[2024-01-25 19:53:50,433] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:53:50,434] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:53:50,434] [INFO] DQC Reference Directory: /var/lib/cwl/stg58fba8ee-5c7b-46b3-a3fd-b0c8b0a4cc00/dqc_reference
[2024-01-25 19:53:51,643] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:53:51,643] [INFO] Task started: Prodigal
[2024-01-25 19:53:51,644] [INFO] Running command: gunzip -c /var/lib/cwl/stga600b2d5-37c7-4c5d-a61a-6a2dca9315cb/GCF_030160575.1_ASM3016057v1_genomic.fna.gz | prodigal -d GCF_030160575.1_ASM3016057v1_genomic.fna/cds.fna -a GCF_030160575.1_ASM3016057v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:54:09,152] [INFO] Task succeeded: Prodigal
[2024-01-25 19:54:09,152] [INFO] Task started: HMMsearch
[2024-01-25 19:54:09,152] [INFO] Running command: hmmsearch --tblout GCF_030160575.1_ASM3016057v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58fba8ee-5c7b-46b3-a3fd-b0c8b0a4cc00/dqc_reference/reference_markers.hmm GCF_030160575.1_ASM3016057v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:54:09,484] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:54:09,485] [INFO] Found 6/6 markers.
[2024-01-25 19:54:09,540] [INFO] Query marker FASTA was written to GCF_030160575.1_ASM3016057v1_genomic.fna/markers.fasta
[2024-01-25 19:54:09,540] [INFO] Task started: Blastn
[2024-01-25 19:54:09,540] [INFO] Running command: blastn -query GCF_030160575.1_ASM3016057v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58fba8ee-5c7b-46b3-a3fd-b0c8b0a4cc00/dqc_reference/reference_markers.fasta -out GCF_030160575.1_ASM3016057v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:10,494] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:10,497] [INFO] Selected 13 target genomes.
[2024-01-25 19:54:10,497] [INFO] Target genome list was writen to GCF_030160575.1_ASM3016057v1_genomic.fna/target_genomes.txt
[2024-01-25 19:54:10,515] [INFO] Task started: fastANI
[2024-01-25 19:54:10,515] [INFO] Running command: fastANI --query /var/lib/cwl/stga600b2d5-37c7-4c5d-a61a-6a2dca9315cb/GCF_030160575.1_ASM3016057v1_genomic.fna.gz --refList GCF_030160575.1_ASM3016057v1_genomic.fna/target_genomes.txt --output GCF_030160575.1_ASM3016057v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:54:27,920] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:27,921] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58fba8ee-5c7b-46b3-a3fd-b0c8b0a4cc00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:54:27,921] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58fba8ee-5c7b-46b3-a3fd-b0c8b0a4cc00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:54:27,939] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:54:27,939] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:54:27,939] [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
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	99.9971	2248	2255	95	conclusive
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	94.0519	1642	2255	95	below_threshold
Shinella zoogloeoides	strain=DSM 287	GCA_009826855.1	352475	352475	type	True	87.9296	1126	2255	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	87.8961	1129	2255	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	87.8642	1238	2255	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	86.4647	1352	2255	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	86.0063	1187	2255	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	85.9643	1149	2255	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	85.8883	1165	2255	95	below_threshold
Novosphingobium marinum	strain=CGMCC 1.12918	GCA_014640055.1	1514948	1514948	type	True	76.0839	141	2255	95	below_threshold
Novosphingobium marinum	strain=DSM 29043	GCA_013408095.1	1514948	1514948	type	True	76.0228	140	2255	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	75.9681	204	2255	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	75.7101	231	2255	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:54:27,940] [INFO] DFAST Taxonomy check result was written to GCF_030160575.1_ASM3016057v1_genomic.fna/tc_result.tsv
[2024-01-25 19:54:27,941] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:54:27,941] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:54:27,941] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58fba8ee-5c7b-46b3-a3fd-b0c8b0a4cc00/dqc_reference/checkm_data
[2024-01-25 19:54:27,942] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:54:28,006] [INFO] Task started: CheckM
[2024-01-25 19:54:28,006] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030160575.1_ASM3016057v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030160575.1_ASM3016057v1_genomic.fna/checkm_input GCF_030160575.1_ASM3016057v1_genomic.fna/checkm_result
[2024-01-25 19:55:30,690] [INFO] Task succeeded: CheckM
[2024-01-25 19:55:30,692] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:55:30,708] [INFO] ===== Completeness check finished =====
[2024-01-25 19:55:30,708] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:55:30,709] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030160575.1_ASM3016057v1_genomic.fna/markers.fasta)
[2024-01-25 19:55:30,710] [INFO] Task started: Blastn
[2024-01-25 19:55:30,710] [INFO] Running command: blastn -query GCF_030160575.1_ASM3016057v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58fba8ee-5c7b-46b3-a3fd-b0c8b0a4cc00/dqc_reference/reference_markers_gtdb.fasta -out GCF_030160575.1_ASM3016057v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:32,593] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:32,595] [INFO] Selected 10 target genomes.
[2024-01-25 19:55:32,596] [INFO] Target genome list was writen to GCF_030160575.1_ASM3016057v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:55:32,606] [INFO] Task started: fastANI
[2024-01-25 19:55:32,606] [INFO] Running command: fastANI --query /var/lib/cwl/stga600b2d5-37c7-4c5d-a61a-6a2dca9315cb/GCF_030160575.1_ASM3016057v1_genomic.fna.gz --refList GCF_030160575.1_ASM3016057v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030160575.1_ASM3016057v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:55:46,083] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:46,090] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:55:46,090] [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_004341885.1	s__Shinella granuli	94.0425	1643	2255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	98.18	98.18	0.91	0.91	2	-
GCF_001262505.1	s__Shinella sp001262505	90.8055	1628	2255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	98.95	98.39	0.91	0.87	4	-
GCF_016839145.1	s__Shinella sp016839145	88.0663	1268	2255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009826855.1	s__Shinella zoogloeoides	87.9296	1126	2255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203155.1	s__Shinella fusca	87.906	1233	2255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003574625.1	s__Shinella zoogloeoides_A	87.8383	1285	2255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001713395.1	s__Shinella sp001713395	86.731	1437	2255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483305.1	s__Brevundimonas sp002483305	77.518	189	2255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408095.1	s__Novosphingobium marinum	76.0343	139	2255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001028625.1	s__Pelagerythrobacter marensis	75.7305	92	2255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:55:46,091] [INFO] GTDB search result was written to GCF_030160575.1_ASM3016057v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:55:46,092] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:55:46,094] [INFO] DFAST_QC result json was written to GCF_030160575.1_ASM3016057v1_genomic.fna/dqc_result.json
[2024-01-25 19:55:46,095] [INFO] DFAST_QC completed!
[2024-01-25 19:55:46,095] [INFO] Total running time: 0h1m56s