[2023-06-27 09:21:32,989] [INFO] DFAST_QC pipeline started.
[2023-06-27 09:21:32,991] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 09:21:32,991] [INFO] DQC Reference Directory: /var/lib/cwl/stg65742c39-61c2-4ce2-87a6-49b19e8a2a73/dqc_reference
[2023-06-27 09:21:34,229] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 09:21:34,230] [INFO] Task started: Prodigal
[2023-06-27 09:21:34,230] [INFO] Running command: gunzip -c /var/lib/cwl/stg894d9366-8bef-47b4-8577-972b987e3330/GCA_026400515.1_ASM2640051v1_genomic.fna.gz | prodigal -d GCA_026400515.1_ASM2640051v1_genomic.fna/cds.fna -a GCA_026400515.1_ASM2640051v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 09:21:40,887] [INFO] Task succeeded: Prodigal
[2023-06-27 09:21:40,888] [INFO] Task started: HMMsearch
[2023-06-27 09:21:40,888] [INFO] Running command: hmmsearch --tblout GCA_026400515.1_ASM2640051v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65742c39-61c2-4ce2-87a6-49b19e8a2a73/dqc_reference/reference_markers.hmm GCA_026400515.1_ASM2640051v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 09:21:41,108] [INFO] Task succeeded: HMMsearch
[2023-06-27 09:21:41,110] [INFO] Found 6/6 markers.
[2023-06-27 09:21:41,141] [INFO] Query marker FASTA was written to GCA_026400515.1_ASM2640051v1_genomic.fna/markers.fasta
[2023-06-27 09:21:41,142] [INFO] Task started: Blastn
[2023-06-27 09:21:41,142] [INFO] Running command: blastn -query GCA_026400515.1_ASM2640051v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65742c39-61c2-4ce2-87a6-49b19e8a2a73/dqc_reference/reference_markers.fasta -out GCA_026400515.1_ASM2640051v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 09:21:41,832] [INFO] Task succeeded: Blastn
[2023-06-27 09:21:41,835] [INFO] Selected 37 target genomes.
[2023-06-27 09:21:41,836] [INFO] Target genome list was writen to GCA_026400515.1_ASM2640051v1_genomic.fna/target_genomes.txt
[2023-06-27 09:21:41,848] [INFO] Task started: fastANI
[2023-06-27 09:21:41,848] [INFO] Running command: fastANI --query /var/lib/cwl/stg894d9366-8bef-47b4-8577-972b987e3330/GCA_026400515.1_ASM2640051v1_genomic.fna.gz --refList GCA_026400515.1_ASM2640051v1_genomic.fna/target_genomes.txt --output GCA_026400515.1_ASM2640051v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 09:22:10,412] [INFO] Task succeeded: fastANI
[2023-06-27 09:22:10,413] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg65742c39-61c2-4ce2-87a6-49b19e8a2a73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 09:22:10,414] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg65742c39-61c2-4ce2-87a6-49b19e8a2a73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 09:22:10,436] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 09:22:10,436] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 09:22:10,437] [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
Bosea psychrotolerans	strain=1131	GCA_002917105.1	1871628	1871628	type	True	76.59	90	513	95	below_threshold
Rhodoblastus acidophilus	strain=DSM 137	GCA_002937135.1	1074	1074	suspected-type	True	76.4821	73	513	95	below_threshold
Bosea robiniae	strain=DSM 26672	GCA_900102525.1	1036780	1036780	type	True	76.4634	81	513	95	below_threshold
Rhodoblastus acidophilus	strain=DSM 137	GCA_900187365.1	1074	1074	suspected-type	True	76.4562	74	513	95	below_threshold
Rhodoblastus acidophilus	strain=DSM 137	GCA_003258765.1	1074	1074	suspected-type	True	76.4548	74	513	95	below_threshold
Phreatobacter stygius	strain=KCTC 52518	GCA_005144885.1	1940610	1940610	type	True	76.4252	103	513	95	below_threshold
Bosea thiooxidans	strain=DSM 9653	GCA_900168195.1	53254	53254	type	True	76.4169	71	513	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	76.3772	50	513	95	below_threshold
Bradyrhizobium ottawaense	strain=OO99	GCA_002278135.2	931866	931866	type	True	76.3531	65	513	95	below_threshold
Afipia massiliensis	strain=DSM 17498	GCA_014203115.1	211460	211460	type	True	76.3353	56	513	95	below_threshold
Bosea lathyri	strain=DSM 26656	GCA_900108245.1	1036778	1036778	type	True	76.2728	90	513	95	below_threshold
Saliniramus fredricksonii	strain=HL-109	GCA_900094735.1	1653334	1653334	type	True	76.2625	74	513	95	below_threshold
Camelimonas fluminis	strain=KCTC 42282	GCA_014656355.1	1576911	1576911	type	True	76.1943	54	513	95	below_threshold
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001418005.1	363953	363953	type	True	76.1342	52	513	95	below_threshold
Chelatococcus sambhunathii	strain=DSM 18167	GCA_001517345.1	363953	363953	type	True	76.1342	52	513	95	below_threshold
Bosea vaviloviae	strain=Vaf18	GCA_001741865.1	1526658	1526658	type	True	76.1248	91	513	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	76.0867	77	513	95	below_threshold
Bradyrhizobium paxllaeri	strain=LMTR 21	GCA_001693515.2	190148	190148	type	True	76.0798	71	513	95	below_threshold
Alsobacter soli	strain=SH9	GCA_003004785.1	2109933	2109933	type	True	76.0754	78	513	95	below_threshold
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	76.0753	56	513	95	below_threshold
Mesorhizobium jarvisii	strain=ATCC 33669	GCA_013170785.1	1777867	1777867	type	True	76.0752	56	513	95	below_threshold
Microvirga aerilata	strain=5420S-16	GCA_016743775.1	670292	670292	type	True	76.0216	62	513	95	below_threshold
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	75.9384	93	513	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001517385.1	466044	466044	type	True	75.7827	58	513	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001418225.1	466044	466044	type	True	75.7827	58	513	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	75.7623	54	513	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 09:22:10,446] [INFO] DFAST Taxonomy check result was written to GCA_026400515.1_ASM2640051v1_genomic.fna/tc_result.tsv
[2023-06-27 09:22:10,447] [INFO] ===== Taxonomy check completed =====
[2023-06-27 09:22:10,447] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 09:22:10,447] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65742c39-61c2-4ce2-87a6-49b19e8a2a73/dqc_reference/checkm_data
[2023-06-27 09:22:10,449] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 09:22:10,482] [INFO] Task started: CheckM
[2023-06-27 09:22:10,482] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026400515.1_ASM2640051v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026400515.1_ASM2640051v1_genomic.fna/checkm_input GCA_026400515.1_ASM2640051v1_genomic.fna/checkm_result
[2023-06-27 09:22:36,716] [INFO] Task succeeded: CheckM
[2023-06-27 09:22:36,718] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.72%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 09:22:36,749] [INFO] ===== Completeness check finished =====
[2023-06-27 09:22:36,750] [INFO] ===== Start GTDB Search =====
[2023-06-27 09:22:36,750] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026400515.1_ASM2640051v1_genomic.fna/markers.fasta)
[2023-06-27 09:22:36,751] [INFO] Task started: Blastn
[2023-06-27 09:22:36,751] [INFO] Running command: blastn -query GCA_026400515.1_ASM2640051v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65742c39-61c2-4ce2-87a6-49b19e8a2a73/dqc_reference/reference_markers_gtdb.fasta -out GCA_026400515.1_ASM2640051v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 09:22:37,928] [INFO] Task succeeded: Blastn
[2023-06-27 09:22:37,934] [INFO] Selected 36 target genomes.
[2023-06-27 09:22:37,935] [INFO] Target genome list was writen to GCA_026400515.1_ASM2640051v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 09:22:37,973] [INFO] Task started: fastANI
[2023-06-27 09:22:37,974] [INFO] Running command: fastANI --query /var/lib/cwl/stg894d9366-8bef-47b4-8577-972b987e3330/GCA_026400515.1_ASM2640051v1_genomic.fna.gz --refList GCA_026400515.1_ASM2640051v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026400515.1_ASM2640051v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 09:23:04,625] [INFO] Task succeeded: fastANI
[2023-06-27 09:23:04,656] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 09:23:04,656] [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_903930675.1	s__CAIYZJ01 sp903930675	98.3501	464	513	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__CAIYZJ01	95.0	97.85	97.85	0.78	0.78	2	conclusive
GCA_903824185.1	s__CAIYZJ01 sp903824185	77.7061	189	513	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__CAIYZJ01	95.0	99.80	99.69	0.95	0.94	4	-
GCA_903900975.1	s__CAIUPE01 sp903900975	77.1236	63	513	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__CAIUPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019083985.1	s__TNE-4 sp019083985	76.7832	99	513	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__TNE-4	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018882635.1	s__TNE-4 sp018882635	76.5773	72	513	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__TNE-4	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104955.1	s__28-YEA-48 sp900104955	76.4689	70	513	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__28-YEA-48	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102525.1	s__Bosea robiniae	76.4634	81	513	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	97.62	97.45	0.92	0.88	4	-
GCF_900187365.1	s__Rhodoblastus acidophilus	76.4562	74	513	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Rhodoblastus	95.0	99.99	99.99	0.99	0.99	3	-
GCF_900168195.1	s__Bosea thiooxidans	76.4169	71	513	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.77	99.77	0.94	0.94	2	-
GCF_011777495.1	s__Microvirga sp011777495	76.3703	54	513	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002278135.2	s__Bradyrhizobium ottawaense	76.3531	65	513	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	98.77	95.31	0.93	0.88	13	-
GCA_900473415.1	s__Bosea sp900473415	76.3118	76	513	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900094735.1	s__Salinarimonas sp900094735	76.2625	74	513	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Salinarimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_004144595.1	s__Bosea sp004144595	76.1758	69	513	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008253865.1	s__Bosea sp008253865	76.1525	92	513	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898115.1	s__Bosea sp001898115	76.1472	67	513	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.21	98.43	0.96	0.93	3	-
GCF_900156025.1	s__Bosea sp900156025	76.139	83	513	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.08	99.08	0.82	0.82	2	-
GCF_001741865.1	s__Bosea vaviloviae	76.1248	91	513	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003004785.1	s__Alsobacter soli	76.0754	78	513	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Alsobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900470775.1	s__Bosea sp900470775	76.0532	91	513	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003046175.1	s__Bosea sp003046175	76.0417	88	513	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001295925.1	s__Bosea sp001295925	76.0407	76	513	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001298265.1	s__Bosea vaviloviae_B	76.0341	83	513	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308015.1	s__Bosea sp017308015	75.9536	74	513	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000517005.1	s__Microvirga lupini	75.9506	66	513	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018398335.1	s__Chelatococcus sp018398335	75.8087	55	513	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003151255.1	s__Microvirga sp003151255	75.5274	50	513	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 09:23:04,659] [INFO] GTDB search result was written to GCA_026400515.1_ASM2640051v1_genomic.fna/result_gtdb.tsv
[2023-06-27 09:23:04,671] [INFO] ===== GTDB Search completed =====
[2023-06-27 09:23:04,681] [INFO] DFAST_QC result json was written to GCA_026400515.1_ASM2640051v1_genomic.fna/dqc_result.json
[2023-06-27 09:23:04,682] [INFO] DFAST_QC completed!
[2023-06-27 09:23:04,682] [INFO] Total running time: 0h1m32s