[2024-01-24 12:06:10,394] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:10,398] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:10,398] [INFO] DQC Reference Directory: /var/lib/cwl/stg7fe7f97b-cce3-4d90-9999-c37f7b5b533a/dqc_reference
[2024-01-24 12:06:13,246] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:13,247] [INFO] Task started: Prodigal
[2024-01-24 12:06:13,247] [INFO] Running command: gunzip -c /var/lib/cwl/stg47f302f5-3147-4b61-bfe0-77745b13af6a/GCF_003324485.1_ASM332448v1_genomic.fna.gz | prodigal -d GCF_003324485.1_ASM332448v1_genomic.fna/cds.fna -a GCF_003324485.1_ASM332448v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:30,035] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:30,035] [INFO] Task started: HMMsearch
[2024-01-24 12:06:30,035] [INFO] Running command: hmmsearch --tblout GCF_003324485.1_ASM332448v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7fe7f97b-cce3-4d90-9999-c37f7b5b533a/dqc_reference/reference_markers.hmm GCF_003324485.1_ASM332448v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:30,370] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:30,371] [INFO] Found 6/6 markers.
[2024-01-24 12:06:30,414] [INFO] Query marker FASTA was written to GCF_003324485.1_ASM332448v1_genomic.fna/markers.fasta
[2024-01-24 12:06:30,415] [INFO] Task started: Blastn
[2024-01-24 12:06:30,415] [INFO] Running command: blastn -query GCF_003324485.1_ASM332448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7fe7f97b-cce3-4d90-9999-c37f7b5b533a/dqc_reference/reference_markers.fasta -out GCF_003324485.1_ASM332448v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:31,216] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:31,219] [INFO] Selected 17 target genomes.
[2024-01-24 12:06:31,219] [INFO] Target genome list was writen to GCF_003324485.1_ASM332448v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:31,225] [INFO] Task started: fastANI
[2024-01-24 12:06:31,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg47f302f5-3147-4b61-bfe0-77745b13af6a/GCF_003324485.1_ASM332448v1_genomic.fna.gz --refList GCF_003324485.1_ASM332448v1_genomic.fna/target_genomes.txt --output GCF_003324485.1_ASM332448v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:50,170] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:50,171] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7fe7f97b-cce3-4d90-9999-c37f7b5b533a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:50,171] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7fe7f97b-cce3-4d90-9999-c37f7b5b533a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:50,184] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:50,184] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:50,184] [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
Cohaesibacter intestini	strain=YE-B6	GCA_003324485.1	2211145	2211145	type	True	100.0	1584	1585	95	conclusive
Cohaesibacter marisflavi	strain=CGMCC 1.9157	GCA_900115225.1	655353	655353	type	True	78.9909	458	1585	95	below_threshold
Cohaesibacter haloalkalitolerans	strain=JC131	GCA_003574655.1	1162980	1162980	type	True	78.55	484	1585	95	below_threshold
Cohaesibacter gelatinilyticus	strain=DSM 18289	GCA_900215605.1	372072	372072	type	True	77.9982	273	1585	95	below_threshold
Cohaesibacter celericrescens	strain=H1304	GCA_002866925.1	2067669	2067669	type	True	77.5273	366	1585	95	below_threshold
Roseibium suaedae	strain=DSM 22153	GCA_900142725.1	735517	735517	type	True	76.5145	130	1585	95	below_threshold
Ciceribacter thiooxidans	strain=F43B	GCA_014126615.1	1969821	1969821	type	True	76.2829	62	1585	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	76.1296	88	1585	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	75.9435	65	1585	95	below_threshold
Rhizobium laguerreae	strain=FB206	GCA_002008165.1	1076926	1076926	type	True	75.8401	87	1585	95	below_threshold
Pseudovibrio flavus	strain=RKSG542	GCA_009711345.1	2529854	2529854	type	True	75.7972	57	1585	95	below_threshold
Bradyrhizobium cenepequi	strain=CNPSo 4026	GCA_020329485.1	2821403	2821403	type	True	75.7971	63	1585	95	below_threshold
Thalassospira profundimaris	strain=WP0211	GCA_000300275.1	502049	502049	suspected-type	True	75.7301	58	1585	95	below_threshold
Pleomorphomonas carboxyditropha	strain=SVCO-16	GCA_002770725.1	2023338	2023338	type	True	75.7217	81	1585	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:50,186] [INFO] DFAST Taxonomy check result was written to GCF_003324485.1_ASM332448v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:50,187] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:50,187] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:50,187] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7fe7f97b-cce3-4d90-9999-c37f7b5b533a/dqc_reference/checkm_data
[2024-01-24 12:06:50,189] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:50,245] [INFO] Task started: CheckM
[2024-01-24 12:06:50,245] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003324485.1_ASM332448v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003324485.1_ASM332448v1_genomic.fna/checkm_input GCF_003324485.1_ASM332448v1_genomic.fna/checkm_result
[2024-01-24 12:07:41,601] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:41,603] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:41,632] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:41,632] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:41,633] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003324485.1_ASM332448v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:41,633] [INFO] Task started: Blastn
[2024-01-24 12:07:41,633] [INFO] Running command: blastn -query GCF_003324485.1_ASM332448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7fe7f97b-cce3-4d90-9999-c37f7b5b533a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003324485.1_ASM332448v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:42,980] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:42,983] [INFO] Selected 12 target genomes.
[2024-01-24 12:07:42,983] [INFO] Target genome list was writen to GCF_003324485.1_ASM332448v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:42,997] [INFO] Task started: fastANI
[2024-01-24 12:07:42,998] [INFO] Running command: fastANI --query /var/lib/cwl/stg47f302f5-3147-4b61-bfe0-77745b13af6a/GCF_003324485.1_ASM332448v1_genomic.fna.gz --refList GCF_003324485.1_ASM332448v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003324485.1_ASM332448v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:54,706] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:54,722] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:54,723] [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_003324485.1	s__Cohaesibacter intestini	100.0	1584	1585	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Cohaesibacteraceae;g__Cohaesibacter	95.0	98.38	98.38	0.96	0.96	2	conclusive
GCF_900115225.1	s__Cohaesibacter marisflavi	78.9899	459	1585	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Cohaesibacteraceae;g__Cohaesibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215505.1	s__Cohaesibacter sp900215505	78.8738	518	1585	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Cohaesibacteraceae;g__Cohaesibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003574655.1	s__Cohaesibacter haloalkalitolerans	78.55	484	1585	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Cohaesibacteraceae;g__Cohaesibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215605.1	s__Cohaesibacter gelatinilyticus	77.9982	273	1585	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Cohaesibacteraceae;g__Cohaesibacter	95.0	98.86	98.83	0.96	0.96	3	-
GCF_002866925.1	s__Cohaesibacter celericrescens	77.525	367	1585	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Cohaesibacteraceae;g__Cohaesibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000172795.2	s__Rhizobium sp000172795	76.1402	87	1585	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902706285.1	s__Rhizobium sp902706285	75.976	89	1585	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002770725.1	s__Pleomorphomonas carboxyditropha	75.7231	81	1585	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Pleomorphomonas	95.0	98.10	98.10	0.89	0.89	2	-
GCA_002698425.1	s__Oricola sp002698425	75.7006	93	1585	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:54,724] [INFO] GTDB search result was written to GCF_003324485.1_ASM332448v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:54,725] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:54,728] [INFO] DFAST_QC result json was written to GCF_003324485.1_ASM332448v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:54,728] [INFO] DFAST_QC completed!
[2024-01-24 12:07:54,728] [INFO] Total running time: 0h1m44s