11:52:31,386] [INFO] Running command: blastn -query GCF_900113955.1_IMG-taxon_2617270870_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg66379315-aafa-431a-9b09-461e6c58cab7/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113955.1_IMG-taxon_2617270870_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:32,711] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:32,715] [INFO] Selected 6 target genomes.
[2024-01-24 11:52:32,715] [INFO] Target genome list was writen to GCF_900113955.1_IMG-taxon_2617270870_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:32,721] [INFO] Task started: fastANI
[2024-01-24 11:52:32,722] [INFO] Running command: fastANI --query /var/lib/cwl/stga9a5c67b-ff16-440c-b57b-1572799cc24f/GCF_900113955.1_IMG-taxon_2617270870_annotated_assembly_genomic.fna.gz --refList GCF_900113955.1_IMG-taxon_2617270870_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113955.1_IMG-taxon_2617270870_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:38,542] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:38,553] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:38,553] [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_900113955.1	s__Celeribacter neptunius	100.0	1455	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001550095.1	s__Celeribacter ethanolicus	83.1407	922	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	98.17	98.15	0.91	0.89	3	-
GCF_011806455.1	s__Celeribacter sp011806455	82.43	845	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	97.95	97.95	0.96	0.96	2	-
GCF_003050785.1	s__Celeribacter persicus	82.3686	851	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114135.1	s__Celeribacter halophilus	80.8161	686	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	98.37	95.14	0.95	0.87	4	-
GCF_000819565.1	s__Celeribacter indicus	80.81	692	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Celeribacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:38,555] [INFO] GTDB search result was written to GCF_900113955.1_IMG-taxon_2617270870_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:38,555] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:38,558] [INFO] DFAST_QC result json was written to GCF_900113955.1_IMG-taxon_2617270870_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 11:52:38,558] [INFO] DFAST_QC completed!
[2024-01-24 11:52:38,558] [INFO] Total running time: 0h1m19s