[2024-01-24 12:40:06,901] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:06,902] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:06,903] [INFO] DQC Reference Directory: /var/lib/cwl/stg770164a4-9432-48b1-a2ac-cfb480d1c1bf/dqc_reference
[2024-01-24 12:40:08,202] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:08,203] [INFO] Task started: Prodigal
[2024-01-24 12:40:08,203] [INFO] Running command: gunzip -c /var/lib/cwl/stg35cdede1-1e63-4aa4-9a75-a365aef49730/GCF_021390325.1_ASM2139032v1_genomic.fna.gz | prodigal -d GCF_021390325.1_ASM2139032v1_genomic.fna/cds.fna -a GCF_021390325.1_ASM2139032v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:21,695] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:21,696] [INFO] Task started: HMMsearch
[2024-01-24 12:40:21,696] [INFO] Running command: hmmsearch --tblout GCF_021390325.1_ASM2139032v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg770164a4-9432-48b1-a2ac-cfb480d1c1bf/dqc_reference/reference_markers.hmm GCF_021390325.1_ASM2139032v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:21,937] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:21,939] [INFO] Found 6/6 markers.
[2024-01-24 12:40:21,982] [INFO] Query marker FASTA was written to GCF_021390325.1_ASM2139032v1_genomic.fna/markers.fasta
[2024-01-24 12:40:21,983] [INFO] Task started: Blastn
[2024-01-24 12:40:21,983] [INFO] Running command: blastn -query GCF_021390325.1_ASM2139032v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg770164a4-9432-48b1-a2ac-cfb480d1c1bf/dqc_reference/reference_markers.fasta -out GCF_021390325.1_ASM2139032v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:23,048] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:23,052] [INFO] Selected 14 target genomes.
[2024-01-24 12:40:23,053] [INFO] Target genome list was writen to GCF_021390325.1_ASM2139032v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:23,055] [INFO] Task started: fastANI
[2024-01-24 12:40:23,056] [INFO] Running command: fastANI --query /var/lib/cwl/stg35cdede1-1e63-4aa4-9a75-a365aef49730/GCF_021390325.1_ASM2139032v1_genomic.fna.gz --refList GCF_021390325.1_ASM2139032v1_genomic.fna/target_genomes.txt --output GCF_021390325.1_ASM2139032v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:37,194] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:37,195] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg770164a4-9432-48b1-a2ac-cfb480d1c1bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:37,195] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg770164a4-9432-48b1-a2ac-cfb480d1c1bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:37,207] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:40:37,208] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:40:37,208] [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
Jiella pacifica	strain=40Bstr34	GCA_010500815.1	2696469	2696469	type	True	89.1303	1308	1701	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	85.0753	1193	1701	95	below_threshold
Jiella endophytica	strain=CBS5Q-3	GCA_004519335.1	2558362	2558362	type	True	84.7565	1170	1701	95	below_threshold
Aurantimonas manganoxydans	strain=DSM 21871	GCA_001463865.1	651183	651183	type	True	80.9592	746	1701	95	below_threshold
Aurantimonas endophytica	strain=DSM 103570	GCA_014196845.1	1522175	1522175	type	True	80.9176	754	1701	95	below_threshold
Aurantimonas manganoxydans	strain=SI85-9A1	GCA_000153465.1	651183	651183	type	True	80.9117	765	1701	95	below_threshold
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	80.8852	778	1701	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	80.7493	772	1701	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	79.6528	645	1701	95	below_threshold
Aureimonas endophytica	strain=CGMCC 1.15367	GCA_014642635.1	2027858	2027858	type	True	79.348	677	1701	95	below_threshold
Fulvimarina pelagi	strain=DSM 15513	GCA_001463845.1	217511	217511	type	True	78.539	465	1701	95	below_threshold
Fulvimarina pelagi	strain=HTCC2506	GCA_000153705.1	217511	217511	type	True	78.52	471	1701	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	78.0366	539	1701	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	77.1621	499	1701	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:37,210] [INFO] DFAST Taxonomy check result was written to GCF_021390325.1_ASM2139032v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:37,211] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:37,211] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:37,212] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg770164a4-9432-48b1-a2ac-cfb480d1c1bf/dqc_reference/checkm_data
[2024-01-24 12:40:37,213] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:37,264] [INFO] Task started: CheckM
[2024-01-24 12:40:37,264] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021390325.1_ASM2139032v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021390325.1_ASM2139032v1_genomic.fna/checkm_input GCF_021390325.1_ASM2139032v1_genomic.fna/checkm_result
[2024-01-24 12:41:35,860] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:35,861] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:35,879] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:35,879] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:35,880] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021390325.1_ASM2139032v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:35,880] [INFO] Task started: Blastn
[2024-01-24 12:41:35,880] [INFO] Running command: blastn -query GCF_021390325.1_ASM2139032v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg770164a4-9432-48b1-a2ac-cfb480d1c1bf/dqc_reference/reference_markers_gtdb.fasta -out GCF_021390325.1_ASM2139032v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:38,028] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:38,032] [INFO] Selected 6 target genomes.
[2024-01-24 12:41:38,032] [INFO] Target genome list was writen to GCF_021390325.1_ASM2139032v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:38,034] [INFO] Task started: fastANI
[2024-01-24 12:41:38,034] [INFO] Running command: fastANI --query /var/lib/cwl/stg35cdede1-1e63-4aa4-9a75-a365aef49730/GCF_021390325.1_ASM2139032v1_genomic.fna.gz --refList GCF_021390325.1_ASM2139032v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021390325.1_ASM2139032v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:46,484] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:46,490] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:41:46,490] [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_010500815.1	s__Jiella pacifica	89.1546	1306	1701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088275.1	s__Jiella sp002088275	85.3475	1177	1701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017353515.1	s__Jiella sp017353515	85.084	1192	1701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700095.1	s__Jiella sp002700095	84.9768	1159	1701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004519335.1	s__Jiella endophytica	84.7956	1162	1701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017815135.1	s__Jiella sp017815135	83.8286	1074	1701	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:46,492] [INFO] GTDB search result was written to GCF_021390325.1_ASM2139032v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:46,492] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:46,495] [INFO] DFAST_QC result json was written to GCF_021390325.1_ASM2139032v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:46,495] [INFO] DFAST_QC completed!
[2024-01-24 12:41:46,495] [INFO] Total running time: 0h1m40s