[2023-06-17 13:27:55,920] [INFO] DFAST_QC pipeline started.
[2023-06-17 13:27:55,923] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 13:27:55,923] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e7c39e0-891c-48d2-bc18-2c7c7e9a9c65/dqc_reference
[2023-06-17 13:27:57,212] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 13:27:57,213] [INFO] Task started: Prodigal
[2023-06-17 13:27:57,213] [INFO] Running command: gunzip -c /var/lib/cwl/stgbabed7c0-c636-4e74-8544-70df40ac3e4c/GCA_028290185.1_ASM2829018v1_genomic.fna.gz | prodigal -d GCA_028290185.1_ASM2829018v1_genomic.fna/cds.fna -a GCA_028290185.1_ASM2829018v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 13:28:05,496] [INFO] Task succeeded: Prodigal
[2023-06-17 13:28:05,497] [INFO] Task started: HMMsearch
[2023-06-17 13:28:05,497] [INFO] Running command: hmmsearch --tblout GCA_028290185.1_ASM2829018v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e7c39e0-891c-48d2-bc18-2c7c7e9a9c65/dqc_reference/reference_markers.hmm GCA_028290185.1_ASM2829018v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 13:28:05,727] [INFO] Task succeeded: HMMsearch
[2023-06-17 13:28:05,728] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbabed7c0-c636-4e74-8544-70df40ac3e4c/GCA_028290185.1_ASM2829018v1_genomic.fna.gz]
[2023-06-17 13:28:05,766] [INFO] Query marker FASTA was written to GCA_028290185.1_ASM2829018v1_genomic.fna/markers.fasta
[2023-06-17 13:28:05,767] [INFO] Task started: Blastn
[2023-06-17 13:28:05,767] [INFO] Running command: blastn -query GCA_028290185.1_ASM2829018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e7c39e0-891c-48d2-bc18-2c7c7e9a9c65/dqc_reference/reference_markers.fasta -out GCA_028290185.1_ASM2829018v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 13:28:06,489] [INFO] Task succeeded: Blastn
[2023-06-17 13:28:06,493] [INFO] Selected 17 target genomes.
[2023-06-17 13:28:06,493] [INFO] Target genome list was writen to GCA_028290185.1_ASM2829018v1_genomic.fna/target_genomes.txt
[2023-06-17 13:28:06,502] [INFO] Task started: fastANI
[2023-06-17 13:28:06,503] [INFO] Running command: fastANI --query /var/lib/cwl/stgbabed7c0-c636-4e74-8544-70df40ac3e4c/GCA_028290185.1_ASM2829018v1_genomic.fna.gz --refList GCA_028290185.1_ASM2829018v1_genomic.fna/target_genomes.txt --output GCA_028290185.1_ASM2829018v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 13:28:26,603] [INFO] Task succeeded: fastANI
[2023-06-17 13:28:26,604] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e7c39e0-891c-48d2-bc18-2c7c7e9a9c65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 13:28:26,604] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e7c39e0-891c-48d2-bc18-2c7c7e9a9c65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 13:28:26,624] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 13:28:26,624] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 13:28:26,624] [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
Rhodopseudomonas rhenobacensis	strain=DSM 12706	GCA_014203125.1	87461	87461	type	True	81.1574	435	824	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	81.07	481	824	95	below_threshold
Bradyrhizobium pachyrhizi	strain=PAC 48	GCA_001189245.1	280333	280333	type	True	80.5152	506	824	95	below_threshold
Bradyrhizobium septentrionale	strain=1S1	GCA_011516645.4	1404411	1404411	type	True	80.4875	530	824	95	below_threshold
Bradyrhizobium tropiciagri	strain=SEMIA 6148	GCA_001189845.1	312253	312253	type	True	80.4518	519	824	95	below_threshold
Bradyrhizobium lablabi	strain=CCBAU 23086	GCA_001440475.1	722472	722472	suspected-type	True	80.3349	516	824	95	below_threshold
Bradyrhizobium paxllaeri	strain=LMTR 21	GCA_001693515.2	190148	190148	type	True	80.3199	507	824	95	below_threshold
Bradyrhizobium jicamae	strain=PAC68	GCA_001440395.1	280332	280332	type	True	80.2892	503	824	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	80.2843	493	824	95	below_threshold
Rhodopseudomonas pseudopalustris	strain=DSM 123	GCA_900110435.1	1513892	1513892	type	True	80.2327	424	824	95	below_threshold
Bradyrhizobium valentinum	strain=LmjM3	GCA_001440405.1	1518501	1518501	type	True	80.1586	495	824	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	80.1289	487	824	95	below_threshold
Bradyrhizobium macuxiense	strain=BR 10303	GCA_001542415.1	1755647	1755647	type	True	80.1164	473	824	95	below_threshold
Rhodopseudomonas pentothenatexigens	strain=JA575	GCA_003385925.1	999699	999699	type	True	80.0323	412	824	95	below_threshold
Rhodopseudomonas pentothenatexigens	strain=JA575	GCA_900218015.1	999699	999699	type	True	80.0122	413	824	95	below_threshold
Rhodopseudomonas faecalis	strain=JCM 11668	GCA_003217325.1	99655	99655	type	True	79.3402	331	824	95	below_threshold
Afipia clevelandensis	strain=ATCC 49720	GCA_000336555.1	1034	1034	type	True	78.9225	343	824	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 13:28:26,626] [INFO] DFAST Taxonomy check result was written to GCA_028290185.1_ASM2829018v1_genomic.fna/tc_result.tsv
[2023-06-17 13:28:26,627] [INFO] ===== Taxonomy check completed =====
[2023-06-17 13:28:26,627] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 13:28:26,627] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e7c39e0-891c-48d2-bc18-2c7c7e9a9c65/dqc_reference/checkm_data
[2023-06-17 13:28:26,629] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 13:28:26,670] [INFO] Task started: CheckM
[2023-06-17 13:28:26,670] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028290185.1_ASM2829018v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028290185.1_ASM2829018v1_genomic.fna/checkm_input GCA_028290185.1_ASM2829018v1_genomic.fna/checkm_result
[2023-06-17 13:28:55,666] [INFO] Task succeeded: CheckM
[2023-06-17 13:28:55,667] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 13:28:55,692] [INFO] ===== Completeness check finished =====
[2023-06-17 13:28:55,692] [INFO] ===== Start GTDB Search =====
[2023-06-17 13:28:55,693] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028290185.1_ASM2829018v1_genomic.fna/markers.fasta)
[2023-06-17 13:28:55,693] [INFO] Task started: Blastn
[2023-06-17 13:28:55,693] [INFO] Running command: blastn -query GCA_028290185.1_ASM2829018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6e7c39e0-891c-48d2-bc18-2c7c7e9a9c65/dqc_reference/reference_markers_gtdb.fasta -out GCA_028290185.1_ASM2829018v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 13:28:56,786] [INFO] Task succeeded: Blastn
[2023-06-17 13:28:56,791] [INFO] Selected 13 target genomes.
[2023-06-17 13:28:56,791] [INFO] Target genome list was writen to GCA_028290185.1_ASM2829018v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 13:28:56,801] [INFO] Task started: fastANI
[2023-06-17 13:28:56,801] [INFO] Running command: fastANI --query /var/lib/cwl/stgbabed7c0-c636-4e74-8544-70df40ac3e4c/GCA_028290185.1_ASM2829018v1_genomic.fna.gz --refList GCA_028290185.1_ASM2829018v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028290185.1_ASM2829018v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 13:29:10,698] [INFO] Task succeeded: fastANI
[2023-06-17 13:29:10,713] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 13:29:10,713] [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
GCA_014377915.1	s__Tardiphaga sp014377915	83.5226	559	824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007018905.1	s__Tardiphaga sp007018905	83.4186	563	824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga	95.0	99.57	99.15	0.93	0.92	5	-
GCF_003096755.1	s__Tardiphaga sp003096755	82.493	626	824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001618955.1	s__Tardiphaga robiniae_A	82.4215	614	824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013359755.1	s__Tardiphaga robiniae	82.3937	605	824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga	95.0	96.54	96.42	0.88	0.87	5	-
GCF_900114605.1	s__Tardiphaga sp900114605	82.0744	613	824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga	95.0	98.23	98.23	0.94	0.94	2	-
GCF_008329525.1	s__Tardiphaga sp008329525	82.0276	604	824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203125.1	s__Rhodopseudomonas rhenobacensis	81.1886	433	824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000935205.1	s__Rhodopseudomonas palustris_E	80.9377	410	824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013745.1	s__Rhodopseudomonas palustris_D	80.8275	431	824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004173095.1	s__Tardiphaga sp004173095	80.4335	414	824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542415.1	s__Bradyrhizobium macuxiense	80.1076	475	824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282615.1	s__Bradyrhizobium sp000282615	80.1001	484	824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 13:29:10,715] [INFO] GTDB search result was written to GCA_028290185.1_ASM2829018v1_genomic.fna/result_gtdb.tsv
[2023-06-17 13:29:10,716] [INFO] ===== GTDB Search completed =====
[2023-06-17 13:29:10,720] [INFO] DFAST_QC result json was written to GCA_028290185.1_ASM2829018v1_genomic.fna/dqc_result.json
[2023-06-17 13:29:10,720] [INFO] DFAST_QC completed!
[2023-06-17 13:29:10,720] [INFO] Total running time: 0h1m15s