[2024-01-24 14:28:02,342] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:02,350] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:02,350] [INFO] DQC Reference Directory: /var/lib/cwl/stgccae0094-04c6-4b5d-a0fa-b9192d696b95/dqc_reference
[2024-01-24 14:28:03,630] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:03,631] [INFO] Task started: Prodigal
[2024-01-24 14:28:03,631] [INFO] Running command: gunzip -c /var/lib/cwl/stg856c9c8b-a403-4e4c-9cc5-bce6a6603a13/GCF_026552795.1_ASM2655279v1_genomic.fna.gz | prodigal -d GCF_026552795.1_ASM2655279v1_genomic.fna/cds.fna -a GCF_026552795.1_ASM2655279v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:18,141] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:18,141] [INFO] Task started: HMMsearch
[2024-01-24 14:28:18,141] [INFO] Running command: hmmsearch --tblout GCF_026552795.1_ASM2655279v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgccae0094-04c6-4b5d-a0fa-b9192d696b95/dqc_reference/reference_markers.hmm GCF_026552795.1_ASM2655279v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:18,508] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:18,509] [INFO] Found 6/6 markers.
[2024-01-24 14:28:18,552] [INFO] Query marker FASTA was written to GCF_026552795.1_ASM2655279v1_genomic.fna/markers.fasta
[2024-01-24 14:28:18,553] [INFO] Task started: Blastn
[2024-01-24 14:28:18,553] [INFO] Running command: blastn -query GCF_026552795.1_ASM2655279v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccae0094-04c6-4b5d-a0fa-b9192d696b95/dqc_reference/reference_markers.fasta -out GCF_026552795.1_ASM2655279v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:19,618] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:19,622] [INFO] Selected 24 target genomes.
[2024-01-24 14:28:19,622] [INFO] Target genome list was writen to GCF_026552795.1_ASM2655279v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:19,651] [INFO] Task started: fastANI
[2024-01-24 14:28:19,651] [INFO] Running command: fastANI --query /var/lib/cwl/stg856c9c8b-a403-4e4c-9cc5-bce6a6603a13/GCF_026552795.1_ASM2655279v1_genomic.fna.gz --refList GCF_026552795.1_ASM2655279v1_genomic.fna/target_genomes.txt --output GCF_026552795.1_ASM2655279v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:47,715] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:47,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgccae0094-04c6-4b5d-a0fa-b9192d696b95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:47,716] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgccae0094-04c6-4b5d-a0fa-b9192d696b95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:47,735] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:28:47,735] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:28:47,735] [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
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	80.4396	668	1680	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.3267	701	1680	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	80.3223	702	1680	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	80.194	743	1680	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	80.1588	767	1680	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	79.9077	634	1680	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	79.8123	612	1680	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	79.7057	579	1680	95	below_threshold
Ciceribacter lividus	strain=DSM 25528	GCA_003337715.1	1197950	1197950	type	True	79.6168	560	1680	95	below_threshold
Neorhizobium vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	79.559	660	1680	95	below_threshold
Ciceribacter thiooxidans	strain=F43B	GCA_014126615.1	1969821	1969821	type	True	79.4552	556	1680	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	79.4028	643	1680	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	79.3433	628	1680	95	below_threshold
Agrobacterium rhizogenes	strain=NBRC 13257	GCA_000696095.1	359	359	type	True	79.314	623	1680	95	below_threshold
Rhizobium etli	strain=CFN 42	GCA_000092045.1	29449	29449	suspected-type	True	79.1434	605	1680	95	below_threshold
Rhizobium wuzhouense	strain=W44	GCA_003205195.1	1986026	1986026	type	True	79.108	557	1680	95	below_threshold
Sinorhizobium fredii	strain=USDA 205	GCA_001461695.1	380	380	type	True	79.0691	588	1680	95	below_threshold
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	79.0519	546	1680	95	below_threshold
Agrobacterium salinitolerans	strain=YIC 5082	GCA_002008225.1	1183413	1183413	type	True	78.977	593	1680	95	below_threshold
Rhizobium wenxiniae	strain=DSM 100734	GCA_014201355.1	1737357	1737357	type	True	78.8632	573	1680	95	below_threshold
Rhizobium wenxiniae	strain=CGMCC 1.15279	GCA_014641515.1	1737357	1737357	type	True	78.8515	570	1680	95	below_threshold
Neorhizobium huautlense	strain=DSM 21817	GCA_002968575.1	67774	67774	type	True	78.814	494	1680	95	below_threshold
Martelella mediterranea	strain=DSM 17316	GCA_000376125.1	293089	293089	type	True	78.6237	465	1680	95	below_threshold
Martelella mediterranea	strain=MACL11	GCA_002043005.1	293089	293089	type	True	78.6071	468	1680	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:47,737] [INFO] DFAST Taxonomy check result was written to GCF_026552795.1_ASM2655279v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:47,738] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:47,738] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:47,738] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgccae0094-04c6-4b5d-a0fa-b9192d696b95/dqc_reference/checkm_data
[2024-01-24 14:28:47,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:47,791] [INFO] Task started: CheckM
[2024-01-24 14:28:47,791] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026552795.1_ASM2655279v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026552795.1_ASM2655279v1_genomic.fna/checkm_input GCF_026552795.1_ASM2655279v1_genomic.fna/checkm_result
[2024-01-24 14:29:34,392] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:34,394] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 12.50%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:34,418] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:34,418] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:34,418] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026552795.1_ASM2655279v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:34,419] [INFO] Task started: Blastn
[2024-01-24 14:29:34,419] [INFO] Running command: blastn -query GCF_026552795.1_ASM2655279v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccae0094-04c6-4b5d-a0fa-b9192d696b95/dqc_reference/reference_markers_gtdb.fasta -out GCF_026552795.1_ASM2655279v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:36,216] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:36,220] [INFO] Selected 27 target genomes.
[2024-01-24 14:29:36,221] [INFO] Target genome list was writen to GCF_026552795.1_ASM2655279v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:36,271] [INFO] Task started: fastANI
[2024-01-24 14:29:36,271] [INFO] Running command: fastANI --query /var/lib/cwl/stg856c9c8b-a403-4e4c-9cc5-bce6a6603a13/GCF_026552795.1_ASM2655279v1_genomic.fna.gz --refList GCF_026552795.1_ASM2655279v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026552795.1_ASM2655279v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:30:08,792] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:08,847] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:30:08,847] [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	82.7065	906	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_B	95.0	98.16	98.16	0.88	0.88	2	-
GCF_004341885.1	s__Shinella granuli	80.2026	743	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Shinella	95.0	98.18	98.18	0.91	0.91	2	-
GCF_003122325.1	s__Rhizobium album	80.131	663	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177415.1	s__Neorhizobium oryzae_A	80.0299	708	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002600635.1	s__Allorhizobium sp002600635	79.9378	688	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927355.1	s__Allorhizobium sp012927355	79.7278	650	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004135.1	s__Rhizobium_A straminoryzae	79.6898	621	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium_A	95.0	98.62	98.62	0.94	0.94	2	-
GCF_000282095.2	s__Neorhizobium sp000282095	79.672	683	1680	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	79.6504	665	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	97.95	97.84	0.92	0.90	4	-
GCF_900155885.1	s__RU20A sp900155885	79.649	579	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RU20A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195095.1	s__Rhizobium sp014195095	79.6423	704	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900473245.1	s__Allorhizobium sp900473245	79.6248	625	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	98.81	98.34	0.95	0.93	20	-
GCF_001651875.1	s__Sinorhizobium saheli	79.5646	581	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	99.97	99.97	0.96	0.96	2	-
GCA_900466005.1	s__Allorhizobium sp900466005	79.5402	584	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	99.03	99.00	0.93	0.93	3	-
GCF_002940685.1	s__Ensifer adhaerens_E	79.4903	616	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014126615.1	s__Allorhizobium thiooxidans	79.4711	553	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005205.3	s__Agrobacterium rhizogenes_A	79.4304	611	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	98.60	97.88	0.94	0.88	11	-
GCF_003425685.1	s__Neorhizobium sp003425685	79.4164	659	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001662075.1	s__Rhizobium bangladeshense_B	79.3403	609	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000696095.1	s__Rhizobium rhizogenes	79.2859	628	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.11	97.39	0.91	0.86	92	-
GCF_013322215.1	s__Rhizobium rhizogenes_D	79.2358	575	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014197145.1	s__Gellertiella hungarica	79.1202	521	1680	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	79.0741	542	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002008225.1	s__Agrobacterium salinitolerans	78.9779	593	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Agrobacterium	95.0	97.86	95.71	0.92	0.87	11	-
GCF_014201355.1	s__Neorhizobium wenxiniae	78.8491	575	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.63	97.27	0.93	0.87	3	-
GCA_900472575.1	s__Neorhizobium cellulosilyticum	78.6779	580	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	97.58	97.10	0.87	0.85	7	-
GCF_002043005.1	s__Martelella mediterranea	78.6405	464	1680	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Martelella	95.0	97.32	95.96	0.90	0.83	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:30:08,848] [INFO] GTDB search result was written to GCF_026552795.1_ASM2655279v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:30:08,849] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:30:08,853] [INFO] DFAST_QC result json was written to GCF_026552795.1_ASM2655279v1_genomic.fna/dqc_result.json
[2024-01-24 14:30:08,854] [INFO] DFAST_QC completed!
[2024-01-24 14:30:08,854] [INFO] Total running time: 0h2m7s