[2024-01-24 14:06:29,833] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:29,835] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:29,835] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ad48a5e-d652-4c7a-8a36-e6b5414882f5/dqc_reference
[2024-01-24 14:06:31,226] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:31,227] [INFO] Task started: Prodigal
[2024-01-24 14:06:31,227] [INFO] Running command: gunzip -c /var/lib/cwl/stg1076b8b9-fa3c-449d-b941-969a93aab4c5/GCF_017873175.1_ASM1787317v1_genomic.fna.gz | prodigal -d GCF_017873175.1_ASM1787317v1_genomic.fna/cds.fna -a GCF_017873175.1_ASM1787317v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:52,275] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:52,275] [INFO] Task started: HMMsearch
[2024-01-24 14:06:52,275] [INFO] Running command: hmmsearch --tblout GCF_017873175.1_ASM1787317v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ad48a5e-d652-4c7a-8a36-e6b5414882f5/dqc_reference/reference_markers.hmm GCF_017873175.1_ASM1787317v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:52,612] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:52,614] [INFO] Found 6/6 markers.
[2024-01-24 14:06:52,764] [INFO] Query marker FASTA was written to GCF_017873175.1_ASM1787317v1_genomic.fna/markers.fasta
[2024-01-24 14:06:52,765] [INFO] Task started: Blastn
[2024-01-24 14:06:52,765] [INFO] Running command: blastn -query GCF_017873175.1_ASM1787317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ad48a5e-d652-4c7a-8a36-e6b5414882f5/dqc_reference/reference_markers.fasta -out GCF_017873175.1_ASM1787317v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:53,776] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:53,779] [INFO] Selected 12 target genomes.
[2024-01-24 14:06:53,780] [INFO] Target genome list was writen to GCF_017873175.1_ASM1787317v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:53,807] [INFO] Task started: fastANI
[2024-01-24 14:06:53,807] [INFO] Running command: fastANI --query /var/lib/cwl/stg1076b8b9-fa3c-449d-b941-969a93aab4c5/GCF_017873175.1_ASM1787317v1_genomic.fna.gz --refList GCF_017873175.1_ASM1787317v1_genomic.fna/target_genomes.txt --output GCF_017873175.1_ASM1787317v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:09,335] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:09,335] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ad48a5e-d652-4c7a-8a36-e6b5414882f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:09,336] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ad48a5e-d652-4c7a-8a36-e6b5414882f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:09,349] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:07:09,350] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:09,350] [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 petrolearium	strain=DSM 26482	GCA_017873175.1	515361	515361	type	True	100.0	2293	2294	95	conclusive
Neorhizobium vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	82.9597	1272	2294	95	below_threshold
Neorhizobium galegae	strain=HAMBI 540	GCA_000731315.1	399	399	suspected-type	True	82.7766	1283	2294	95	below_threshold
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	82.1132	1115	2294	95	below_threshold
Rhizobium populisoli	strain=XQZ8	GCA_019430945.1	2859785	2859785	type	True	81.8289	1223	2294	95	below_threshold
Neorhizobium huautlense	strain=DSM 21817	GCA_002968575.1	67774	67774	type	True	81.7849	1125	2294	95	below_threshold
Neorhizobium lilium	strain=24NR	GCA_004053875.1	2503024	2503024	type	True	79.8661	784	2294	95	below_threshold
Rhizobium smilacinae	strain=PTYR-5	GCA_006335145.1	1395944	1395944	type	True	79.8303	824	2294	95	below_threshold
Pseudorhizobium banfieldiae	strain=NT-26	GCA_000967425.1	1125847	1125847	type	True	79.5891	679	2294	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	79.5571	750	2294	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	79.2482	639	2294	95	below_threshold
Ciceribacter thiooxidans	strain=F43B	GCA_014126615.1	1969821	1969821	type	True	79.1493	624	2294	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:09,352] [INFO] DFAST Taxonomy check result was written to GCF_017873175.1_ASM1787317v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:09,352] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:09,353] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:09,353] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ad48a5e-d652-4c7a-8a36-e6b5414882f5/dqc_reference/checkm_data
[2024-01-24 14:07:09,354] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:09,416] [INFO] Task started: CheckM
[2024-01-24 14:07:09,417] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017873175.1_ASM1787317v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017873175.1_ASM1787317v1_genomic.fna/checkm_input GCF_017873175.1_ASM1787317v1_genomic.fna/checkm_result
[2024-01-24 14:08:08,112] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:08,113] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:08,130] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:08,130] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:08,131] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017873175.1_ASM1787317v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:08,131] [INFO] Task started: Blastn
[2024-01-24 14:08:08,131] [INFO] Running command: blastn -query GCF_017873175.1_ASM1787317v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ad48a5e-d652-4c7a-8a36-e6b5414882f5/dqc_reference/reference_markers_gtdb.fasta -out GCF_017873175.1_ASM1787317v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:10,202] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:10,205] [INFO] Selected 14 target genomes.
[2024-01-24 14:08:10,205] [INFO] Target genome list was writen to GCF_017873175.1_ASM1787317v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:10,214] [INFO] Task started: fastANI
[2024-01-24 14:08:10,214] [INFO] Running command: fastANI --query /var/lib/cwl/stg1076b8b9-fa3c-449d-b941-969a93aab4c5/GCF_017873175.1_ASM1787317v1_genomic.fna.gz --refList GCF_017873175.1_ASM1787317v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017873175.1_ASM1787317v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:31,377] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:31,389] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:31,390] [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_017873175.1	s__Neorhizobium petrolearium	100.0	2293	2294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	95.77	95.77	0.89	0.89	2	conclusive
GCF_900177415.1	s__Neorhizobium oryzae_A	84.8236	1318	2294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282095.2	s__Neorhizobium sp000282095	83.1015	1291	2294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003425685.1	s__Neorhizobium sp003425685	83.0772	1381	2294	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	83.0332	1287	2294	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	83.0202	1255	2294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	97.95	97.84	0.92	0.90	4	-
GCA_900471605.1	s__Neorhizobium sp900471605	82.9843	1273	2294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.26	98.25	0.92	0.92	3	-
GCF_000732195.1	s__Neorhizobium vignae	82.9552	1273	2294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000985895.1	s__Neorhizobium galegae_B	82.942	1271	2294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.06	98.00	0.96	0.95	4	-
GCF_002968635.1	s__Neorhizobium alkalisoli	82.1199	1114	2294	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	81.9827	1086	2294	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	81.7831	1124	2294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	98.14	97.99	0.92	0.90	5	-
GCF_007829835.1	s__Neorhizobium sp002431175	80.596	970	2294	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	95.71	95.71	0.88	0.88	2	-
GCA_900469345.1	s__Neorhizobium sp900469345	79.9809	829	2294	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 14:08:31,391] [INFO] GTDB search result was written to GCF_017873175.1_ASM1787317v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:31,392] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:31,395] [INFO] DFAST_QC result json was written to GCF_017873175.1_ASM1787317v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:31,395] [INFO] DFAST_QC completed!
[2024-01-24 14:08:31,396] [INFO] Total running time: 0h2m2s