[2024-01-24 11:51:06,930] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:06,932] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:06,932] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc5bb14a-6181-46bd-a5ba-6e45c27afcb6/dqc_reference
[2024-01-24 11:51:08,157] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:08,157] [INFO] Task started: Prodigal
[2024-01-24 11:51:08,158] [INFO] Running command: gunzip -c /var/lib/cwl/stge1145a0b-bd51-4fb3-b039-4137c0db7b85/GCF_024609765.1_ASM2460976v1_genomic.fna.gz | prodigal -d GCF_024609765.1_ASM2460976v1_genomic.fna/cds.fna -a GCF_024609765.1_ASM2460976v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:21,958] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:21,959] [INFO] Task started: HMMsearch
[2024-01-24 11:51:21,959] [INFO] Running command: hmmsearch --tblout GCF_024609765.1_ASM2460976v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc5bb14a-6181-46bd-a5ba-6e45c27afcb6/dqc_reference/reference_markers.hmm GCF_024609765.1_ASM2460976v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:22,337] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:22,338] [INFO] Found 6/6 markers.
[2024-01-24 11:51:22,387] [INFO] Query marker FASTA was written to GCF_024609765.1_ASM2460976v1_genomic.fna/markers.fasta
[2024-01-24 11:51:22,388] [INFO] Task started: Blastn
[2024-01-24 11:51:22,388] [INFO] Running command: blastn -query GCF_024609765.1_ASM2460976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc5bb14a-6181-46bd-a5ba-6e45c27afcb6/dqc_reference/reference_markers.fasta -out GCF_024609765.1_ASM2460976v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:23,572] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:23,576] [INFO] Selected 10 target genomes.
[2024-01-24 11:51:23,577] [INFO] Target genome list was writen to GCF_024609765.1_ASM2460976v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:23,583] [INFO] Task started: fastANI
[2024-01-24 11:51:23,583] [INFO] Running command: fastANI --query /var/lib/cwl/stge1145a0b-bd51-4fb3-b039-4137c0db7b85/GCF_024609765.1_ASM2460976v1_genomic.fna.gz --refList GCF_024609765.1_ASM2460976v1_genomic.fna/target_genomes.txt --output GCF_024609765.1_ASM2460976v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:37,433] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:37,434] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc5bb14a-6181-46bd-a5ba-6e45c27afcb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:37,434] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc5bb14a-6181-46bd-a5ba-6e45c27afcb6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:37,443] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:37,443] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:37,443] [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 pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	100.0	1701	1704	95	conclusive
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	86.3748	1061	1704	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	86.1536	1163	1704	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	86.0824	1188	1704	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	85.6108	994	1704	95	below_threshold
Shinella zoogloeoides	strain=DSM 287	GCA_009826855.1	352475	352475	type	True	85.5688	991	1704	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	84.1162	984	1704	95	below_threshold
Shinella kummerowiae	strain=CCBAU 25048	GCA_009827055.1	417745	417745	type	True	84.0905	1077	1704	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	83.7307	1077	1704	95	below_threshold
Shinella daejeonensis	strain=JCM 16236	GCA_024281235.1	659017	659017	type	True	83.6634	951	1704	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:37,445] [INFO] DFAST Taxonomy check result was written to GCF_024609765.1_ASM2460976v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:37,445] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:37,446] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:37,446] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc5bb14a-6181-46bd-a5ba-6e45c27afcb6/dqc_reference/checkm_data
[2024-01-24 11:51:37,447] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:37,499] [INFO] Task started: CheckM
[2024-01-24 11:51:37,500] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024609765.1_ASM2460976v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024609765.1_ASM2460976v1_genomic.fna/checkm_input GCF_024609765.1_ASM2460976v1_genomic.fna/checkm_result
[2024-01-24 11:52:21,061] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:21,062] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:21,091] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:21,092] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:21,092] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024609765.1_ASM2460976v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:21,093] [INFO] Task started: Blastn
[2024-01-24 11:52:21,093] [INFO] Running command: blastn -query GCF_024609765.1_ASM2460976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc5bb14a-6181-46bd-a5ba-6e45c27afcb6/dqc_reference/reference_markers_gtdb.fasta -out GCF_024609765.1_ASM2460976v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:23,523] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:23,528] [INFO] Selected 7 target genomes.
[2024-01-24 11:52:23,528] [INFO] Target genome list was writen to GCF_024609765.1_ASM2460976v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:23,534] [INFO] Task started: fastANI
[2024-01-24 11:52:23,535] [INFO] Running command: fastANI --query /var/lib/cwl/stge1145a0b-bd51-4fb3-b039-4137c0db7b85/GCF_024609765.1_ASM2460976v1_genomic.fna.gz --refList GCF_024609765.1_ASM2460976v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024609765.1_ASM2460976v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:34,383] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:34,394] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:52:34,394] [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_014203155.1	s__Shinella fusca	86.3559	1063	1704	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	86.1456	1166	1704	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	98.18	98.18	0.91	0.91	2	-
GCF_016839145.1	s__Shinella sp016839145	86.0908	1113	1704	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	85.7799	1072	1704	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	85.5589	992	1704	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	84.5082	1124	1704	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	84.1239	1074	1704	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 11:52:34,396] [INFO] GTDB search result was written to GCF_024609765.1_ASM2460976v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:34,396] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:34,399] [INFO] DFAST_QC result json was written to GCF_024609765.1_ASM2460976v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:34,399] [INFO] DFAST_QC completed!
[2024-01-24 11:52:34,399] [INFO] Total running time: 0h1m27s