[2023-06-28 20:07:26,283] [INFO] DFAST_QC pipeline started.
[2023-06-28 20:07:26,286] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 20:07:26,286] [INFO] DQC Reference Directory: /var/lib/cwl/stg22af6f76-7abb-49a3-b587-e300da36b6fc/dqc_reference
[2023-06-28 20:07:27,641] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 20:07:27,642] [INFO] Task started: Prodigal
[2023-06-28 20:07:27,642] [INFO] Running command: gunzip -c /var/lib/cwl/stgc37d50fb-d7a4-4833-95bd-88fef2493ad4/GCA_020853435.1_ASM2085343v1_genomic.fna.gz | prodigal -d GCA_020853435.1_ASM2085343v1_genomic.fna/cds.fna -a GCA_020853435.1_ASM2085343v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 20:07:33,494] [INFO] Task succeeded: Prodigal
[2023-06-28 20:07:33,494] [INFO] Task started: HMMsearch
[2023-06-28 20:07:33,494] [INFO] Running command: hmmsearch --tblout GCA_020853435.1_ASM2085343v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22af6f76-7abb-49a3-b587-e300da36b6fc/dqc_reference/reference_markers.hmm GCA_020853435.1_ASM2085343v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 20:07:33,709] [INFO] Task succeeded: HMMsearch
[2023-06-28 20:07:33,711] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc37d50fb-d7a4-4833-95bd-88fef2493ad4/GCA_020853435.1_ASM2085343v1_genomic.fna.gz]
[2023-06-28 20:07:33,748] [INFO] Query marker FASTA was written to GCA_020853435.1_ASM2085343v1_genomic.fna/markers.fasta
[2023-06-28 20:07:33,749] [INFO] Task started: Blastn
[2023-06-28 20:07:33,749] [INFO] Running command: blastn -query GCA_020853435.1_ASM2085343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22af6f76-7abb-49a3-b587-e300da36b6fc/dqc_reference/reference_markers.fasta -out GCA_020853435.1_ASM2085343v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:07:34,396] [INFO] Task succeeded: Blastn
[2023-06-28 20:07:34,400] [INFO] Selected 19 target genomes.
[2023-06-28 20:07:34,401] [INFO] Target genome list was writen to GCA_020853435.1_ASM2085343v1_genomic.fna/target_genomes.txt
[2023-06-28 20:07:34,403] [INFO] Task started: fastANI
[2023-06-28 20:07:34,403] [INFO] Running command: fastANI --query /var/lib/cwl/stgc37d50fb-d7a4-4833-95bd-88fef2493ad4/GCA_020853435.1_ASM2085343v1_genomic.fna.gz --refList GCA_020853435.1_ASM2085343v1_genomic.fna/target_genomes.txt --output GCA_020853435.1_ASM2085343v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 20:07:49,295] [INFO] Task succeeded: fastANI
[2023-06-28 20:07:49,296] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22af6f76-7abb-49a3-b587-e300da36b6fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 20:07:49,296] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22af6f76-7abb-49a3-b587-e300da36b6fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 20:07:49,310] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 20:07:49,311] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 20:07:49,311] [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
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	76.5922	118	661	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.5604	131	661	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.3468	84	661	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	76.3389	146	661	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.3108	143	661	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.2749	100	661	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	76.2668	83	661	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	76.2182	144	661	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.1511	169	661	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	76.1085	162	661	95	below_threshold
Dongia mobilis	strain=CGMCC 1.7660	GCA_004363235.1	578943	578943	type	True	76.0978	102	661	95	below_threshold
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	76.0709	137	661	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.0293	129	661	95	below_threshold
Pararhodospirillum oryzae	strain=NBRC 107573	GCA_007992075.1	478448	478448	type	True	75.9629	68	661	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	75.6973	109	661	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	75.6919	122	661	95	below_threshold
Methylobacterium dankookense	strain=SW08-7	GCA_902141855.1	560405	560405	type	True	75.6813	125	661	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 20:07:49,313] [INFO] DFAST Taxonomy check result was written to GCA_020853435.1_ASM2085343v1_genomic.fna/tc_result.tsv
[2023-06-28 20:07:49,313] [INFO] ===== Taxonomy check completed =====
[2023-06-28 20:07:49,313] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 20:07:49,314] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22af6f76-7abb-49a3-b587-e300da36b6fc/dqc_reference/checkm_data
[2023-06-28 20:07:49,315] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 20:07:49,348] [INFO] Task started: CheckM
[2023-06-28 20:07:49,348] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020853435.1_ASM2085343v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020853435.1_ASM2085343v1_genomic.fna/checkm_input GCA_020853435.1_ASM2085343v1_genomic.fna/checkm_result
[2023-06-28 20:08:13,148] [INFO] Task succeeded: CheckM
[2023-06-28 20:08:13,150] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.84%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 20:08:13,171] [INFO] ===== Completeness check finished =====
[2023-06-28 20:08:13,172] [INFO] ===== Start GTDB Search =====
[2023-06-28 20:08:13,172] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020853435.1_ASM2085343v1_genomic.fna/markers.fasta)
[2023-06-28 20:08:13,172] [INFO] Task started: Blastn
[2023-06-28 20:08:13,173] [INFO] Running command: blastn -query GCA_020853435.1_ASM2085343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22af6f76-7abb-49a3-b587-e300da36b6fc/dqc_reference/reference_markers_gtdb.fasta -out GCA_020853435.1_ASM2085343v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:08:14,094] [INFO] Task succeeded: Blastn
[2023-06-28 20:08:14,098] [INFO] Selected 14 target genomes.
[2023-06-28 20:08:14,099] [INFO] Target genome list was writen to GCA_020853435.1_ASM2085343v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 20:08:14,122] [INFO] Task started: fastANI
[2023-06-28 20:08:14,122] [INFO] Running command: fastANI --query /var/lib/cwl/stgc37d50fb-d7a4-4833-95bd-88fef2493ad4/GCA_020853435.1_ASM2085343v1_genomic.fna.gz --refList GCA_020853435.1_ASM2085343v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020853435.1_ASM2085343v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 20:08:22,454] [INFO] Task succeeded: fastANI
[2023-06-28 20:08:22,467] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 20:08:22,468] [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_001830475.1	s__2-12-FULL-67-15 sp001830475	88.0624	304	661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-12-FULL-67-15;g__2-12-FULL-67-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009693905.1	s__2-12-FULL-67-15 sp009693905	85.4061	308	661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-12-FULL-67-15;g__2-12-FULL-67-15	95.0	99.79	99.79	0.72	0.72	2	-
GCA_016872535.1	s__2-12-FULL-67-15 sp016872535	83.2063	451	661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-12-FULL-67-15;g__2-12-FULL-67-15	95.0	95.80	95.80	0.86	0.86	2	-
GCA_016187325.1	s__JACPJY01 sp016187325	77.2215	150	661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__JACPJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016202695.1	s__JACQOE01 sp016202695	76.6251	162	661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__JACQOE01;f__JACQOE01;g__JACQOE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011022235.1	s__Magnetospirillum aberrantis	76.2469	84	661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827815.1	s__Azospirillum brasilense_C	76.0902	155	661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.36	95.98	0.93	0.90	3	-
GCA_013003675.1	s__JABDIP01 sp013003675	75.9477	96	661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__JABDIP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197805.1	s__Rhodospirillum_A centenum	75.8998	103	661	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Rhodospirillum_A	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-28 20:08:22,469] [INFO] GTDB search result was written to GCA_020853435.1_ASM2085343v1_genomic.fna/result_gtdb.tsv
[2023-06-28 20:08:22,470] [INFO] ===== GTDB Search completed =====
[2023-06-28 20:08:22,473] [INFO] DFAST_QC result json was written to GCA_020853435.1_ASM2085343v1_genomic.fna/dqc_result.json
[2023-06-28 20:08:22,474] [INFO] DFAST_QC completed!
[2023-06-28 20:08:22,474] [INFO] Total running time: 0h0m56s