[2024-01-24 11:09:50,719] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:09:50,722] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:09:50,722] [INFO] DQC Reference Directory: /var/lib/cwl/stgc824285b-f547-4bea-a548-a4839c30aff9/dqc_reference
[2024-01-24 11:09:53,303] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:09:53,304] [INFO] Task started: Prodigal
[2024-01-24 11:09:53,304] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6cea5f4-0a0e-4e49-9998-7e05a29f1818/GCF_014196535.1_ASM1419653v1_genomic.fna.gz | prodigal -d GCF_014196535.1_ASM1419653v1_genomic.fna/cds.fna -a GCF_014196535.1_ASM1419653v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:10:07,626] [INFO] Task succeeded: Prodigal
[2024-01-24 11:10:07,627] [INFO] Task started: HMMsearch
[2024-01-24 11:10:07,627] [INFO] Running command: hmmsearch --tblout GCF_014196535.1_ASM1419653v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc824285b-f547-4bea-a548-a4839c30aff9/dqc_reference/reference_markers.hmm GCF_014196535.1_ASM1419653v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:10:07,902] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:10:07,904] [INFO] Found 6/6 markers.
[2024-01-24 11:10:07,943] [INFO] Query marker FASTA was written to GCF_014196535.1_ASM1419653v1_genomic.fna/markers.fasta
[2024-01-24 11:10:07,943] [INFO] Task started: Blastn
[2024-01-24 11:10:07,943] [INFO] Running command: blastn -query GCF_014196535.1_ASM1419653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc824285b-f547-4bea-a548-a4839c30aff9/dqc_reference/reference_markers.fasta -out GCF_014196535.1_ASM1419653v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:10:08,921] [INFO] Task succeeded: Blastn
[2024-01-24 11:10:08,926] [INFO] Selected 28 target genomes.
[2024-01-24 11:10:08,926] [INFO] Target genome list was writen to GCF_014196535.1_ASM1419653v1_genomic.fna/target_genomes.txt
[2024-01-24 11:10:08,986] [INFO] Task started: fastANI
[2024-01-24 11:10:08,987] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6cea5f4-0a0e-4e49-9998-7e05a29f1818/GCF_014196535.1_ASM1419653v1_genomic.fna.gz --refList GCF_014196535.1_ASM1419653v1_genomic.fna/target_genomes.txt --output GCF_014196535.1_ASM1419653v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:10:37,151] [INFO] Task succeeded: fastANI
[2024-01-24 11:10:37,151] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc824285b-f547-4bea-a548-a4839c30aff9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:10:37,152] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc824285b-f547-4bea-a548-a4839c30aff9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:10:37,172] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:10:37,172] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:10:37,173] [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
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	79.5802	598	1576	95	below_threshold
Ciceribacter selenitireducens	strain=ATCC BAA-1503	GCA_000518785.1	448181	448181	type	True	79.5636	586	1576	95	below_threshold
Rhizobium daejeonense	strain=CCBAU10050	GCA_011045155.1	240521	240521	type	True	79.5102	560	1576	95	below_threshold
Rhizobium daejeonense	strain=L61	GCA_014280875.1	240521	240521	type	True	79.4749	556	1576	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	79.4425	555	1576	95	below_threshold
Rhizobium oryzihabitans	strain=M15	GCA_010669145.1	2267833	2267833	type	True	79.4329	575	1576	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	79.4034	550	1576	95	below_threshold
Agrobacterium tumefaciens	strain=B6	GCA_001541315.1	358	358	suspected-type	True	79.3008	565	1576	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	79.2475	602	1576	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	79.1865	585	1576	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	79.176	512	1576	95	below_threshold
Agrobacterium tumefaciens	strain=ICMP 5856T	GCA_009498475.1	358	358	suspected-type	True	79.1711	585	1576	95	below_threshold
Agrobacterium salinitolerans	strain=YIC 5082	GCA_002008225.1	1183413	1183413	type	True	79.1536	547	1576	95	below_threshold
Shinella kummerowiae	strain=CCBAU 25048	GCA_009827055.1	417745	417745	type	True	79.0218	576	1576	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	78.9796	532	1576	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	78.9341	558	1576	95	below_threshold
Rhizobium wenxiniae	strain=CGMCC 1.15279	GCA_014641515.1	1737357	1737357	type	True	78.9266	513	1576	95	below_threshold
Neorhizobium vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	78.9231	563	1576	95	below_threshold
Rhizobium sophoriradicis	strain=CCBAU 03470	GCA_003939025.1	1535245	1535245	type	True	78.907	524	1576	95	below_threshold
Rhizobium binae	strain=BLR195	GCA_019684455.1	1138190	1138190	type	True	78.891	571	1576	95	below_threshold
Rhizobium wenxiniae	strain=DSM 100734	GCA_014201355.1	1737357	1737357	type	True	78.8907	518	1576	95	below_threshold
Rhizobium binae	strain=BLR195	GCA_017357225.1	1138190	1138190	type	True	78.8646	572	1576	95	below_threshold
Rhizobium multihospitium	strain=HAMBI 2975	GCA_900094585.1	410764	410764	type	True	78.7916	526	1576	95	below_threshold
Rhizobium indicum	strain=JKLM 12A2	GCA_005862305.2	2583231	2583231	type	True	78.742	546	1576	95	below_threshold
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	78.707	463	1576	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	78.6578	490	1576	95	below_threshold
Neorhizobium huautlense	strain=DSM 21817	GCA_002968575.1	67774	67774	type	True	78.6053	449	1576	95	below_threshold
Rhizobium grahamii	strain=CCGE 502	GCA_000298315.2	1120045	1120045	type	True	78.5848	420	1576	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:10:37,174] [INFO] DFAST Taxonomy check result was written to GCF_014196535.1_ASM1419653v1_genomic.fna/tc_result.tsv
[2024-01-24 11:10:37,175] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:10:37,175] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:10:37,175] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc824285b-f547-4bea-a548-a4839c30aff9/dqc_reference/checkm_data
[2024-01-24 11:10:37,177] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:10:37,236] [INFO] Task started: CheckM
[2024-01-24 11:10:37,237] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196535.1_ASM1419653v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196535.1_ASM1419653v1_genomic.fna/checkm_input GCF_014196535.1_ASM1419653v1_genomic.fna/checkm_result
[2024-01-24 11:11:21,560] [INFO] Task succeeded: CheckM
[2024-01-24 11:11:21,562] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:11:21,585] [INFO] ===== Completeness check finished =====
[2024-01-24 11:11:21,585] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:11:21,586] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196535.1_ASM1419653v1_genomic.fna/markers.fasta)
[2024-01-24 11:11:21,586] [INFO] Task started: Blastn
[2024-01-24 11:11:21,586] [INFO] Running command: blastn -query GCF_014196535.1_ASM1419653v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc824285b-f547-4bea-a548-a4839c30aff9/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196535.1_ASM1419653v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:11:23,556] [INFO] Task succeeded: Blastn
[2024-01-24 11:11:23,560] [INFO] Selected 29 target genomes.
[2024-01-24 11:11:23,560] [INFO] Target genome list was writen to GCF_014196535.1_ASM1419653v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:11:23,582] [INFO] Task started: fastANI
[2024-01-24 11:11:23,583] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6cea5f4-0a0e-4e49-9998-7e05a29f1818/GCF_014196535.1_ASM1419653v1_genomic.fna.gz --refList GCF_014196535.1_ASM1419653v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196535.1_ASM1419653v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:11:55,678] [INFO] Task succeeded: fastANI
[2024-01-24 11:11:55,707] [INFO] Found 29 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:11:55,707] [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_014196535.1	s__Rhizobium_B borbori	100.0	1575	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_B	95.0	98.16	98.16	0.88	0.88	2	conclusive
GCF_002600635.1	s__Allorhizobium sp002600635	79.7422	616	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004514435.1	s__Shinella sp004514435	79.5193	550	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	99.21	98.45	0.95	0.91	3	-
GCF_003122325.1	s__Rhizobium album	79.4799	600	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014280875.1	s__Allorhizobium daejeonense	79.4667	558	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_002005205.3	s__Agrobacterium rhizogenes_A	79.426	594	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.60	97.88	0.94	0.88	11	-
GCF_016839145.1	s__Shinella sp016839145	79.4109	570	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003574625.1	s__Shinella zoogloeoides_A	79.4045	566	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203155.1	s__Shinella fusca	79.3879	552	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000949895.1	s__Agrobacterium arsenijevicii	79.3114	539	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341885.1	s__Shinella granuli	79.2557	601	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	98.18	98.18	0.91	0.91	2	-
GCF_002211285.1	s__Rhizobium sp002211285	79.2463	544	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744915.1	s__Agrobacterium tumefaciens_I	79.2206	578	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017877135.1	s__Rhizobium_A galegae_A	79.2169	581	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927355.1	s__Allorhizobium sp012927355	79.2136	567	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000949865.1	s__Agrobacterium nepotum	79.1607	543	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003025035.1	s__Rhizobium paranaense	79.0824	445	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.97	99.97	0.99	0.99	2	-
GCF_000746385.1	s__Rhizobium sp000746385	78.9997	523	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.83	96.83	0.89	0.89	2	-
GCF_000799775.1	s__Rhizobium sp000799775	78.9965	536	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	95.27	95.13	0.81	0.79	16	-
GCF_014201355.1	s__Neorhizobium wenxiniae	78.8984	516	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.63	97.27	0.93	0.87	3	-
GCF_017876795.1	s__Rhizobium leguminosarum_P	78.8515	552	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001692325.1	s__Rhizobium sp001692325	78.7985	509	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.36	95.29	0.93	0.90	3	-
GCF_000271845.1	s__Rhizobium leguminosarum_G	78.7954	561	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197145.1	s__Gellertiella hungarica	78.7876	477	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Gellertiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002968635.1	s__Neorhizobium alkalisoli	78.6975	462	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341625.1	s__Rhizobium sp004341625	78.6402	474	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.83	97.83	0.87	0.87	2	-
GCA_003241215.1	s__Agrobacterium fabrum_A	78.625	432	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002968575.1	s__Neorhizobium huautlense	78.5839	452	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.14	97.99	0.92	0.90	5	-
GCA_003527225.1	s__Allorhizobium sp003527225	78.4065	429	1576	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:11:55,709] [INFO] GTDB search result was written to GCF_014196535.1_ASM1419653v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:11:55,709] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:11:55,734] [INFO] DFAST_QC result json was written to GCF_014196535.1_ASM1419653v1_genomic.fna/dqc_result.json
[2024-01-24 11:11:55,735] [INFO] DFAST_QC completed!
[2024-01-24 11:11:55,735] [INFO] Total running time: 0h2m5s