[2023-06-17 00:46:19,304] [INFO] DFAST_QC pipeline started.
[2023-06-17 00:46:19,307] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 00:46:19,307] [INFO] DQC Reference Directory: /var/lib/cwl/stg80ade448-f421-4e5f-8343-47d9b054cfee/dqc_reference
[2023-06-17 00:46:20,594] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 00:46:20,595] [INFO] Task started: Prodigal
[2023-06-17 00:46:20,595] [INFO] Running command: gunzip -c /var/lib/cwl/stgf74c26f5-ba85-4833-959f-d4d48d436668/GCA_013911885.1_ASM1391188v1_genomic.fna.gz | prodigal -d GCA_013911885.1_ASM1391188v1_genomic.fna/cds.fna -a GCA_013911885.1_ASM1391188v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 00:46:28,785] [INFO] Task succeeded: Prodigal
[2023-06-17 00:46:28,785] [INFO] Task started: HMMsearch
[2023-06-17 00:46:28,786] [INFO] Running command: hmmsearch --tblout GCA_013911885.1_ASM1391188v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80ade448-f421-4e5f-8343-47d9b054cfee/dqc_reference/reference_markers.hmm GCA_013911885.1_ASM1391188v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 00:46:28,983] [INFO] Task succeeded: HMMsearch
[2023-06-17 00:46:28,984] [INFO] Found 6/6 markers.
[2023-06-17 00:46:29,009] [INFO] Query marker FASTA was written to GCA_013911885.1_ASM1391188v1_genomic.fna/markers.fasta
[2023-06-17 00:46:29,009] [INFO] Task started: Blastn
[2023-06-17 00:46:29,009] [INFO] Running command: blastn -query GCA_013911885.1_ASM1391188v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80ade448-f421-4e5f-8343-47d9b054cfee/dqc_reference/reference_markers.fasta -out GCA_013911885.1_ASM1391188v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 00:46:29,749] [INFO] Task succeeded: Blastn
[2023-06-17 00:46:29,753] [INFO] Selected 34 target genomes.
[2023-06-17 00:46:29,754] [INFO] Target genome list was writen to GCA_013911885.1_ASM1391188v1_genomic.fna/target_genomes.txt
[2023-06-17 00:46:29,761] [INFO] Task started: fastANI
[2023-06-17 00:46:29,762] [INFO] Running command: fastANI --query /var/lib/cwl/stgf74c26f5-ba85-4833-959f-d4d48d436668/GCA_013911885.1_ASM1391188v1_genomic.fna.gz --refList GCA_013911885.1_ASM1391188v1_genomic.fna/target_genomes.txt --output GCA_013911885.1_ASM1391188v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 00:46:53,440] [INFO] Task succeeded: fastANI
[2023-06-17 00:46:53,441] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80ade448-f421-4e5f-8343-47d9b054cfee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 00:46:53,441] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80ade448-f421-4e5f-8343-47d9b054cfee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 00:46:53,463] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 00:46:53,464] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 00:46:53,464] [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
Methylobrevis pamukkalensis	strain=PK2	GCA_001720135.1	1439726	1439726	type	True	77.0857	83	908	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001517385.1	466044	466044	type	True	76.721	78	908	95	below_threshold
Pannonibacter indicus	strain=DSM 23407	GCA_001418225.1	466044	466044	type	True	76.721	78	908	95	below_threshold
Aurantimonas aggregata	strain=KCTC 52919	GCA_010500835.1	2047720	2047720	type	True	76.3728	95	908	95	below_threshold
Ensifer alkalisoli	strain=YIC4027	GCA_001723275.1	1752398	1752398	type	True	76.3264	85	908	95	below_threshold
Tepidamorphus gemmatus	strain=DSM 19345	GCA_004346195.1	747076	747076	type	True	76.297	67	908	95	below_threshold
Ensifer sojae	strain=CCBAU 05684	GCA_002288525.1	716925	716925	type	True	76.2421	85	908	95	below_threshold
Ensifer sojae	strain=CCBAU 05684	GCA_000261485.1	716925	716925	type	True	76.2343	87	908	95	below_threshold
Ensifer alkalisoli	strain=YIC4027	GCA_008932245.1	1752398	1752398	type	True	76.2123	91	908	95	below_threshold
Sinorhizobium kostiense	strain=DSM 13372	GCA_017874595.1	76747	76747	type	True	76.2077	87	908	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	76.2008	79	908	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	76.1652	96	908	95	below_threshold
Roseibium marinum	strain=DSM 17023	GCA_002906165.1	281252	281252	type	True	76.1507	82	908	95	below_threshold
Kaistia granuli	strain=Ko04	GCA_000380505.1	363259	363259	type	True	76.1463	95	908	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	76.0747	51	908	95	below_threshold
Bauldia litoralis	strain=ATCC 35022	GCA_900104485.1	665467	665467	type	True	76.0489	72	908	95	below_threshold
Stappia taiwanensis	strain=CCM 7757	GCA_014635285.1	992267	992267	type	True	76.0371	94	908	95	below_threshold
Rhizobium rosettiformans	strain=W3	GCA_004912135.1	1368430	1368430	type	True	76.0231	82	908	95	below_threshold
Afipia felis	strain=ATCC 53690	GCA_000314735.2	1035	1035	type	True	76.0043	64	908	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	75.9937	91	908	95	below_threshold
Afipia felis	strain=NCTC12499	GCA_900445155.1	1035	1035	type	True	75.9909	63	908	95	below_threshold
Rhizobium rosettiformans	strain=DSM 26376	GCA_014202175.1	1368430	1368430	type	True	75.9836	83	908	95	below_threshold
Pannonibacter phragmitetus	strain=DSM 14782	GCA_000382365.1	121719	121719	suspected-type	True	75.973	83	908	95	below_threshold
Rhizobium wuzhouense	strain=W44	GCA_003205195.1	1986026	1986026	type	True	75.9391	90	908	95	below_threshold
Pannonibacter phragmitetus	strain=NCTC13350	GCA_900454465.1	121719	121719	suspected-type	True	75.9365	85	908	95	below_threshold
Stappia stellulata	strain=DSM 5886	GCA_000423705.1	71235	71235	type	True	75.8844	91	908	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	75.7998	59	908	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	75.77	64	908	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	75.7011	68	908	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	75.6342	72	908	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	75.3219	62	908	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 00:46:53,466] [INFO] DFAST Taxonomy check result was written to GCA_013911885.1_ASM1391188v1_genomic.fna/tc_result.tsv
[2023-06-17 00:46:53,466] [INFO] ===== Taxonomy check completed =====
[2023-06-17 00:46:53,467] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 00:46:53,467] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80ade448-f421-4e5f-8343-47d9b054cfee/dqc_reference/checkm_data
[2023-06-17 00:46:53,468] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 00:46:53,496] [INFO] Task started: CheckM
[2023-06-17 00:46:53,496] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013911885.1_ASM1391188v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013911885.1_ASM1391188v1_genomic.fna/checkm_input GCA_013911885.1_ASM1391188v1_genomic.fna/checkm_result
[2023-06-17 00:47:21,824] [INFO] Task succeeded: CheckM
[2023-06-17 00:47:21,825] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 00:47:21,924] [INFO] ===== Completeness check finished =====
[2023-06-17 00:47:21,925] [INFO] ===== Start GTDB Search =====
[2023-06-17 00:47:21,925] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013911885.1_ASM1391188v1_genomic.fna/markers.fasta)
[2023-06-17 00:47:21,925] [INFO] Task started: Blastn
[2023-06-17 00:47:21,925] [INFO] Running command: blastn -query GCA_013911885.1_ASM1391188v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80ade448-f421-4e5f-8343-47d9b054cfee/dqc_reference/reference_markers_gtdb.fasta -out GCA_013911885.1_ASM1391188v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 00:47:23,225] [INFO] Task succeeded: Blastn
[2023-06-17 00:47:23,229] [INFO] Selected 26 target genomes.
[2023-06-17 00:47:23,229] [INFO] Target genome list was writen to GCA_013911885.1_ASM1391188v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 00:47:23,248] [INFO] Task started: fastANI
[2023-06-17 00:47:23,248] [INFO] Running command: fastANI --query /var/lib/cwl/stgf74c26f5-ba85-4833-959f-d4d48d436668/GCA_013911885.1_ASM1391188v1_genomic.fna.gz --refList GCA_013911885.1_ASM1391188v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013911885.1_ASM1391188v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 00:47:43,262] [INFO] Task succeeded: fastANI
[2023-06-17 00:47:43,280] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 00:47:43,280] [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_013911885.1	s__JACESI01 sp013911885	100.0	908	908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__JACESI01;g__JACESI01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001418225.1	s__Pannonibacter indicus	76.721	78	908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	96.01	95.55	0.94	0.89	12	-
GCF_001298265.1	s__Bosea vaviloviae_B	76.3993	80	908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643215.1	s__Roseibium sp017643215	76.2696	66	908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002288525.1	s__Sinorhizobium sojae	76.2421	85	908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003966715.1	s__Blastochloris tepida	76.2008	79	908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002906165.1	s__Roseibium marinum	76.1507	82	908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829155.1	s__Rhizobium sp900467885	76.1506	84	908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.99	98.86	0.92	0.89	10	-
GCF_001651875.1	s__Sinorhizobium saheli	76.1505	94	908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	99.97	99.97	0.96	0.96	2	-
GCF_012641405.1	s__Rhizobium sp012641405	76.1061	83	908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.52	99.52	0.93	0.93	2	-
GCA_016716745.1	s__GCA-013693735 sp016716745	76.0947	91	908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__GCA-013693735	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001262505.1	s__Shinella sp001262505	76.0665	106	908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	98.95	98.39	0.91	0.87	4	-
GCF_014635285.1	s__Stappia taiwanensis	76.0371	94	908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004912135.1	s__Allorhizobium rosettiformans	76.0231	82	908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.40	95.42	0.87	0.84	7	-
GCA_017307955.1	s__Kaistia sp017307955	76.022	99	908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005205.3	s__Agrobacterium rhizogenes_A	76.0112	100	908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.60	97.88	0.94	0.88	11	-
GCF_000382365.1	s__Pannonibacter phragmitetus	75.973	83	908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018760785.1	s__Rhizobium_A sp018760785	75.9587	104	908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003205195.1	s__Allorhizobium wuzhouense	75.9391	90	908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	97.59	97.59	0.92	0.92	2	-
GCF_016629525.1	s__Kaistia sp016629525	75.9339	104	908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423705.1	s__Stappia stellulata	75.8844	91	908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001624695.1	s__Roseibium sp001624695	75.8416	81	908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014692675.1	s__Roseibium aggregatum_C	75.8004	91	908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Roseibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003062295.1	s__Bradyrhizobium algeriense	75.6096	84	908	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 00:47:43,283] [INFO] GTDB search result was written to GCA_013911885.1_ASM1391188v1_genomic.fna/result_gtdb.tsv
[2023-06-17 00:47:43,283] [INFO] ===== GTDB Search completed =====
[2023-06-17 00:47:43,289] [INFO] DFAST_QC result json was written to GCA_013911885.1_ASM1391188v1_genomic.fna/dqc_result.json
[2023-06-17 00:47:43,289] [INFO] DFAST_QC completed!
[2023-06-17 00:47:43,289] [INFO] Total running time: 0h1m24s