[2024-01-25 19:10:20,985] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:10:20,986] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:10:20,987] [INFO] DQC Reference Directory: /var/lib/cwl/stga28e1375-f4f0-4b02-822c-06fc2b42896f/dqc_reference
[2024-01-25 19:10:22,132] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:10:22,132] [INFO] Task started: Prodigal
[2024-01-25 19:10:22,133] [INFO] Running command: gunzip -c /var/lib/cwl/stgc2e46262-18a3-4907-b3d8-0c32e466e8b5/GCF_003425685.1_ASM342568v1_genomic.fna.gz | prodigal -d GCF_003425685.1_ASM342568v1_genomic.fna/cds.fna -a GCF_003425685.1_ASM342568v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:10:40,251] [INFO] Task succeeded: Prodigal
[2024-01-25 19:10:40,251] [INFO] Task started: HMMsearch
[2024-01-25 19:10:40,251] [INFO] Running command: hmmsearch --tblout GCF_003425685.1_ASM342568v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga28e1375-f4f0-4b02-822c-06fc2b42896f/dqc_reference/reference_markers.hmm GCF_003425685.1_ASM342568v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:10:40,560] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:10:40,561] [INFO] Found 6/6 markers.
[2024-01-25 19:10:40,615] [INFO] Query marker FASTA was written to GCF_003425685.1_ASM342568v1_genomic.fna/markers.fasta
[2024-01-25 19:10:40,615] [INFO] Task started: Blastn
[2024-01-25 19:10:40,615] [INFO] Running command: blastn -query GCF_003425685.1_ASM342568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga28e1375-f4f0-4b02-822c-06fc2b42896f/dqc_reference/reference_markers.fasta -out GCF_003425685.1_ASM342568v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:41,529] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:41,532] [INFO] Selected 12 target genomes.
[2024-01-25 19:10:41,532] [INFO] Target genome list was writen to GCF_003425685.1_ASM342568v1_genomic.fna/target_genomes.txt
[2024-01-25 19:10:41,539] [INFO] Task started: fastANI
[2024-01-25 19:10:41,539] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2e46262-18a3-4907-b3d8-0c32e466e8b5/GCF_003425685.1_ASM342568v1_genomic.fna.gz --refList GCF_003425685.1_ASM342568v1_genomic.fna/target_genomes.txt --output GCF_003425685.1_ASM342568v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:10:57,743] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:57,744] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga28e1375-f4f0-4b02-822c-06fc2b42896f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:10:57,744] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga28e1375-f4f0-4b02-822c-06fc2b42896f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:10:57,752] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:10:57,752] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:10:57,752] [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 vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	84.2183	1438	2287	95	below_threshold
Neorhizobium galegae	strain=HAMBI 540	GCA_000731315.1	399	399	suspected-type	True	84.1459	1431	2287	95	below_threshold
Rhizobium populisoli	strain=XQZ8	GCA_019430945.1	2859785	2859785	type	True	83.7573	1399	2287	95	below_threshold
Rhizobium petrolearium	strain=DSM 26482	GCA_017873175.1	515361	515361	type	True	82.9522	1375	2287	95	below_threshold
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	82.3158	1180	2287	95	below_threshold
Neorhizobium huautlense	strain=DSM 21817	GCA_002968575.1	67774	67774	type	True	82.0594	1134	2287	95	below_threshold
Neorhizobium lilium	strain=24NR	GCA_004053875.1	2503024	2503024	type	True	80.5437	830	2287	95	below_threshold
Rhizobium wenxiniae	strain=CGMCC 1.15279	GCA_014641515.1	1737357	1737357	type	True	80.4112	899	2287	95	below_threshold
Rhizobium wenxiniae	strain=DSM 100734	GCA_014201355.1	1737357	1737357	type	True	80.3881	907	2287	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	79.9114	711	2287	95	below_threshold
Rhizobium viscosum	strain=DSM 7307	GCA_014873945.1	1673	1673	type	True	79.7426	770	2287	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	79.5401	657	2287	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:10:57,754] [INFO] DFAST Taxonomy check result was written to GCF_003425685.1_ASM342568v1_genomic.fna/tc_result.tsv
[2024-01-25 19:10:57,755] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:10:57,755] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:10:57,755] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga28e1375-f4f0-4b02-822c-06fc2b42896f/dqc_reference/checkm_data
[2024-01-25 19:10:57,756] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:10:57,820] [INFO] Task started: CheckM
[2024-01-25 19:10:57,820] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003425685.1_ASM342568v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003425685.1_ASM342568v1_genomic.fna/checkm_input GCF_003425685.1_ASM342568v1_genomic.fna/checkm_result
[2024-01-25 19:11:49,504] [INFO] Task succeeded: CheckM
[2024-01-25 19:11:49,506] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:11:49,527] [INFO] ===== Completeness check finished =====
[2024-01-25 19:11:49,527] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:11:49,528] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003425685.1_ASM342568v1_genomic.fna/markers.fasta)
[2024-01-25 19:11:49,528] [INFO] Task started: Blastn
[2024-01-25 19:11:49,529] [INFO] Running command: blastn -query GCF_003425685.1_ASM342568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga28e1375-f4f0-4b02-822c-06fc2b42896f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003425685.1_ASM342568v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:51,475] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:51,479] [INFO] Selected 11 target genomes.
[2024-01-25 19:11:51,479] [INFO] Target genome list was writen to GCF_003425685.1_ASM342568v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:11:51,491] [INFO] Task started: fastANI
[2024-01-25 19:11:51,491] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2e46262-18a3-4907-b3d8-0c32e466e8b5/GCF_003425685.1_ASM342568v1_genomic.fna.gz --refList GCF_003425685.1_ASM342568v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003425685.1_ASM342568v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:12:07,953] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:07,961] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:12:07,961] [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_003425685.1	s__Neorhizobium sp003425685	100.0	2284	2287	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000282095.2	s__Neorhizobium sp000282095	84.5841	1454	2287	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	84.5564	1358	2287	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	84.4646	1421	2287	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	84.444	1441	2287	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.26	98.25	0.92	0.92	3	-
GCA_000985895.1	s__Neorhizobium galegae_B	84.3899	1392	2287	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.06	98.00	0.96	0.95	4	-
GCA_000985875.1	s__Neorhizobium galegae_C	84.3895	1397	2287	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	97.95	97.84	0.92	0.90	4	-
GCF_000732195.1	s__Neorhizobium vignae	84.2174	1438	2287	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002968635.1	s__Neorhizobium alkalisoli	82.3102	1181	2287	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	82.1069	1161	2287	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002968575.1	s__Neorhizobium huautlense	82.0384	1138	2287	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.14	97.99	0.92	0.90	5	-
--------------------------------------------------------------------------------
[2024-01-25 19:12:07,963] [INFO] GTDB search result was written to GCF_003425685.1_ASM342568v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:12:07,963] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:12:07,966] [INFO] DFAST_QC result json was written to GCF_003425685.1_ASM342568v1_genomic.fna/dqc_result.json
[2024-01-25 19:12:07,966] [INFO] DFAST_QC completed!
[2024-01-25 19:12:07,966] [INFO] Total running time: 0h1m47s