[2024-01-24 14:40:01,109] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:40:01,110] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:40:01,110] [INFO] DQC Reference Directory: /var/lib/cwl/stg8266992a-0739-494d-9038-c0f919ca76a5/dqc_reference
[2024-01-24 14:40:02,442] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:40:02,443] [INFO] Task started: Prodigal
[2024-01-24 14:40:02,444] [INFO] Running command: gunzip -c /var/lib/cwl/stg8591b9b7-2cee-4891-8129-8f84db200603/GCF_003314975.1_ASM331497v1_genomic.fna.gz | prodigal -d GCF_003314975.1_ASM331497v1_genomic.fna/cds.fna -a GCF_003314975.1_ASM331497v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:40:12,386] [INFO] Task succeeded: Prodigal
[2024-01-24 14:40:12,386] [INFO] Task started: HMMsearch
[2024-01-24 14:40:12,386] [INFO] Running command: hmmsearch --tblout GCF_003314975.1_ASM331497v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8266992a-0739-494d-9038-c0f919ca76a5/dqc_reference/reference_markers.hmm GCF_003314975.1_ASM331497v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:40:12,713] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:40:12,714] [INFO] Found 6/6 markers.
[2024-01-24 14:40:12,748] [INFO] Query marker FASTA was written to GCF_003314975.1_ASM331497v1_genomic.fna/markers.fasta
[2024-01-24 14:40:12,748] [INFO] Task started: Blastn
[2024-01-24 14:40:12,749] [INFO] Running command: blastn -query GCF_003314975.1_ASM331497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8266992a-0739-494d-9038-c0f919ca76a5/dqc_reference/reference_markers.fasta -out GCF_003314975.1_ASM331497v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:13,513] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:13,516] [INFO] Selected 19 target genomes.
[2024-01-24 14:40:13,516] [INFO] Target genome list was writen to GCF_003314975.1_ASM331497v1_genomic.fna/target_genomes.txt
[2024-01-24 14:40:13,523] [INFO] Task started: fastANI
[2024-01-24 14:40:13,523] [INFO] Running command: fastANI --query /var/lib/cwl/stg8591b9b7-2cee-4891-8129-8f84db200603/GCF_003314975.1_ASM331497v1_genomic.fna.gz --refList GCF_003314975.1_ASM331497v1_genomic.fna/target_genomes.txt --output GCF_003314975.1_ASM331497v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:28,709] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:28,710] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8266992a-0739-494d-9038-c0f919ca76a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:28,710] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8266992a-0739-494d-9038-c0f919ca76a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:28,722] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:40:28,722] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:28,722] [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
Marinomonas aquiplantarum	strain=CECT 7732	GCA_003314975.1	491951	491951	type	True	100.0	1241	1241	95	conclusive
Marinomonas posidonica	strain=IVIA-Po-181	GCA_000214215.1	936476	936476	type	True	87.4085	962	1241	95	below_threshold
Marinomonas rhizomae	strain=CECT 7377	GCA_003315485.1	491948	491948	type	True	79.7129	460	1241	95	below_threshold
Marinomonas rhizomae	strain=IVIA-Po-145	GCA_003721275.1	491948	491948	type	True	79.6693	453	1241	95	below_threshold
Marinomonas foliarum	strain=CECT 7731	GCA_003337275.1	491950	491950	type	True	79.0792	392	1241	95	below_threshold
Marinomonas polaris	strain=DSM 16579	GCA_900129155.1	293552	293552	type	True	79.0334	424	1241	95	below_threshold
Marinomonas alcarazii	strain=CECT 7730	GCA_003208215.1	491949	491949	type	True	79.0254	378	1241	95	below_threshold
Marinomonas primoryensis	strain=MPKMM3633	GCA_013372285.1	178399	178399	type	True	78.8455	377	1241	95	below_threshold
Marinomonas pollencensis	strain=CECT 7375	GCA_003387375.1	491954	491954	type	True	78.7696	292	1241	95	below_threshold
Marinomonas ushuaiensis	strain=DSM 15871	GCA_000521805.1	263818	263818	type	True	78.6992	318	1241	95	below_threshold
Marinomonas colpomeniae	strain=SM2066	GCA_014803385.1	2774408	2774408	type	True	78.5256	323	1241	95	below_threshold
Marinomonas flavescens	strain=ANRC-JHZ47	GCA_004352835.1	2529379	2529379	type	True	78.5183	268	1241	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:28,724] [INFO] DFAST Taxonomy check result was written to GCF_003314975.1_ASM331497v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:28,724] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:28,724] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:28,725] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8266992a-0739-494d-9038-c0f919ca76a5/dqc_reference/checkm_data
[2024-01-24 14:40:28,726] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:28,767] [INFO] Task started: CheckM
[2024-01-24 14:40:28,767] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003314975.1_ASM331497v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003314975.1_ASM331497v1_genomic.fna/checkm_input GCF_003314975.1_ASM331497v1_genomic.fna/checkm_result
[2024-01-24 14:41:03,879] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:03,881] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:41:03,903] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:03,904] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:03,904] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003314975.1_ASM331497v1_genomic.fna/markers.fasta)
[2024-01-24 14:41:03,905] [INFO] Task started: Blastn
[2024-01-24 14:41:03,905] [INFO] Running command: blastn -query GCF_003314975.1_ASM331497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8266992a-0739-494d-9038-c0f919ca76a5/dqc_reference/reference_markers_gtdb.fasta -out GCF_003314975.1_ASM331497v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:04,989] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:04,993] [INFO] Selected 14 target genomes.
[2024-01-24 14:41:04,994] [INFO] Target genome list was writen to GCF_003314975.1_ASM331497v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:05,005] [INFO] Task started: fastANI
[2024-01-24 14:41:05,005] [INFO] Running command: fastANI --query /var/lib/cwl/stg8591b9b7-2cee-4891-8129-8f84db200603/GCF_003314975.1_ASM331497v1_genomic.fna.gz --refList GCF_003314975.1_ASM331497v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003314975.1_ASM331497v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:15,444] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:15,459] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:15,460] [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_003314975.1	s__Marinomonas aquiplantarum	100.0	1241	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001625355.1	s__Marinomonas sp001625355	89.3121	1017	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000214215.1	s__Marinomonas posidonica	87.3951	963	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315485.1	s__Marinomonas rhizomae	79.7037	460	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003337275.1	s__Marinomonas foliarum	79.0829	391	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.18	98.18	0.87	0.87	2	-
GCF_003208215.1	s__Marinomonas alcarazii	79.0265	376	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.70	98.70	0.93	0.93	2	-
GCF_900129155.1	s__Marinomonas polaris	79.0166	425	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	97.53	97.35	0.90	0.88	9	-
GCF_004352855.1	s__Marinomonas sp004352855	78.9613	299	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000508165.1	s__Marinomonas profundimaris	78.9171	419	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387375.1	s__Marinomonas pollencensis	78.7682	292	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521805.1	s__Marinomonas ushuaiensis	78.6992	318	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014803385.1	s__Marinomonas colpomeniae	78.5256	323	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008122525.1	s__Marinomonas sp008122525	78.4289	309	1241	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:41:15,462] [INFO] GTDB search result was written to GCF_003314975.1_ASM331497v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:15,462] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:15,466] [INFO] DFAST_QC result json was written to GCF_003314975.1_ASM331497v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:15,467] [INFO] DFAST_QC completed!
[2024-01-24 14:41:15,467] [INFO] Total running time: 0h1m14s