[2024-01-24 15:26:47,604] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:47,609] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:47,609] [INFO] DQC Reference Directory: /var/lib/cwl/stge6d2ab96-fb9a-4a50-a189-62c1026f8de0/dqc_reference
[2024-01-24 15:26:48,780] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:48,780] [INFO] Task started: Prodigal
[2024-01-24 15:26:48,781] [INFO] Running command: gunzip -c /var/lib/cwl/stgc434dbf2-a083-4196-a212-1eaac47e9915/GCF_003258595.1_ASM325859v1_genomic.fna.gz | prodigal -d GCF_003258595.1_ASM325859v1_genomic.fna/cds.fna -a GCF_003258595.1_ASM325859v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:11,261] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:11,262] [INFO] Task started: HMMsearch
[2024-01-24 15:27:11,262] [INFO] Running command: hmmsearch --tblout GCF_003258595.1_ASM325859v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6d2ab96-fb9a-4a50-a189-62c1026f8de0/dqc_reference/reference_markers.hmm GCF_003258595.1_ASM325859v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:11,602] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:11,603] [INFO] Found 6/6 markers.
[2024-01-24 15:27:11,660] [INFO] Query marker FASTA was written to GCF_003258595.1_ASM325859v1_genomic.fna/markers.fasta
[2024-01-24 15:27:11,660] [INFO] Task started: Blastn
[2024-01-24 15:27:11,660] [INFO] Running command: blastn -query GCF_003258595.1_ASM325859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6d2ab96-fb9a-4a50-a189-62c1026f8de0/dqc_reference/reference_markers.fasta -out GCF_003258595.1_ASM325859v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:12,618] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:12,622] [INFO] Selected 17 target genomes.
[2024-01-24 15:27:12,623] [INFO] Target genome list was writen to GCF_003258595.1_ASM325859v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:12,631] [INFO] Task started: fastANI
[2024-01-24 15:27:12,631] [INFO] Running command: fastANI --query /var/lib/cwl/stgc434dbf2-a083-4196-a212-1eaac47e9915/GCF_003258595.1_ASM325859v1_genomic.fna.gz --refList GCF_003258595.1_ASM325859v1_genomic.fna/target_genomes.txt --output GCF_003258595.1_ASM325859v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:35,173] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:35,174] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6d2ab96-fb9a-4a50-a189-62c1026f8de0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:35,174] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6d2ab96-fb9a-4a50-a189-62c1026f8de0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:35,188] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:35,188] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:35,188] [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
Acuticoccus sediminis	strain=PTG4-2	GCA_003258595.1	2184697	2184697	type	True	100.0	2565	2567	95	conclusive
Acuticoccus yangtzensis	strain=JL1095	GCA_001927245.1	1443441	1443441	type	True	82.464	1211	2567	95	below_threshold
Acuticoccus yangtzensis	strain=JL1095	GCA_003073145.1	1443441	1443441	type	True	82.4477	1225	2567	95	below_threshold
Acuticoccus kandeliae	strain=J103	GCA_003073115.1	2073160	2073160	type	True	79.5931	1031	2567	95	below_threshold
Acuticoccus mangrovi	strain=B2012	GCA_016411865.1	2796142	2796142	type	True	79.4851	923	2567	95	below_threshold
Pannonibacter phragmitetus	strain=NCTC13350	GCA_900454465.1	121719	121719	suspected-type	True	76.73	258	2567	95	below_threshold
Methylobrevis pamukkalensis	strain=PK2	GCA_001720135.1	1439726	1439726	type	True	76.7271	438	2567	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	76.5098	600	2567	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	76.4412	404	2567	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_000379145.1	29448	29448	type	True	76.3607	452	2567	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	76.3518	460	2567	95	below_threshold
Bradyrhizobium elkanii	strain=NBRC 14791	GCA_006539665.1	29448	29448	type	True	76.32	448	2567	95	below_threshold
Bradyrhizobium pachyrhizi	strain=PAC 48	GCA_001189245.1	280333	280333	type	True	76.2943	430	2567	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	76.2551	309	2567	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	76.2547	669	2567	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.0782	242	2567	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	75.9588	237	2567	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:35,190] [INFO] DFAST Taxonomy check result was written to GCF_003258595.1_ASM325859v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:35,191] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:35,191] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:35,191] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6d2ab96-fb9a-4a50-a189-62c1026f8de0/dqc_reference/checkm_data
[2024-01-24 15:27:35,192] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:35,272] [INFO] Task started: CheckM
[2024-01-24 15:27:35,273] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003258595.1_ASM325859v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003258595.1_ASM325859v1_genomic.fna/checkm_input GCF_003258595.1_ASM325859v1_genomic.fna/checkm_result
[2024-01-24 15:28:47,104] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:47,105] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:47,133] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:47,133] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:47,134] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003258595.1_ASM325859v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:47,134] [INFO] Task started: Blastn
[2024-01-24 15:28:47,134] [INFO] Running command: blastn -query GCF_003258595.1_ASM325859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6d2ab96-fb9a-4a50-a189-62c1026f8de0/dqc_reference/reference_markers_gtdb.fasta -out GCF_003258595.1_ASM325859v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:48,893] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:48,896] [INFO] Selected 21 target genomes.
[2024-01-24 15:28:48,896] [INFO] Target genome list was writen to GCF_003258595.1_ASM325859v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:48,920] [INFO] Task started: fastANI
[2024-01-24 15:28:48,920] [INFO] Running command: fastANI --query /var/lib/cwl/stgc434dbf2-a083-4196-a212-1eaac47e9915/GCF_003258595.1_ASM325859v1_genomic.fna.gz --refList GCF_003258595.1_ASM325859v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003258595.1_ASM325859v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:29:12,518] [INFO] Task succeeded: fastANI
[2024-01-24 15:29:12,539] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:29:12,539] [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
GCF_003258595.1	s__Acuticoccus sediminis	100.0	2565	2567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Acuticoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001927245.1	s__Acuticoccus yangtzensis	82.4589	1210	2567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Acuticoccus	95.0	98.76	97.53	0.97	0.95	3	-
GCF_016411865.1	s__Acuticoccus sp016411865	79.5341	913	2567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Acuticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374525.1	s__Amorphus coralli	77.5149	427	2567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Amorphus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000192745.1	s__Polymorphum gilvum	76.8862	451	2567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Polymorphum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013839445.1	s__Chthonobacter albigriseus	76.8772	396	2567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Chthonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001463765.1	s__Aureimonas sp001463765	76.8239	374	2567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362745.1	s__Oharaeibacter diazotrophicus	76.8076	635	2567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Oharaeibacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_017872635.1	s__Starkeya sp017872635	76.7839	441	2567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003241485.1	s__Angulomicrobium novellum_A	76.7216	367	2567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382365.1	s__Pannonibacter phragmitetus	76.6486	256	2567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Pannonibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001425485.1	s__Aureimonas_A sp001425485	76.5934	446	2567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014196425.1	s__Hansschlegelia beijingensis	76.4861	371	2567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methylopilaceae;g__Hansschlegelia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898115.1	s__Bosea sp001898115	76.4642	404	2567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	99.21	98.43	0.96	0.93	3	-
GCA_004963905.1	s__Mesorhizobium sp004963905	76.4328	417	2567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039875.1	s__Methylobacterium sp008039875	76.4023	446	2567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.26	97.89	0.94	0.87	4	-
GCF_004022705.2	s__Mesorhizobium sp004022705	76.3741	358	2567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	99.85	98.91	0.98	0.93	18	-
GCF_016653355.1	s__Rhodoplanes elegans	76.3314	526	2567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodoplanes	95.0	99.89	99.89	0.96	0.96	2	-
GCF_018130215.1	s__Bradyrhizobium jicamae_A	76.2936	397	2567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	99.26	99.26	0.93	0.93	2	-
GCF_016756495.1	s__Mesorhizobium sp016756495	76.2896	359	2567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019365.1	s__Methylobacterium sp000019365	76.165	603	2567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.09	99.09	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:29:12,541] [INFO] GTDB search result was written to GCF_003258595.1_ASM325859v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:29:12,542] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:29:12,546] [INFO] DFAST_QC result json was written to GCF_003258595.1_ASM325859v1_genomic.fna/dqc_result.json
[2024-01-24 15:29:12,546] [INFO] DFAST_QC completed!
[2024-01-24 15:29:12,546] [INFO] Total running time: 0h2m25s