[2024-01-25 20:13:50,542] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:13:50,544] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:13:50,544] [INFO] DQC Reference Directory: /var/lib/cwl/stgda316cbc-576d-4b16-8ee7-0b27d62c3c25/dqc_reference
[2024-01-25 20:13:51,686] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:13:51,687] [INFO] Task started: Prodigal
[2024-01-25 20:13:51,687] [INFO] Running command: gunzip -c /var/lib/cwl/stg3faac2c0-9e14-4928-b4c0-4d8ac918cb2a/GCF_014641515.1_ASM1464151v1_genomic.fna.gz | prodigal -d GCF_014641515.1_ASM1464151v1_genomic.fna/cds.fna -a GCF_014641515.1_ASM1464151v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:14:10,076] [INFO] Task succeeded: Prodigal
[2024-01-25 20:14:10,076] [INFO] Task started: HMMsearch
[2024-01-25 20:14:10,076] [INFO] Running command: hmmsearch --tblout GCF_014641515.1_ASM1464151v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda316cbc-576d-4b16-8ee7-0b27d62c3c25/dqc_reference/reference_markers.hmm GCF_014641515.1_ASM1464151v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:14:10,432] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:14:10,433] [INFO] Found 6/6 markers.
[2024-01-25 20:14:10,484] [INFO] Query marker FASTA was written to GCF_014641515.1_ASM1464151v1_genomic.fna/markers.fasta
[2024-01-25 20:14:10,485] [INFO] Task started: Blastn
[2024-01-25 20:14:10,485] [INFO] Running command: blastn -query GCF_014641515.1_ASM1464151v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda316cbc-576d-4b16-8ee7-0b27d62c3c25/dqc_reference/reference_markers.fasta -out GCF_014641515.1_ASM1464151v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:11,466] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:11,470] [INFO] Selected 14 target genomes.
[2024-01-25 20:14:11,470] [INFO] Target genome list was writen to GCF_014641515.1_ASM1464151v1_genomic.fna/target_genomes.txt
[2024-01-25 20:14:11,474] [INFO] Task started: fastANI
[2024-01-25 20:14:11,474] [INFO] Running command: fastANI --query /var/lib/cwl/stg3faac2c0-9e14-4928-b4c0-4d8ac918cb2a/GCF_014641515.1_ASM1464151v1_genomic.fna.gz --refList GCF_014641515.1_ASM1464151v1_genomic.fna/target_genomes.txt --output GCF_014641515.1_ASM1464151v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:14:29,024] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:29,024] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda316cbc-576d-4b16-8ee7-0b27d62c3c25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:14:29,025] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda316cbc-576d-4b16-8ee7-0b27d62c3c25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:14:29,034] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:14:29,034] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:14:29,034] [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 wenxiniae	strain=CGMCC 1.15279	GCA_014641515.1	1737357	1737357	type	True	100.0	2132	2133	95	conclusive
Rhizobium wenxiniae	strain=DSM 100734	GCA_014201355.1	1737357	1737357	type	True	99.9984	2128	2133	95	conclusive
Rhizobium smilacinae	strain=PTYR-5	GCA_006335145.1	1395944	1395944	type	True	85.6597	1478	2133	95	below_threshold
Rhizobium populisoli	strain=XQZ8	GCA_019430945.1	2859785	2859785	type	True	80.8547	949	2133	95	below_threshold
Neorhizobium vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	80.6803	928	2133	95	below_threshold
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	79.9939	787	2133	95	below_threshold
Neorhizobium lilium	strain=24NR	GCA_004053875.1	2503024	2503024	type	True	79.7085	737	2133	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	79.5171	699	2133	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	79.476	634	2133	95	below_threshold
Rhizobium etli	strain=CFN 42	GCA_000092045.1	29449	29449	suspected-type	True	79.2211	614	2133	95	below_threshold
Pseudorhizobium banfieldiae	strain=NT-26	GCA_000967425.1	1125847	1125847	type	True	79.1399	547	2133	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	79.1095	576	2133	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	79.1074	660	2133	95	below_threshold
Pseudorhizobium flavum	strain=YW14	GCA_002000045.1	1335061	1335061	type	True	78.9395	562	2133	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:14:29,035] [INFO] DFAST Taxonomy check result was written to GCF_014641515.1_ASM1464151v1_genomic.fna/tc_result.tsv
[2024-01-25 20:14:29,036] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:14:29,036] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:14:29,036] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda316cbc-576d-4b16-8ee7-0b27d62c3c25/dqc_reference/checkm_data
[2024-01-25 20:14:29,037] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:14:29,095] [INFO] Task started: CheckM
[2024-01-25 20:14:29,095] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014641515.1_ASM1464151v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014641515.1_ASM1464151v1_genomic.fna/checkm_input GCF_014641515.1_ASM1464151v1_genomic.fna/checkm_result
[2024-01-25 20:15:20,140] [INFO] Task succeeded: CheckM
[2024-01-25 20:15:20,141] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:15:20,185] [INFO] ===== Completeness check finished =====
[2024-01-25 20:15:20,185] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:15:20,186] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014641515.1_ASM1464151v1_genomic.fna/markers.fasta)
[2024-01-25 20:15:20,186] [INFO] Task started: Blastn
[2024-01-25 20:15:20,186] [INFO] Running command: blastn -query GCF_014641515.1_ASM1464151v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda316cbc-576d-4b16-8ee7-0b27d62c3c25/dqc_reference/reference_markers_gtdb.fasta -out GCF_014641515.1_ASM1464151v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:22,219] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:22,222] [INFO] Selected 8 target genomes.
[2024-01-25 20:15:22,223] [INFO] Target genome list was writen to GCF_014641515.1_ASM1464151v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:15:22,230] [INFO] Task started: fastANI
[2024-01-25 20:15:22,231] [INFO] Running command: fastANI --query /var/lib/cwl/stg3faac2c0-9e14-4928-b4c0-4d8ac918cb2a/GCF_014641515.1_ASM1464151v1_genomic.fna.gz --refList GCF_014641515.1_ASM1464151v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014641515.1_ASM1464151v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:15:34,290] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:34,296] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:15:34,296] [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_014201355.1	s__Neorhizobium wenxiniae	99.9984	2128	2133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.63	97.27	0.93	0.87	3	conclusive
GCA_900472575.1	s__Neorhizobium cellulosilyticum	92.353	1652	2133	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	87.5744	1139	2133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002376235.1	s__Neorhizobium sp002376235	87.4255	1429	2133	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	87.0713	1457	2133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	99.00	97.21	0.95	0.90	4	-
GCA_900466875.1	s__Neorhizobium sp900466875	86.5686	1401	2133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006335145.1	s__Neorhizobium smilacinae	85.6525	1479	2133	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	83.4685	1187	2133	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:15:34,298] [INFO] GTDB search result was written to GCF_014641515.1_ASM1464151v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:15:34,298] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:15:34,300] [INFO] DFAST_QC result json was written to GCF_014641515.1_ASM1464151v1_genomic.fna/dqc_result.json
[2024-01-25 20:15:34,301] [INFO] DFAST_QC completed!
[2024-01-25 20:15:34,301] [INFO] Total running time: 0h1m44s