[2024-01-24 13:21:47,046] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:47,048] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:47,048] [INFO] DQC Reference Directory: /var/lib/cwl/stg4cbcc147-9f89-4e52-98d9-7c55fee28deb/dqc_reference
[2024-01-24 13:21:48,319] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:48,320] [INFO] Task started: Prodigal
[2024-01-24 13:21:48,320] [INFO] Running command: gunzip -c /var/lib/cwl/stged29375c-ef98-4e4d-9fb8-eeafb0459b7b/GCF_006335145.1_ASM633514v1_genomic.fna.gz | prodigal -d GCF_006335145.1_ASM633514v1_genomic.fna/cds.fna -a GCF_006335145.1_ASM633514v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:07,030] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:07,031] [INFO] Task started: HMMsearch
[2024-01-24 13:22:07,031] [INFO] Running command: hmmsearch --tblout GCF_006335145.1_ASM633514v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4cbcc147-9f89-4e52-98d9-7c55fee28deb/dqc_reference/reference_markers.hmm GCF_006335145.1_ASM633514v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:07,369] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:07,371] [INFO] Found 6/6 markers.
[2024-01-24 13:22:07,424] [INFO] Query marker FASTA was written to GCF_006335145.1_ASM633514v1_genomic.fna/markers.fasta
[2024-01-24 13:22:07,424] [INFO] Task started: Blastn
[2024-01-24 13:22:07,424] [INFO] Running command: blastn -query GCF_006335145.1_ASM633514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4cbcc147-9f89-4e52-98d9-7c55fee28deb/dqc_reference/reference_markers.fasta -out GCF_006335145.1_ASM633514v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:08,494] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:08,497] [INFO] Selected 15 target genomes.
[2024-01-24 13:22:08,497] [INFO] Target genome list was writen to GCF_006335145.1_ASM633514v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:08,504] [INFO] Task started: fastANI
[2024-01-24 13:22:08,505] [INFO] Running command: fastANI --query /var/lib/cwl/stged29375c-ef98-4e4d-9fb8-eeafb0459b7b/GCF_006335145.1_ASM633514v1_genomic.fna.gz --refList GCF_006335145.1_ASM633514v1_genomic.fna/target_genomes.txt --output GCF_006335145.1_ASM633514v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:27,886] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:27,887] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4cbcc147-9f89-4e52-98d9-7c55fee28deb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:27,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4cbcc147-9f89-4e52-98d9-7c55fee28deb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:27,901] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:27,901] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:27,902] [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
Rhizobium smilacinae	strain=PTYR-5	GCA_006335145.1	1395944	1395944	type	True	100.0	1991	1993	95	conclusive
Rhizobium wenxiniae	strain=CGMCC 1.15279	GCA_014641515.1	1737357	1737357	type	True	85.7203	1464	1993	95	below_threshold
Rhizobium wenxiniae	strain=DSM 100734	GCA_014201355.1	1737357	1737357	type	True	85.6677	1484	1993	95	below_threshold
Neorhizobium vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	80.795	907	1993	95	below_threshold
Rhizobium populisoli	strain=XQZ8	GCA_019430945.1	2859785	2859785	type	True	80.7727	963	1993	95	below_threshold
Neorhizobium galegae	strain=HAMBI 540	GCA_000731315.1	399	399	suspected-type	True	80.6664	920	1993	95	below_threshold
Neorhizobium lilium	strain=24NR	GCA_004053875.1	2503024	2503024	type	True	79.6487	779	1993	95	below_threshold
Rhizobium pseudoryzae	strain=DSM 19479	GCA_011046245.1	379684	379684	type	True	79.6083	716	1993	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	79.2943	680	1993	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	79.2157	659	1993	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	79.1817	659	1993	95	below_threshold
Agrobacterium salinitolerans	strain=YIC 5082	GCA_002008225.1	1183413	1183413	type	True	79.059	637	1993	95	below_threshold
Pseudorhizobium banfieldiae	strain=NT-26	GCA_000967425.1	1125847	1125847	type	True	79.0267	546	1993	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	78.7394	564	1993	95	below_threshold
Agrobacterium larrymoorei	strain=CFBP5473	GCA_005145045.1	160699	160699	type	True	78.5021	538	1993	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:27,904] [INFO] DFAST Taxonomy check result was written to GCF_006335145.1_ASM633514v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:27,904] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:27,905] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:27,905] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4cbcc147-9f89-4e52-98d9-7c55fee28deb/dqc_reference/checkm_data
[2024-01-24 13:22:27,906] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:27,967] [INFO] Task started: CheckM
[2024-01-24 13:22:27,967] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006335145.1_ASM633514v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006335145.1_ASM633514v1_genomic.fna/checkm_input GCF_006335145.1_ASM633514v1_genomic.fna/checkm_result
[2024-01-24 13:23:21,908] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:21,910] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:21,941] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:21,942] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:21,942] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006335145.1_ASM633514v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:21,943] [INFO] Task started: Blastn
[2024-01-24 13:23:21,943] [INFO] Running command: blastn -query GCF_006335145.1_ASM633514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4cbcc147-9f89-4e52-98d9-7c55fee28deb/dqc_reference/reference_markers_gtdb.fasta -out GCF_006335145.1_ASM633514v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:23,951] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:23,957] [INFO] Selected 9 target genomes.
[2024-01-24 13:23:23,957] [INFO] Target genome list was writen to GCF_006335145.1_ASM633514v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:23,984] [INFO] Task started: fastANI
[2024-01-24 13:23:23,984] [INFO] Running command: fastANI --query /var/lib/cwl/stged29375c-ef98-4e4d-9fb8-eeafb0459b7b/GCF_006335145.1_ASM633514v1_genomic.fna.gz --refList GCF_006335145.1_ASM633514v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006335145.1_ASM633514v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:36,782] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:36,794] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:36,794] [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_006335145.1	s__Neorhizobium smilacinae	100.0	1991	1993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900466875.1	s__Neorhizobium sp900466875	87.3738	1364	1993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900469445.1	s__Neorhizobium sp900469445	85.9306	1367	1993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	99.00	97.21	0.95	0.90	4	-
GCA_900472575.1	s__Neorhizobium cellulosilyticum	85.8611	1425	1993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	97.58	97.10	0.87	0.85	7	-
GCA_002500765.1	s__Neorhizobium sp002500765	85.8361	1117	1993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201355.1	s__Neorhizobium wenxiniae	85.6506	1487	1993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.63	97.27	0.93	0.87	3	-
GCA_002376235.1	s__Neorhizobium sp002376235	85.3729	1344	1993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003597675.1	s__Neorhizobium sp003597675	83.1191	1193	1993	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343585.1	s__Neorhizobium sp004343585	81.4266	942	1993	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 13:23:36,795] [INFO] GTDB search result was written to GCF_006335145.1_ASM633514v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:36,796] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:36,799] [INFO] DFAST_QC result json was written to GCF_006335145.1_ASM633514v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:36,800] [INFO] DFAST_QC completed!
[2024-01-24 13:23:36,800] [INFO] Total running time: 0h1m50s