[2024-01-24 13:45:45,617] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:45,619] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:45,619] [INFO] DQC Reference Directory: /var/lib/cwl/stg387298b9-d12e-4d1f-bd76-0f8303692d07/dqc_reference
[2024-01-24 13:45:46,931] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:46,932] [INFO] Task started: Prodigal
[2024-01-24 13:45:46,932] [INFO] Running command: gunzip -c /var/lib/cwl/stga0831a96-d72e-48a1-885a-d968a1e745c7/GCF_022899355.1_ASM2289935v1_genomic.fna.gz | prodigal -d GCF_022899355.1_ASM2289935v1_genomic.fna/cds.fna -a GCF_022899355.1_ASM2289935v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:07,028] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:07,029] [INFO] Task started: HMMsearch
[2024-01-24 13:46:07,029] [INFO] Running command: hmmsearch --tblout GCF_022899355.1_ASM2289935v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg387298b9-d12e-4d1f-bd76-0f8303692d07/dqc_reference/reference_markers.hmm GCF_022899355.1_ASM2289935v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:07,543] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:07,544] [INFO] Found 6/6 markers.
[2024-01-24 13:46:07,611] [INFO] Query marker FASTA was written to GCF_022899355.1_ASM2289935v1_genomic.fna/markers.fasta
[2024-01-24 13:46:07,612] [INFO] Task started: Blastn
[2024-01-24 13:46:07,612] [INFO] Running command: blastn -query GCF_022899355.1_ASM2289935v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg387298b9-d12e-4d1f-bd76-0f8303692d07/dqc_reference/reference_markers.fasta -out GCF_022899355.1_ASM2289935v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:08,668] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:08,672] [INFO] Selected 13 target genomes.
[2024-01-24 13:46:08,673] [INFO] Target genome list was writen to GCF_022899355.1_ASM2289935v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:08,681] [INFO] Task started: fastANI
[2024-01-24 13:46:08,682] [INFO] Running command: fastANI --query /var/lib/cwl/stga0831a96-d72e-48a1-885a-d968a1e745c7/GCF_022899355.1_ASM2289935v1_genomic.fna.gz --refList GCF_022899355.1_ASM2289935v1_genomic.fna/target_genomes.txt --output GCF_022899355.1_ASM2289935v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:25,374] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:25,375] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg387298b9-d12e-4d1f-bd76-0f8303692d07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:25,375] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg387298b9-d12e-4d1f-bd76-0f8303692d07/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:25,399] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:25,399] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:25,400] [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	100.0	2269	2273	95	conclusive
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	94.1127	1657	2273	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	87.9947	1134	2273	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	87.9608	1239	2273	95	below_threshold
Shinella zoogloeoides	strain=DSM 287	GCA_009826855.1	352475	352475	type	True	87.9229	1131	2273	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	86.4831	1367	2273	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	86.0083	1178	2273	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	85.9921	1153	2273	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	85.939	1187	2273	95	below_threshold
Novosphingobium marinum	strain=CGMCC 1.12918	GCA_014640055.1	1514948	1514948	type	True	76.1918	135	2273	95	below_threshold
Novosphingobium marinum	strain=DSM 29043	GCA_013408095.1	1514948	1514948	type	True	76.1461	133	2273	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	75.9437	215	2273	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	75.8368	236	2273	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:25,402] [INFO] DFAST Taxonomy check result was written to GCF_022899355.1_ASM2289935v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:25,403] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:25,403] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:25,404] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg387298b9-d12e-4d1f-bd76-0f8303692d07/dqc_reference/checkm_data
[2024-01-24 13:46:25,406] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:25,477] [INFO] Task started: CheckM
[2024-01-24 13:46:25,477] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022899355.1_ASM2289935v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022899355.1_ASM2289935v1_genomic.fna/checkm_input GCF_022899355.1_ASM2289935v1_genomic.fna/checkm_result
[2024-01-24 13:47:25,998] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:26,000] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:26,029] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:26,029] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:26,029] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022899355.1_ASM2289935v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:26,030] [INFO] Task started: Blastn
[2024-01-24 13:47:26,030] [INFO] Running command: blastn -query GCF_022899355.1_ASM2289935v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg387298b9-d12e-4d1f-bd76-0f8303692d07/dqc_reference/reference_markers_gtdb.fasta -out GCF_022899355.1_ASM2289935v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:27,949] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:27,952] [INFO] Selected 10 target genomes.
[2024-01-24 13:47:27,952] [INFO] Target genome list was writen to GCF_022899355.1_ASM2289935v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:27,966] [INFO] Task started: fastANI
[2024-01-24 13:47:27,967] [INFO] Running command: fastANI --query /var/lib/cwl/stga0831a96-d72e-48a1-885a-d968a1e745c7/GCF_022899355.1_ASM2289935v1_genomic.fna.gz --refList GCF_022899355.1_ASM2289935v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022899355.1_ASM2289935v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:41,060] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:41,073] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:47:41,073] [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	94.1008	1658	2273	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	90.8699	1646	2273	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	88.0136	1286	2273	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	87.9625	1239	2273	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	87.9346	1130	2273	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	87.8718	1315	2273	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	86.807	1459	2273	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	77.5112	189	2273	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	76.1461	133	2273	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	75.7884	93	2273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:41,075] [INFO] GTDB search result was written to GCF_022899355.1_ASM2289935v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:41,076] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:41,079] [INFO] DFAST_QC result json was written to GCF_022899355.1_ASM2289935v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:41,079] [INFO] DFAST_QC completed!
[2024-01-24 13:47:41,080] [INFO] Total running time: 0h1m55s