[2024-01-24 13:32:56,333] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:56,345] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:56,348] [INFO] DQC Reference Directory: /var/lib/cwl/stg319afab8-53dc-4bcc-9296-71fe375847b0/dqc_reference
[2024-01-24 13:32:58,116] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:58,117] [INFO] Task started: Prodigal
[2024-01-24 13:32:58,117] [INFO] Running command: gunzip -c /var/lib/cwl/stgebdaafa1-d033-4d0c-a7ed-651966800fa4/GCF_003046475.1_ASM304647v1_genomic.fna.gz | prodigal -d GCF_003046475.1_ASM304647v1_genomic.fna/cds.fna -a GCF_003046475.1_ASM304647v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:10,324] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:10,324] [INFO] Task started: HMMsearch
[2024-01-24 13:33:10,324] [INFO] Running command: hmmsearch --tblout GCF_003046475.1_ASM304647v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg319afab8-53dc-4bcc-9296-71fe375847b0/dqc_reference/reference_markers.hmm GCF_003046475.1_ASM304647v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:10,747] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:10,748] [INFO] Found 6/6 markers.
[2024-01-24 13:33:10,785] [INFO] Query marker FASTA was written to GCF_003046475.1_ASM304647v1_genomic.fna/markers.fasta
[2024-01-24 13:33:10,786] [INFO] Task started: Blastn
[2024-01-24 13:33:10,786] [INFO] Running command: blastn -query GCF_003046475.1_ASM304647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg319afab8-53dc-4bcc-9296-71fe375847b0/dqc_reference/reference_markers.fasta -out GCF_003046475.1_ASM304647v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:11,844] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:11,847] [INFO] Selected 14 target genomes.
[2024-01-24 13:33:11,847] [INFO] Target genome list was writen to GCF_003046475.1_ASM304647v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:11,875] [INFO] Task started: fastANI
[2024-01-24 13:33:11,875] [INFO] Running command: fastANI --query /var/lib/cwl/stgebdaafa1-d033-4d0c-a7ed-651966800fa4/GCF_003046475.1_ASM304647v1_genomic.fna.gz --refList GCF_003046475.1_ASM304647v1_genomic.fna/target_genomes.txt --output GCF_003046475.1_ASM304647v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:27,701] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:27,701] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg319afab8-53dc-4bcc-9296-71fe375847b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:27,702] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg319afab8-53dc-4bcc-9296-71fe375847b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:27,711] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:33:27,711] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:33:27,711] [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
Rhizobium azooxidifex	strain=DSM 100211	GCA_014196765.1	1636188	1636188	type	True	83.5654	1006	1519	95	below_threshold
Rhizobium subbaraonis	strain=JC85	GCA_900220975.1	908946	908946	type	True	82.812	935	1519	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	82.7807	856	1519	95	below_threshold
Rhizobium rhizolycopersici	strain=DBTS2	GCA_013378445.1	2746702	2746702	type	True	82.7571	951	1519	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	82.3915	846	1519	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	82.283	924	1519	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	82.212	934	1519	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	82.0469	813	1519	95	below_threshold
Shinella zoogloeoides	strain=DSM 287	GCA_009826855.1	352475	352475	type	True	81.9919	811	1519	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	81.4575	781	1519	95	below_threshold
Shinella kummerowiae	strain=CCBAU 25048	GCA_009827055.1	417745	417745	type	True	81.3985	857	1519	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	81.3947	798	1519	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	81.1655	829	1519	95	below_threshold
Shinella daejeonensis	strain=JCM 16236	GCA_024281235.1	659017	659017	type	True	80.6648	743	1519	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:27,712] [INFO] DFAST Taxonomy check result was written to GCF_003046475.1_ASM304647v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:27,713] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:27,713] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:27,713] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg319afab8-53dc-4bcc-9296-71fe375847b0/dqc_reference/checkm_data
[2024-01-24 13:33:27,714] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:27,761] [INFO] Task started: CheckM
[2024-01-24 13:33:27,761] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003046475.1_ASM304647v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003046475.1_ASM304647v1_genomic.fna/checkm_input GCF_003046475.1_ASM304647v1_genomic.fna/checkm_result
[2024-01-24 13:34:02,948] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:02,949] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:02,965] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:02,965] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:02,966] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003046475.1_ASM304647v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:02,966] [INFO] Task started: Blastn
[2024-01-24 13:34:02,966] [INFO] Running command: blastn -query GCF_003046475.1_ASM304647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg319afab8-53dc-4bcc-9296-71fe375847b0/dqc_reference/reference_markers_gtdb.fasta -out GCF_003046475.1_ASM304647v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:05,143] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:05,146] [INFO] Selected 8 target genomes.
[2024-01-24 13:34:05,146] [INFO] Target genome list was writen to GCF_003046475.1_ASM304647v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:05,151] [INFO] Task started: fastANI
[2024-01-24 13:34:05,151] [INFO] Running command: fastANI --query /var/lib/cwl/stgebdaafa1-d033-4d0c-a7ed-651966800fa4/GCF_003046475.1_ASM304647v1_genomic.fna.gz --refList GCF_003046475.1_ASM304647v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003046475.1_ASM304647v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:15,512] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:15,519] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:15,519] [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_003046475.1	s__Mycoplana dimorpha	100.0	1516	1519	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900469965.1	s__Mycoplana sp900469965	84.1548	998	1519	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	98.03	97.96	0.94	0.92	10	-
GCF_014196765.1	s__Mycoplana azooxidifex	83.5629	1006	1519	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014851675.1	s__Mycoplana sp014851675	83.2498	986	1519	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900220975.1	s__Mycoplana subbaraonis	82.812	935	1519	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013378445.1	s__Mycoplana rhizolycopersici	82.7531	952	1519	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mycoplana	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203155.1	s__Shinella fusca	82.3745	848	1519	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341885.1	s__Shinella granuli	82.3098	920	1519	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	98.18	98.18	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:15,520] [INFO] GTDB search result was written to GCF_003046475.1_ASM304647v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:15,521] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:15,524] [INFO] DFAST_QC result json was written to GCF_003046475.1_ASM304647v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:15,524] [INFO] DFAST_QC completed!
[2024-01-24 13:34:15,524] [INFO] Total running time: 0h1m19s