[2023-06-19 04:59:37,323] [INFO] DFAST_QC pipeline started.
[2023-06-19 04:59:37,325] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 04:59:37,325] [INFO] DQC Reference Directory: /var/lib/cwl/stg0755e8c1-4cc4-488e-b10d-5c7420a510cd/dqc_reference
[2023-06-19 04:59:38,540] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 04:59:38,541] [INFO] Task started: Prodigal
[2023-06-19 04:59:38,541] [INFO] Running command: gunzip -c /var/lib/cwl/stgc1505ba8-b75f-4169-9bed-a8a5853cc0d0/GCA_013141015.1_ASM1314101v1_genomic.fna.gz | prodigal -d GCA_013141015.1_ASM1314101v1_genomic.fna/cds.fna -a GCA_013141015.1_ASM1314101v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 04:59:50,705] [INFO] Task succeeded: Prodigal
[2023-06-19 04:59:50,706] [INFO] Task started: HMMsearch
[2023-06-19 04:59:50,706] [INFO] Running command: hmmsearch --tblout GCA_013141015.1_ASM1314101v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0755e8c1-4cc4-488e-b10d-5c7420a510cd/dqc_reference/reference_markers.hmm GCA_013141015.1_ASM1314101v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 04:59:50,914] [INFO] Task succeeded: HMMsearch
[2023-06-19 04:59:50,917] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc1505ba8-b75f-4169-9bed-a8a5853cc0d0/GCA_013141015.1_ASM1314101v1_genomic.fna.gz]
[2023-06-19 04:59:50,952] [INFO] Query marker FASTA was written to GCA_013141015.1_ASM1314101v1_genomic.fna/markers.fasta
[2023-06-19 04:59:50,952] [INFO] Task started: Blastn
[2023-06-19 04:59:50,952] [INFO] Running command: blastn -query GCA_013141015.1_ASM1314101v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0755e8c1-4cc4-488e-b10d-5c7420a510cd/dqc_reference/reference_markers.fasta -out GCA_013141015.1_ASM1314101v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:59:51,702] [INFO] Task succeeded: Blastn
[2023-06-19 04:59:51,706] [INFO] Selected 25 target genomes.
[2023-06-19 04:59:51,707] [INFO] Target genome list was writen to GCA_013141015.1_ASM1314101v1_genomic.fna/target_genomes.txt
[2023-06-19 04:59:51,710] [INFO] Task started: fastANI
[2023-06-19 04:59:51,710] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1505ba8-b75f-4169-9bed-a8a5853cc0d0/GCA_013141015.1_ASM1314101v1_genomic.fna.gz --refList GCA_013141015.1_ASM1314101v1_genomic.fna/target_genomes.txt --output GCA_013141015.1_ASM1314101v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 05:00:10,593] [INFO] Task succeeded: fastANI
[2023-06-19 05:00:10,593] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0755e8c1-4cc4-488e-b10d-5c7420a510cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 05:00:10,594] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0755e8c1-4cc4-488e-b10d-5c7420a510cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 05:00:10,613] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 05:00:10,613] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 05:00:10,613] [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
Hyphomicrobium denitrificans	strain=ATCC 51888	GCA_000143145.1	53399	53399	type	True	78.1878	289	1279	95	below_threshold
Hyphomicrobium facile	strain=DSM 1565	GCA_900116175.1	51670	51670	type	True	77.7986	253	1279	95	below_threshold
Hyphomicrobium zavarzinii	strain=ZV-622	GCA_000383415.1	48292	48292	type	True	77.2631	210	1279	95	below_threshold
Hyphomicrobium album	strain=XQ2	GCA_009708035.1	2665159	2665159	type	True	77.2448	202	1279	95	below_threshold
Hyphomicrobium sulfonivorans	strain=S1	GCA_016125985.1	121290	121290	type	True	77.2401	179	1279	95	below_threshold
Hyphomicrobium sulfonivorans	strain=S1	GCA_013306565.1	121290	121290	type	True	77.1288	183	1279	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	76.7201	98	1279	95	below_threshold
Brucella suis	strain=1330	GCA_000007505.1	29461	29461	suspected-type	True	76.6757	57	1279	95	below_threshold
Afipia clevelandensis	strain=ATCC 49720	GCA_000336555.1	1034	1034	type	True	76.5482	100	1279	95	below_threshold
Brucella melitensis	strain=16M	GCA_000160295.1	29459	29459	suspected-type	True	76.5234	62	1279	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	76.5042	104	1279	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	76.4789	113	1279	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	76.4655	92	1279	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	76.3928	81	1279	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	76.386	101	1279	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	76.3502	108	1279	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	76.3085	119	1279	95	below_threshold
Rhizobium rhizolycopersici	strain=DBTS2	GCA_013378445.1	2746702	2746702	type	True	76.2201	99	1279	95	below_threshold
Rhizobium subbaraonis	strain=JC85	GCA_900220975.1	908946	908946	type	True	76.1934	93	1279	95	below_threshold
Methylocapsa aurea	strain=KYG	GCA_000746085.1	663610	663610	type	True	76.1608	54	1279	95	below_threshold
Lichenibacterium ramalinae	strain=RmlP001	GCA_004137085.1	2316527	2316527	type	True	76.1519	84	1279	95	below_threshold
Methylorubrum salsuginis	strain=CGMCC 1.6474	GCA_900114375.1	414703	414703	type	True	76.0571	96	1279	95	below_threshold
Camelimonas fluminis	strain=KCTC 42282	GCA_014656355.1	1576911	1576911	type	True	75.9195	83	1279	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.6943	97	1279	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 05:00:10,616] [INFO] DFAST Taxonomy check result was written to GCA_013141015.1_ASM1314101v1_genomic.fna/tc_result.tsv
[2023-06-19 05:00:10,616] [INFO] ===== Taxonomy check completed =====
[2023-06-19 05:00:10,616] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 05:00:10,617] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0755e8c1-4cc4-488e-b10d-5c7420a510cd/dqc_reference/checkm_data
[2023-06-19 05:00:10,618] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 05:00:10,658] [INFO] Task started: CheckM
[2023-06-19 05:00:10,658] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013141015.1_ASM1314101v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013141015.1_ASM1314101v1_genomic.fna/checkm_input GCA_013141015.1_ASM1314101v1_genomic.fna/checkm_result
[2023-06-19 05:00:48,990] [INFO] Task succeeded: CheckM
[2023-06-19 05:00:48,991] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 05:00:49,009] [INFO] ===== Completeness check finished =====
[2023-06-19 05:00:49,010] [INFO] ===== Start GTDB Search =====
[2023-06-19 05:00:49,010] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013141015.1_ASM1314101v1_genomic.fna/markers.fasta)
[2023-06-19 05:00:49,010] [INFO] Task started: Blastn
[2023-06-19 05:00:49,010] [INFO] Running command: blastn -query GCA_013141015.1_ASM1314101v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0755e8c1-4cc4-488e-b10d-5c7420a510cd/dqc_reference/reference_markers_gtdb.fasta -out GCA_013141015.1_ASM1314101v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:00:50,268] [INFO] Task succeeded: Blastn
[2023-06-19 05:00:50,272] [INFO] Selected 13 target genomes.
[2023-06-19 05:00:50,272] [INFO] Target genome list was writen to GCA_013141015.1_ASM1314101v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 05:00:50,279] [INFO] Task started: fastANI
[2023-06-19 05:00:50,280] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1505ba8-b75f-4169-9bed-a8a5853cc0d0/GCA_013141015.1_ASM1314101v1_genomic.fna.gz --refList GCA_013141015.1_ASM1314101v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013141015.1_ASM1314101v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 05:00:59,594] [INFO] Task succeeded: fastANI
[2023-06-19 05:00:59,605] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 05:00:59,606] [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_013141015.1	s__Hyphomicrobium sp013141015	100.0	1275	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016716675.1	s__Hyphomicrobium sp016716675	79.8249	528	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017512425.1	s__Hyphomicrobium sp017512425	79.1487	497	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000143145.1	s__Hyphomicrobium denitrificans	78.1866	289	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	95.20	95.20	0.90	0.90	2	-
GCF_900116175.1	s__Hyphomicrobium facile	77.7527	252	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002928515.1	s__Hyphomicrobium sp002928515	77.5291	240	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	99.95	99.95	0.95	0.95	2	-
GCA_902825785.1	s__Hyphomicrobium sp902825785	77.52	229	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242255.1	s__Hyphomicrobium sp018242255	77.3493	249	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793445.1	s__Hyphomicrobium sp016793445	77.3313	262	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242215.1	s__Hyphomicrobium sp018242215	77.2378	241	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003367195.1	s__Pseudolabrys sp003367195	76.7774	114	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242205.1	s__Pseudolabrys sp018242205	76.6798	116	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Pseudolabrys	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019242655.1	s__JAFASC01 sp019242655	75.6611	52	1279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__JAFASC01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 05:00:59,608] [INFO] GTDB search result was written to GCA_013141015.1_ASM1314101v1_genomic.fna/result_gtdb.tsv
[2023-06-19 05:00:59,609] [INFO] ===== GTDB Search completed =====
[2023-06-19 05:00:59,613] [INFO] DFAST_QC result json was written to GCA_013141015.1_ASM1314101v1_genomic.fna/dqc_result.json
[2023-06-19 05:00:59,614] [INFO] DFAST_QC completed!
[2023-06-19 05:00:59,614] [INFO] Total running time: 0h1m22s