[2023-06-29 16:47:01,823] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:47:01,825] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:47:01,825] [INFO] DQC Reference Directory: /var/lib/cwl/stgdaff16a7-15a5-4c54-83a3-6381fde5e0e3/dqc_reference
[2023-06-29 16:47:03,023] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:47:03,024] [INFO] Task started: Prodigal
[2023-06-29 16:47:03,024] [INFO] Running command: gunzip -c /var/lib/cwl/stg01da18bd-0fa5-4f84-9e33-2a4c97a4e790/GCA_023430705.1_ASM2343070v1_genomic.fna.gz | prodigal -d GCA_023430705.1_ASM2343070v1_genomic.fna/cds.fna -a GCA_023430705.1_ASM2343070v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:47:11,635] [INFO] Task succeeded: Prodigal
[2023-06-29 16:47:11,635] [INFO] Task started: HMMsearch
[2023-06-29 16:47:11,636] [INFO] Running command: hmmsearch --tblout GCA_023430705.1_ASM2343070v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdaff16a7-15a5-4c54-83a3-6381fde5e0e3/dqc_reference/reference_markers.hmm GCA_023430705.1_ASM2343070v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:47:11,838] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:47:11,839] [INFO] Found 6/6 markers.
[2023-06-29 16:47:11,871] [INFO] Query marker FASTA was written to GCA_023430705.1_ASM2343070v1_genomic.fna/markers.fasta
[2023-06-29 16:47:11,872] [INFO] Task started: Blastn
[2023-06-29 16:47:11,872] [INFO] Running command: blastn -query GCA_023430705.1_ASM2343070v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdaff16a7-15a5-4c54-83a3-6381fde5e0e3/dqc_reference/reference_markers.fasta -out GCA_023430705.1_ASM2343070v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:47:12,742] [INFO] Task succeeded: Blastn
[2023-06-29 16:47:12,747] [INFO] Selected 20 target genomes.
[2023-06-29 16:47:12,747] [INFO] Target genome list was writen to GCA_023430705.1_ASM2343070v1_genomic.fna/target_genomes.txt
[2023-06-29 16:47:12,750] [INFO] Task started: fastANI
[2023-06-29 16:47:12,750] [INFO] Running command: fastANI --query /var/lib/cwl/stg01da18bd-0fa5-4f84-9e33-2a4c97a4e790/GCA_023430705.1_ASM2343070v1_genomic.fna.gz --refList GCA_023430705.1_ASM2343070v1_genomic.fna/target_genomes.txt --output GCA_023430705.1_ASM2343070v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:47:27,321] [INFO] Task succeeded: fastANI
[2023-06-29 16:47:27,322] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdaff16a7-15a5-4c54-83a3-6381fde5e0e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:47:27,322] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdaff16a7-15a5-4c54-83a3-6381fde5e0e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:47:27,338] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:47:27,338] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 16:47:27,339] [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
Devosia insulae	strain=DS-56	GCA_000970465.2	408174	408174	type	True	82.3203	703	1012	95	below_threshold
Devosia geojensis	strain=BD-c194	GCA_000969415.1	443610	443610	type	True	78.9431	444	1012	95	below_threshold
Youhaiella tibetensis	strain=CGMCC 1.12719	GCA_014638565.1	1447062	1447062	type	True	78.8717	405	1012	95	below_threshold
Youhaiella tibetensis	strain=fig4	GCA_008000755.1	1447062	1447062	type	True	78.8397	410	1012	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	78.4826	345	1012	95	below_threshold
Devosia enhydra	strain=ATCC 23634	GCA_900119845.1	665118	665118	type	True	78.4825	354	1012	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	78.3132	312	1012	95	below_threshold
Devosia ginsengisoli	strain=Gsoil 520	GCA_007859655.1	400770	400770	type	True	78.2554	381	1012	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	78.2186	338	1012	95	below_threshold
Arsenicitalea aurantiaca	strain=42-50	GCA_003994485.1	1783274	1783274	type	True	78.1081	318	1012	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	77.9841	319	1012	95	below_threshold
Devosia chinhatensis	strain=IPL18	GCA_000969445.1	429727	429727	type	True	77.9697	279	1012	95	below_threshold
Devosia rhizoryzae	strain=LEGU1	GCA_016698665.1	2774137	2774137	type	True	77.8694	274	1012	95	below_threshold
Devosia lucknowensis	strain=L15	GCA_900177655.1	1096929	1096929	type	True	77.8469	317	1012	95	below_threshold
Devosia indica	strain=IO390501	GCA_003056405.1	2079253	2079253	type	True	77.7497	263	1012	95	below_threshold
Devosia subaequoris	strain=HST3-14	GCA_024158985.1	395930	395930	type	True	77.4719	215	1012	95	below_threshold
Devosia pacifica	strain=KCTC 32437	GCA_014652635.1	1335967	1335967	type	True	76.7562	203	1012	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	76.6818	193	1012	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	76.5135	174	1012	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	76.3812	210	1012	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:47:27,341] [INFO] DFAST Taxonomy check result was written to GCA_023430705.1_ASM2343070v1_genomic.fna/tc_result.tsv
[2023-06-29 16:47:27,341] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:47:27,341] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:47:27,341] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdaff16a7-15a5-4c54-83a3-6381fde5e0e3/dqc_reference/checkm_data
[2023-06-29 16:47:27,343] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:47:27,378] [INFO] Task started: CheckM
[2023-06-29 16:47:27,378] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023430705.1_ASM2343070v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023430705.1_ASM2343070v1_genomic.fna/checkm_input GCA_023430705.1_ASM2343070v1_genomic.fna/checkm_result
[2023-06-29 16:47:56,293] [INFO] Task succeeded: CheckM
[2023-06-29 16:47:56,294] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.16%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 16:47:56,310] [INFO] ===== Completeness check finished =====
[2023-06-29 16:47:56,310] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:47:56,310] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023430705.1_ASM2343070v1_genomic.fna/markers.fasta)
[2023-06-29 16:47:56,311] [INFO] Task started: Blastn
[2023-06-29 16:47:56,311] [INFO] Running command: blastn -query GCA_023430705.1_ASM2343070v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdaff16a7-15a5-4c54-83a3-6381fde5e0e3/dqc_reference/reference_markers_gtdb.fasta -out GCA_023430705.1_ASM2343070v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:47:57,876] [INFO] Task succeeded: Blastn
[2023-06-29 16:47:57,880] [INFO] Selected 10 target genomes.
[2023-06-29 16:47:57,880] [INFO] Target genome list was writen to GCA_023430705.1_ASM2343070v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:47:57,882] [INFO] Task started: fastANI
[2023-06-29 16:47:57,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg01da18bd-0fa5-4f84-9e33-2a4c97a4e790/GCA_023430705.1_ASM2343070v1_genomic.fna.gz --refList GCA_023430705.1_ASM2343070v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023430705.1_ASM2343070v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:48:06,679] [INFO] Task succeeded: fastANI
[2023-06-29 16:48:06,688] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 16:48:06,689] [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_017307495.1	s__Devosia_A sp017307495	84.7156	712	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	98.70	98.70	0.95	0.95	2	-
GCF_001402915.1	s__Devosia_A sp001402915	82.4512	746	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899085.1	s__Devosia_A sp001899085	82.4193	740	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	99.98	99.97	0.99	0.99	3	-
GCF_001425235.1	s__Devosia_A sp001425235	82.3816	755	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	97.96	97.96	0.95	0.95	2	-
GCF_000970465.2	s__Devosia_A insulae	82.3344	702	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903842455.1	s__Devosia_A sp903842455	81.1608	582	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713105.1	s__Devosia_A sp016713105	81.0097	584	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899075.1	s__Devosia_A sp001899075	79.6423	510	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000969415.1	s__Devosia geojensis	78.9458	443	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903828145.1	s__Devosia_A sp903828145	78.1626	273	1012	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	99.95	99.93	0.97	0.97	4	-
--------------------------------------------------------------------------------
[2023-06-29 16:48:06,690] [INFO] GTDB search result was written to GCA_023430705.1_ASM2343070v1_genomic.fna/result_gtdb.tsv
[2023-06-29 16:48:06,691] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:48:06,694] [INFO] DFAST_QC result json was written to GCA_023430705.1_ASM2343070v1_genomic.fna/dqc_result.json
[2023-06-29 16:48:06,694] [INFO] DFAST_QC completed!
[2023-06-29 16:48:06,694] [INFO] Total running time: 0h1m5s