[2024-01-24 10:47:09,805] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:09,812] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:09,812] [INFO] DQC Reference Directory: /var/lib/cwl/stg813711c4-90fd-4266-8b26-b14740d86d00/dqc_reference
[2024-01-24 10:47:12,039] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,045] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,046] [INFO] Running command: gunzip -c /var/lib/cwl/stgd70c96cd-1cd6-41d9-8407-99f21ce70375/GCF_008802405.1_ASM880240v1_genomic.fna.gz | prodigal -d GCF_008802405.1_ASM880240v1_genomic.fna/cds.fna -a GCF_008802405.1_ASM880240v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:24,288] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:24,289] [INFO] Task started: HMMsearch
[2024-01-24 10:47:24,289] [INFO] Running command: hmmsearch --tblout GCF_008802405.1_ASM880240v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg813711c4-90fd-4266-8b26-b14740d86d00/dqc_reference/reference_markers.hmm GCF_008802405.1_ASM880240v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:24,577] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:24,578] [INFO] Found 6/6 markers.
[2024-01-24 10:47:24,625] [INFO] Query marker FASTA was written to GCF_008802405.1_ASM880240v1_genomic.fna/markers.fasta
[2024-01-24 10:47:24,626] [INFO] Task started: Blastn
[2024-01-24 10:47:24,626] [INFO] Running command: blastn -query GCF_008802405.1_ASM880240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg813711c4-90fd-4266-8b26-b14740d86d00/dqc_reference/reference_markers.fasta -out GCF_008802405.1_ASM880240v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:25,695] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:25,698] [INFO] Selected 15 target genomes.
[2024-01-24 10:47:25,698] [INFO] Target genome list was writen to GCF_008802405.1_ASM880240v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:26,232] [INFO] Task started: fastANI
[2024-01-24 10:47:26,232] [INFO] Running command: fastANI --query /var/lib/cwl/stgd70c96cd-1cd6-41d9-8407-99f21ce70375/GCF_008802405.1_ASM880240v1_genomic.fna.gz --refList GCF_008802405.1_ASM880240v1_genomic.fna/target_genomes.txt --output GCF_008802405.1_ASM880240v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:41,946] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:41,946] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg813711c4-90fd-4266-8b26-b14740d86d00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:41,947] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg813711c4-90fd-4266-8b26-b14740d86d00/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:41,959] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:41,959] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:41,960] [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
Aureimonas leprariae	strain=YIM 132180	GCA_008802405.1	2615207	2615207	type	True	100.0	1570	1573	95	conclusive
Aureimonas endophytica	strain=CGMCC 1.15367	GCA_014642635.1	2027858	2027858	type	True	82.4777	911	1573	95	below_threshold
Aureimonas psammosilenae	strain=YIM DR1026	GCA_009176975.1	2495496	2495496	type	True	81.5485	830	1573	95	below_threshold
Aureimonas flava	strain=M2BS4Y-1	GCA_003583935.1	2320271	2320271	type	True	80.1108	667	1573	95	below_threshold
Aureimonas phyllosphaerae	strain=DSM 25024	GCA_014196405.1	1166078	1166078	type	True	79.825	689	1573	95	below_threshold
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	79.5511	587	1573	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	79.4586	638	1573	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	79.4444	589	1573	95	below_threshold
Aureimonas mangrovi	strain=LMG 31693	GCA_014058705.1	2758041	2758041	type	True	79.4415	523	1573	95	below_threshold
Aurantimonas endophytica	strain=DSM 103570	GCA_014196845.1	1522175	1522175	type	True	79.4243	579	1573	95	below_threshold
Jiella endophytica	strain=CBS5Q-3	GCA_004519335.1	2558362	2558362	type	True	79.197	613	1573	95	below_threshold
Jiella pacifica	strain=40Bstr34	GCA_010500815.1	2696469	2696469	type	True	78.9643	566	1573	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.7777	571	1573	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	78.5276	416	1573	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	77.6442	374	1573	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:41,961] [INFO] DFAST Taxonomy check result was written to GCF_008802405.1_ASM880240v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:41,962] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:41,962] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:41,962] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg813711c4-90fd-4266-8b26-b14740d86d00/dqc_reference/checkm_data
[2024-01-24 10:47:41,963] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:42,015] [INFO] Task started: CheckM
[2024-01-24 10:47:42,015] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008802405.1_ASM880240v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008802405.1_ASM880240v1_genomic.fna/checkm_input GCF_008802405.1_ASM880240v1_genomic.fna/checkm_result
[2024-01-24 10:48:20,297] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:20,299] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:20,323] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:20,323] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:20,324] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008802405.1_ASM880240v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:20,324] [INFO] Task started: Blastn
[2024-01-24 10:48:20,324] [INFO] Running command: blastn -query GCF_008802405.1_ASM880240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg813711c4-90fd-4266-8b26-b14740d86d00/dqc_reference/reference_markers_gtdb.fasta -out GCF_008802405.1_ASM880240v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:22,541] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:22,547] [INFO] Selected 17 target genomes.
[2024-01-24 10:48:22,547] [INFO] Target genome list was writen to GCF_008802405.1_ASM880240v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:22,585] [INFO] Task started: fastANI
[2024-01-24 10:48:22,585] [INFO] Running command: fastANI --query /var/lib/cwl/stgd70c96cd-1cd6-41d9-8407-99f21ce70375/GCF_008802405.1_ASM880240v1_genomic.fna.gz --refList GCF_008802405.1_ASM880240v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008802405.1_ASM880240v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:40,250] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:40,290] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:40,291] [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_008802405.1	s__Aureimonas_A leprariae	100.0	1570	1573	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014642635.1	s__Aureimonas_A endophytica	82.4632	913	1573	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009176975.1	s__Aureimonas_A psammosilene	81.5441	832	1573	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765365.1	s__VTOM01 sp009765365	80.1754	739	1573	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__VTOM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425485.1	s__Aureimonas_A sp001425485	80.1506	742	1573	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003583935.1	s__Aureimonas flava	80.1027	668	1573	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424685.1	s__Aureimonas_A sp001424685	79.9827	684	1573	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382705.1	s__Aureimonas ureilytica	79.7453	653	1573	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001425575.1	s__Leaf443 sp001425575	79.7294	676	1573	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Leaf443	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002893625.1	s__Mangrovicella endophytica	79.6955	616	1573	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mangrovicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001463705.1	s__Aureimonas sp001463705	79.6832	682	1573	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500835.1	s__Aurantimonas aggregata	79.5399	589	1573	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014058705.1	s__Aureimonas mangrovi	79.4473	523	1573	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017353515.1	s__Jiella sp017353515	79.4397	640	1573	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	79.1981	611	1573	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500815.1	s__Jiella pacifica	78.9556	566	1573	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	78.903	585	1573	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 10:48:40,293] [INFO] GTDB search result was written to GCF_008802405.1_ASM880240v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:40,294] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:40,298] [INFO] DFAST_QC result json was written to GCF_008802405.1_ASM880240v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:40,299] [INFO] DFAST_QC completed!
[2024-01-24 10:48:40,299] [INFO] Total running time: 0h1m30s