[2024-01-24 14:06:07,171] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:07,177] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:07,177] [INFO] DQC Reference Directory: /var/lib/cwl/stge4706802-9831-4dea-a156-60b5929ad32a/dqc_reference
[2024-01-24 14:06:08,552] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:08,553] [INFO] Task started: Prodigal
[2024-01-24 14:06:08,553] [INFO] Running command: gunzip -c /var/lib/cwl/stg69305514-9bef-47f5-b2ec-1b227e65d259/GCF_022601905.1_ASM2260190v1_genomic.fna.gz | prodigal -d GCF_022601905.1_ASM2260190v1_genomic.fna/cds.fna -a GCF_022601905.1_ASM2260190v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:23,841] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:23,842] [INFO] Task started: HMMsearch
[2024-01-24 14:06:23,842] [INFO] Running command: hmmsearch --tblout GCF_022601905.1_ASM2260190v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4706802-9831-4dea-a156-60b5929ad32a/dqc_reference/reference_markers.hmm GCF_022601905.1_ASM2260190v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:24,140] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:24,149] [INFO] Found 6/6 markers.
[2024-01-24 14:06:24,205] [INFO] Query marker FASTA was written to GCF_022601905.1_ASM2260190v1_genomic.fna/markers.fasta
[2024-01-24 14:06:24,205] [INFO] Task started: Blastn
[2024-01-24 14:06:24,206] [INFO] Running command: blastn -query GCF_022601905.1_ASM2260190v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4706802-9831-4dea-a156-60b5929ad32a/dqc_reference/reference_markers.fasta -out GCF_022601905.1_ASM2260190v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:25,280] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:25,283] [INFO] Selected 9 target genomes.
[2024-01-24 14:06:25,284] [INFO] Target genome list was writen to GCF_022601905.1_ASM2260190v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:25,285] [INFO] Task started: fastANI
[2024-01-24 14:06:25,285] [INFO] Running command: fastANI --query /var/lib/cwl/stg69305514-9bef-47f5-b2ec-1b227e65d259/GCF_022601905.1_ASM2260190v1_genomic.fna.gz --refList GCF_022601905.1_ASM2260190v1_genomic.fna/target_genomes.txt --output GCF_022601905.1_ASM2260190v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:36,951] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:36,951] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4706802-9831-4dea-a156-60b5929ad32a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:36,952] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4706802-9831-4dea-a156-60b5929ad32a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:36,960] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:06:36,960] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:06:36,960] [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 sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	91.8189	1342	1643	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	91.7437	1393	1643	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	85.6488	1007	1643	95	below_threshold
Shinella zoogloeoides	strain=DSM 287	GCA_009826855.1	352475	352475	type	True	85.6193	1006	1643	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	85.2672	1150	1643	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	85.2455	1150	1643	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	85.0689	1039	1643	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	84.9792	1098	1643	95	below_threshold
Shinella kummerowiae	strain=CCBAU 25048	GCA_009827055.1	417745	417745	type	True	84.4844	1136	1643	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:36,962] [INFO] DFAST Taxonomy check result was written to GCF_022601905.1_ASM2260190v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:36,962] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:36,962] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:36,963] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4706802-9831-4dea-a156-60b5929ad32a/dqc_reference/checkm_data
[2024-01-24 14:06:36,964] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:37,022] [INFO] Task started: CheckM
[2024-01-24 14:06:37,023] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022601905.1_ASM2260190v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022601905.1_ASM2260190v1_genomic.fna/checkm_input GCF_022601905.1_ASM2260190v1_genomic.fna/checkm_result
[2024-01-24 14:07:22,974] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:22,976] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:23,002] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:23,002] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:23,003] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022601905.1_ASM2260190v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:23,003] [INFO] Task started: Blastn
[2024-01-24 14:07:23,003] [INFO] Running command: blastn -query GCF_022601905.1_ASM2260190v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4706802-9831-4dea-a156-60b5929ad32a/dqc_reference/reference_markers_gtdb.fasta -out GCF_022601905.1_ASM2260190v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:24,982] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:24,986] [INFO] Selected 11 target genomes.
[2024-01-24 14:07:24,986] [INFO] Target genome list was writen to GCF_022601905.1_ASM2260190v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:24,990] [INFO] Task started: fastANI
[2024-01-24 14:07:24,990] [INFO] Running command: fastANI --query /var/lib/cwl/stg69305514-9bef-47f5-b2ec-1b227e65d259/GCF_022601905.1_ASM2260190v1_genomic.fna.gz --refList GCF_022601905.1_ASM2260190v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022601905.1_ASM2260190v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:38,562] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:38,575] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:38,575] [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
GCA_002364745.1	s__Shinella sp002364745	98.1805	1516	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	99.33	99.33	0.84	0.84	2	conclusive
GCF_004514435.1	s__Shinella sp004514435	91.8084	1330	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	99.21	98.45	0.95	0.91	3	-
GCF_009826855.1	s__Shinella zoogloeoides	85.6282	1005	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016839145.1	s__Shinella sp016839145	85.439	1120	1643	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	85.4091	1085	1643	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	85.2552	1149	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	98.18	98.18	0.91	0.91	2	-
GCF_014203155.1	s__Shinella fusca	85.0628	1040	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003432075.1	s__Shinella sp003432075	84.9966	1076	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001262505.1	s__Shinella sp001262505	84.5094	1135	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	98.95	98.39	0.91	0.87	4	-
GCF_009827055.1	s__Shinella kummerowiae	84.4933	1135	1643	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	84.2686	1127	1643	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:38,577] [INFO] GTDB search result was written to GCF_022601905.1_ASM2260190v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:38,577] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:38,580] [INFO] DFAST_QC result json was written to GCF_022601905.1_ASM2260190v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:38,580] [INFO] DFAST_QC completed!
[2024-01-24 14:07:38,580] [INFO] Total running time: 0h1m31s