[2024-01-24 13:37:11,554] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:11,556] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:11,556] [INFO] DQC Reference Directory: /var/lib/cwl/stg047d6687-0102-4a01-b3bc-6616a57b22a7/dqc_reference
[2024-01-24 13:37:12,900] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:12,901] [INFO] Task started: Prodigal
[2024-01-24 13:37:12,901] [INFO] Running command: gunzip -c /var/lib/cwl/stg0277fb83-9934-4528-964b-7d15b2ad6a0d/GCF_009765365.1_ASM976536v1_genomic.fna.gz | prodigal -d GCF_009765365.1_ASM976536v1_genomic.fna/cds.fna -a GCF_009765365.1_ASM976536v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:28,680] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:28,680] [INFO] Task started: HMMsearch
[2024-01-24 13:37:28,680] [INFO] Running command: hmmsearch --tblout GCF_009765365.1_ASM976536v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg047d6687-0102-4a01-b3bc-6616a57b22a7/dqc_reference/reference_markers.hmm GCF_009765365.1_ASM976536v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:29,086] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:29,087] [INFO] Found 6/6 markers.
[2024-01-24 13:37:29,141] [INFO] Query marker FASTA was written to GCF_009765365.1_ASM976536v1_genomic.fna/markers.fasta
[2024-01-24 13:37:29,142] [INFO] Task started: Blastn
[2024-01-24 13:37:29,142] [INFO] Running command: blastn -query GCF_009765365.1_ASM976536v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg047d6687-0102-4a01-b3bc-6616a57b22a7/dqc_reference/reference_markers.fasta -out GCF_009765365.1_ASM976536v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:30,389] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:30,392] [INFO] Selected 21 target genomes.
[2024-01-24 13:37:30,392] [INFO] Target genome list was writen to GCF_009765365.1_ASM976536v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:30,406] [INFO] Task started: fastANI
[2024-01-24 13:37:30,406] [INFO] Running command: fastANI --query /var/lib/cwl/stg0277fb83-9934-4528-964b-7d15b2ad6a0d/GCF_009765365.1_ASM976536v1_genomic.fna.gz --refList GCF_009765365.1_ASM976536v1_genomic.fna/target_genomes.txt --output GCF_009765365.1_ASM976536v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:53,133] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:53,134] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg047d6687-0102-4a01-b3bc-6616a57b22a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:53,134] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg047d6687-0102-4a01-b3bc-6616a57b22a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:53,156] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:37:53,156] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:37:53,157] [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 flava	strain=M2BS4Y-1	GCA_003583935.1	2320271	2320271	type	True	80.4786	703	1941	95	below_threshold
Aureimonas pseudogalii	strain=DSM 102238	GCA_014196835.1	1744844	1744844	type	True	80.2303	783	1941	95	below_threshold
Aureimonas ureilytica	strain=NBRC 106430	GCA_001463945.1	401562	401562	type	True	80.1621	760	1941	95	below_threshold
Aureimonas ureilytica	strain=DSM 18598	GCA_000382705.1	401562	401562	type	True	80.0953	766	1941	95	below_threshold
Aureimonas leprariae	strain=YIM 132180	GCA_008802405.1	2615207	2615207	type	True	79.997	756	1941	95	below_threshold
Aureimonas endophytica	strain=CGMCC 1.15367	GCA_014642635.1	2027858	2027858	type	True	79.9808	816	1941	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	79.793	669	1941	95	below_threshold
Aurantimonas endophytica	strain=DSM 103570	GCA_014196845.1	1522175	1522175	type	True	79.7811	664	1941	95	below_threshold
Aureimonas mangrovi	strain=LMG 31693	GCA_014058705.1	2758041	2758041	type	True	79.6789	568	1941	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	79.641	746	1941	95	below_threshold
Aurantimonas manganoxydans	strain=SI85-9A1	GCA_000153465.1	651183	651183	type	True	79.6272	636	1941	95	below_threshold
Aureimonas psammosilenae	strain=YIM DR1026	GCA_009176975.1	2495496	2495496	type	True	79.6061	691	1941	95	below_threshold
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	79.5702	692	1941	95	below_threshold
Jiella pacifica	strain=40Bstr34	GCA_010500815.1	2696469	2696469	type	True	79.284	680	1941	95	below_threshold
Jiella endophytica	strain=CBS5Q-3	GCA_004519335.1	2558362	2558362	type	True	79.2594	708	1941	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.7898	631	1941	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	78.584	505	1941	95	below_threshold
Fulvimarina endophytica	strain=85	GCA_003403015.1	2293836	2293836	type	True	78.5695	507	1941	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	77.9865	445	1941	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.0115	612	1941	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	76.8718	606	1941	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:53,158] [INFO] DFAST Taxonomy check result was written to GCF_009765365.1_ASM976536v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:53,159] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:53,159] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:53,159] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg047d6687-0102-4a01-b3bc-6616a57b22a7/dqc_reference/checkm_data
[2024-01-24 13:37:53,160] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:53,215] [INFO] Task started: CheckM
[2024-01-24 13:37:53,215] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009765365.1_ASM976536v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009765365.1_ASM976536v1_genomic.fna/checkm_input GCF_009765365.1_ASM976536v1_genomic.fna/checkm_result
[2024-01-24 13:38:40,004] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:40,006] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:40,031] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:40,032] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:40,032] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009765365.1_ASM976536v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:40,033] [INFO] Task started: Blastn
[2024-01-24 13:38:40,033] [INFO] Running command: blastn -query GCF_009765365.1_ASM976536v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg047d6687-0102-4a01-b3bc-6616a57b22a7/dqc_reference/reference_markers_gtdb.fasta -out GCF_009765365.1_ASM976536v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:42,336] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:42,341] [INFO] Selected 18 target genomes.
[2024-01-24 13:38:42,341] [INFO] Target genome list was writen to GCF_009765365.1_ASM976536v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:42,382] [INFO] Task started: fastANI
[2024-01-24 13:38:42,383] [INFO] Running command: fastANI --query /var/lib/cwl/stg0277fb83-9934-4528-964b-7d15b2ad6a0d/GCF_009765365.1_ASM976536v1_genomic.fna.gz --refList GCF_009765365.1_ASM976536v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009765365.1_ASM976536v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:01,530] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:01,549] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:39:01,549] [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_009765365.1	s__VTOM01 sp009765365	100.0	1940	1941	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__VTOM01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001425575.1	s__Leaf443 sp001425575	80.9849	800	1941	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Leaf443	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423245.1	s__Aureimonas sp001423245	80.6995	727	1941	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001463765.1	s__Aureimonas sp001463765	80.2538	728	1941	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196835.1	s__Aureimonas pseudogalii	80.242	781	1941	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001463705.1	s__Aureimonas sp001463705	80.0299	751	1941	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008802405.1	s__Aureimonas_A leprariae	80.0148	754	1941	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_903970965.1	s__Aureimonas sp903970965	79.9732	660	1941	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014642635.1	s__Aureimonas_A endophytica	79.9453	821	1941	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_000421645.1	s__Aurantimonas coralicida	79.864	647	1941	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aurantimonas	95.4342	97.41	96.44	0.92	0.87	5	-
GCF_014196845.1	s__Aurantimonas endophytica	79.8228	658	1941	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	79.6767	567	1941	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	79.6558	745	1941	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	79.609	711	1941	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009176975.1	s__Aureimonas_A psammosilene	79.602	692	1941	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700095.1	s__Jiella sp002700095	79.5064	702	1941	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	79.2797	681	1941	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Jiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003403015.1	s__Fulvimarina endophytica	78.5609	508	1941	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Fulvimarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:39:01,550] [INFO] GTDB search result was written to GCF_009765365.1_ASM976536v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:01,551] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:01,555] [INFO] DFAST_QC result json was written to GCF_009765365.1_ASM976536v1_genomic.fna/dqc_result.json
[2024-01-24 13:39:01,555] [INFO] DFAST_QC completed!
[2024-01-24 13:39:01,555] [INFO] Total running time: 0h1m50s