[2024-01-24 14:55:26,935] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:26,940] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:26,940] [INFO] DQC Reference Directory: /var/lib/cwl/stg5688bbdc-398b-45cc-941b-4508fcd60306/dqc_reference
[2024-01-24 14:55:28,307] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:28,308] [INFO] Task started: Prodigal
[2024-01-24 14:55:28,308] [INFO] Running command: gunzip -c /var/lib/cwl/stg7034c35b-f073-4083-872a-a7cbc9327910/GCF_004053875.1_ASM405387v1_genomic.fna.gz | prodigal -d GCF_004053875.1_ASM405387v1_genomic.fna/cds.fna -a GCF_004053875.1_ASM405387v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:45,092] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:45,093] [INFO] Task started: HMMsearch
[2024-01-24 14:55:45,093] [INFO] Running command: hmmsearch --tblout GCF_004053875.1_ASM405387v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5688bbdc-398b-45cc-941b-4508fcd60306/dqc_reference/reference_markers.hmm GCF_004053875.1_ASM405387v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:45,378] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:45,379] [INFO] Found 6/6 markers.
[2024-01-24 14:55:45,434] [INFO] Query marker FASTA was written to GCF_004053875.1_ASM405387v1_genomic.fna/markers.fasta
[2024-01-24 14:55:45,435] [INFO] Task started: Blastn
[2024-01-24 14:55:45,435] [INFO] Running command: blastn -query GCF_004053875.1_ASM405387v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5688bbdc-398b-45cc-941b-4508fcd60306/dqc_reference/reference_markers.fasta -out GCF_004053875.1_ASM405387v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:46,462] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:46,467] [INFO] Selected 14 target genomes.
[2024-01-24 14:55:46,467] [INFO] Target genome list was writen to GCF_004053875.1_ASM405387v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:46,484] [INFO] Task started: fastANI
[2024-01-24 14:55:46,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg7034c35b-f073-4083-872a-a7cbc9327910/GCF_004053875.1_ASM405387v1_genomic.fna.gz --refList GCF_004053875.1_ASM405387v1_genomic.fna/target_genomes.txt --output GCF_004053875.1_ASM405387v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:02,610] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:02,611] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5688bbdc-398b-45cc-941b-4508fcd60306/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:02,611] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5688bbdc-398b-45cc-941b-4508fcd60306/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:02,623] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:56:02,624] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:02,624] [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 lilium	strain=24NR	GCA_004053875.1	2503024	2503024	type	True	100.0	1733	1734	95	conclusive
Neorhizobium vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	80.6382	843	1734	95	below_threshold
Rhizobium deserti	strain=SPY-1	GCA_004358025.1	2547961	2547961	type	True	80.6329	856	1734	95	below_threshold
Neorhizobium galegae	strain=HAMBI 540	GCA_000731315.1	399	399	suspected-type	True	80.5529	871	1734	95	below_threshold
Rhizobium populisoli	strain=XQZ8	GCA_019430945.1	2859785	2859785	type	True	80.3839	855	1734	95	below_threshold
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	80.073	764	1734	95	below_threshold
Rhizobium petrolearium	strain=DSM 26482	GCA_017873175.1	515361	515361	type	True	80.0451	768	1734	95	below_threshold
Neorhizobium huautlense	strain=DSM 21817	GCA_002968575.1	67774	67774	type	True	79.8579	717	1734	95	below_threshold
Rhizobium wenxiniae	strain=CGMCC 1.15279	GCA_014641515.1	1737357	1737357	type	True	79.7943	714	1734	95	below_threshold
Rhizobium wenxiniae	strain=DSM 100734	GCA_014201355.1	1737357	1737357	type	True	79.7458	726	1734	95	below_threshold
Rhizobium smilacinae	strain=PTYR-5	GCA_006335145.1	1395944	1395944	type	True	79.6315	764	1734	95	below_threshold
Rhizobium pseudoryzae	strain=DSM 19479	GCA_011046245.1	379684	379684	type	True	79.5189	660	1734	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	78.6228	498	1734	95	below_threshold
Rhizobium skierniewicense	strain=Ch11	GCA_023757665.1	984260	984260	type	True	78.1272	386	1734	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:02,625] [INFO] DFAST Taxonomy check result was written to GCF_004053875.1_ASM405387v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:02,626] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:02,626] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:02,626] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5688bbdc-398b-45cc-941b-4508fcd60306/dqc_reference/checkm_data
[2024-01-24 14:56:02,628] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:02,676] [INFO] Task started: CheckM
[2024-01-24 14:56:02,676] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004053875.1_ASM405387v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004053875.1_ASM405387v1_genomic.fna/checkm_input GCF_004053875.1_ASM405387v1_genomic.fna/checkm_result
[2024-01-24 14:56:48,905] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:48,906] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:48,926] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:48,926] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:48,927] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004053875.1_ASM405387v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:48,927] [INFO] Task started: Blastn
[2024-01-24 14:56:48,927] [INFO] Running command: blastn -query GCF_004053875.1_ASM405387v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5688bbdc-398b-45cc-941b-4508fcd60306/dqc_reference/reference_markers_gtdb.fasta -out GCF_004053875.1_ASM405387v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:51,039] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:51,043] [INFO] Selected 18 target genomes.
[2024-01-24 14:56:51,043] [INFO] Target genome list was writen to GCF_004053875.1_ASM405387v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:51,061] [INFO] Task started: fastANI
[2024-01-24 14:56:51,061] [INFO] Running command: fastANI --query /var/lib/cwl/stg7034c35b-f073-4083-872a-a7cbc9327910/GCF_004053875.1_ASM405387v1_genomic.fna.gz --refList GCF_004053875.1_ASM405387v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004053875.1_ASM405387v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:12,723] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:12,738] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:12,739] [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_004053875.1	s__Neorhizobium sp004053875	100.0	1733	1734	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_900469345.1	s__Neorhizobium sp900469345	82.6858	1073	1734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900472675.1	s__Neorhizobium sp900472675	82.3046	1036	1734	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	80.8587	877	1734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	97.95	97.84	0.92	0.90	4	-
GCF_000282095.2	s__Neorhizobium sp000282095	80.822	867	1734	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	80.8018	868	1734	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	80.7438	862	1734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829835.1	s__Neorhizobium sp002431175	80.6771	926	1734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	95.71	95.71	0.88	0.88	2	-
GCF_000732195.1	s__Neorhizobium vignae	80.6454	842	1734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358025.1	s__Neorhizobium deserti	80.6404	855	1734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000731315.1	s__Neorhizobium galegae	80.5491	873	1734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	97.31	95.05	0.87	0.81	4	-
GCA_902167985.1	s__Neorhizobium sp902167985	80.1666	792	1734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873175.1	s__Neorhizobium petrolearium	80.045	768	1734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	95.77	95.77	0.89	0.89	2	-
GCF_003491345.1	s__Neorhizobium sp003491345	79.9809	712	1734	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	79.9463	735	1734	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	79.854	718	1734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.14	97.99	0.92	0.90	5	-
GCF_006335145.1	s__Neorhizobium smilacinae	79.6248	765	1734	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002500765.1	s__Neorhizobium sp002500765	79.5718	590	1734	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 14:57:12,740] [INFO] GTDB search result was written to GCF_004053875.1_ASM405387v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:12,741] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:12,745] [INFO] DFAST_QC result json was written to GCF_004053875.1_ASM405387v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:12,745] [INFO] DFAST_QC completed!
[2024-01-24 14:57:12,745] [INFO] Total running time: 0h1m46s