[2024-01-24 13:40:34,931] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,933] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,933] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a403cbc-1a77-46fc-8e0b-acf6b3f15c2a/dqc_reference
[2024-01-24 13:40:36,419] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,420] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,420] [INFO] Running command: gunzip -c /var/lib/cwl/stg6cf67693-3295-419c-b9a0-4a4cefe07fc2/GCF_002968575.1_ASM296857v1_genomic.fna.gz | prodigal -d GCF_002968575.1_ASM296857v1_genomic.fna/cds.fna -a GCF_002968575.1_ASM296857v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:54,043] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:54,043] [INFO] Task started: HMMsearch
[2024-01-24 13:40:54,043] [INFO] Running command: hmmsearch --tblout GCF_002968575.1_ASM296857v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a403cbc-1a77-46fc-8e0b-acf6b3f15c2a/dqc_reference/reference_markers.hmm GCF_002968575.1_ASM296857v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:54,398] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:54,399] [INFO] Found 6/6 markers.
[2024-01-24 13:40:54,458] [INFO] Query marker FASTA was written to GCF_002968575.1_ASM296857v1_genomic.fna/markers.fasta
[2024-01-24 13:40:54,458] [INFO] Task started: Blastn
[2024-01-24 13:40:54,458] [INFO] Running command: blastn -query GCF_002968575.1_ASM296857v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a403cbc-1a77-46fc-8e0b-acf6b3f15c2a/dqc_reference/reference_markers.fasta -out GCF_002968575.1_ASM296857v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:55,513] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:55,517] [INFO] Selected 11 target genomes.
[2024-01-24 13:40:55,517] [INFO] Target genome list was writen to GCF_002968575.1_ASM296857v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:55,522] [INFO] Task started: fastANI
[2024-01-24 13:40:55,522] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cf67693-3295-419c-b9a0-4a4cefe07fc2/GCF_002968575.1_ASM296857v1_genomic.fna.gz --refList GCF_002968575.1_ASM296857v1_genomic.fna/target_genomes.txt --output GCF_002968575.1_ASM296857v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:09,929] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:09,930] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a403cbc-1a77-46fc-8e0b-acf6b3f15c2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:09,930] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a403cbc-1a77-46fc-8e0b-acf6b3f15c2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:09,941] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:09,942] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:09,942] [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
Neorhizobium huautlense	strain=DSM 21817	GCA_002968575.1	67774	67774	type	True	100.0	1849	1852	95	conclusive
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	88.9526	1411	1852	95	below_threshold
Neorhizobium galegae	strain=HAMBI 540	GCA_000731315.1	399	399	suspected-type	True	82.2711	1137	1852	95	below_threshold
Neorhizobium vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	82.2434	1130	1852	95	below_threshold
Rhizobium petrolearium	strain=DSM 26482	GCA_017873175.1	515361	515361	type	True	81.8825	1107	1852	95	below_threshold
Rhizobium populisoli	strain=XQZ8	GCA_019430945.1	2859785	2859785	type	True	81.3063	1048	1852	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	79.2672	578	1852	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	79.1805	707	1852	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	79.1166	566	1852	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	79.0215	564	1852	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	78.8286	603	1852	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:09,944] [INFO] DFAST Taxonomy check result was written to GCF_002968575.1_ASM296857v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:09,944] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:09,945] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:09,945] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a403cbc-1a77-46fc-8e0b-acf6b3f15c2a/dqc_reference/checkm_data
[2024-01-24 13:41:09,946] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:10,010] [INFO] Task started: CheckM
[2024-01-24 13:41:10,010] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002968575.1_ASM296857v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002968575.1_ASM296857v1_genomic.fna/checkm_input GCF_002968575.1_ASM296857v1_genomic.fna/checkm_result
[2024-01-24 13:42:01,987] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:01,989] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:02,014] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:02,014] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:02,015] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002968575.1_ASM296857v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:02,015] [INFO] Task started: Blastn
[2024-01-24 13:42:02,015] [INFO] Running command: blastn -query GCF_002968575.1_ASM296857v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a403cbc-1a77-46fc-8e0b-acf6b3f15c2a/dqc_reference/reference_markers_gtdb.fasta -out GCF_002968575.1_ASM296857v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:04,074] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:04,082] [INFO] Selected 13 target genomes.
[2024-01-24 13:42:04,082] [INFO] Target genome list was writen to GCF_002968575.1_ASM296857v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:04,092] [INFO] Task started: fastANI
[2024-01-24 13:42:04,093] [INFO] Running command: fastANI --query /var/lib/cwl/stg6cf67693-3295-419c-b9a0-4a4cefe07fc2/GCF_002968575.1_ASM296857v1_genomic.fna.gz --refList GCF_002968575.1_ASM296857v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002968575.1_ASM296857v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:21,786] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:21,810] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:21,810] [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_002968575.1	s__Neorhizobium huautlense	100.0	1849	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.14	97.99	0.92	0.90	5	conclusive
GCF_002968635.1	s__Neorhizobium alkalisoli	88.9526	1411	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900469955.1	s__Neorhizobium sp900469955	88.4071	1394	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177415.1	s__Neorhizobium oryzae_A	82.7411	1121	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017877055.1	s__Neorhizobium galegae_D	82.4425	1118	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900471605.1	s__Neorhizobium sp900471605	82.4348	1147	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.26	98.25	0.92	0.92	3	-
GCF_000282095.2	s__Neorhizobium sp000282095	82.418	1108	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000985875.1	s__Neorhizobium galegae_C	82.3872	1141	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	97.95	97.84	0.92	0.90	4	-
GCA_002968845.1	s__Neorhizobium tomejilense	82.3293	1157	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	97.02	95.22	0.90	0.84	9	-
GCF_000731315.1	s__Neorhizobium galegae	82.2852	1134	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	97.31	95.05	0.87	0.81	4	-
GCF_000732195.1	s__Neorhizobium vignae	82.2351	1131	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003425685.1	s__Neorhizobium sp003425685	82.1089	1147	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358025.1	s__Neorhizobium deserti	79.8328	777	1852	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:21,812] [INFO] GTDB search result was written to GCF_002968575.1_ASM296857v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:21,812] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:21,816] [INFO] DFAST_QC result json was written to GCF_002968575.1_ASM296857v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:21,816] [INFO] DFAST_QC completed!
[2024-01-24 13:42:21,816] [INFO] Total running time: 0h1m47s