[2024-01-24 13:27:58,618] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:58,620] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:58,620] [INFO] DQC Reference Directory: /var/lib/cwl/stg3960240f-6218-4374-9c92-d209350d52fd/dqc_reference
[2024-01-24 13:27:59,860] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:59,861] [INFO] Task started: Prodigal
[2024-01-24 13:27:59,861] [INFO] Running command: gunzip -c /var/lib/cwl/stg4e20e3f4-2015-4976-be73-5b2e110e4866/GCF_014652875.1_ASM1465287v1_genomic.fna.gz | prodigal -d GCF_014652875.1_ASM1465287v1_genomic.fna/cds.fna -a GCF_014652875.1_ASM1465287v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:13,100] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:13,101] [INFO] Task started: HMMsearch
[2024-01-24 13:28:13,101] [INFO] Running command: hmmsearch --tblout GCF_014652875.1_ASM1465287v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3960240f-6218-4374-9c92-d209350d52fd/dqc_reference/reference_markers.hmm GCF_014652875.1_ASM1465287v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:13,401] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:13,403] [INFO] Found 6/6 markers.
[2024-01-24 13:28:13,456] [INFO] Query marker FASTA was written to GCF_014652875.1_ASM1465287v1_genomic.fna/markers.fasta
[2024-01-24 13:28:13,457] [INFO] Task started: Blastn
[2024-01-24 13:28:13,458] [INFO] Running command: blastn -query GCF_014652875.1_ASM1465287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3960240f-6218-4374-9c92-d209350d52fd/dqc_reference/reference_markers.fasta -out GCF_014652875.1_ASM1465287v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:14,536] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:14,539] [INFO] Selected 26 target genomes.
[2024-01-24 13:28:14,539] [INFO] Target genome list was writen to GCF_014652875.1_ASM1465287v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:14,562] [INFO] Task started: fastANI
[2024-01-24 13:28:14,562] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e20e3f4-2015-4976-be73-5b2e110e4866/GCF_014652875.1_ASM1465287v1_genomic.fna.gz --refList GCF_014652875.1_ASM1465287v1_genomic.fna/target_genomes.txt --output GCF_014652875.1_ASM1465287v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:43,023] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:43,023] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3960240f-6218-4374-9c92-d209350d52fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:43,024] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3960240f-6218-4374-9c92-d209350d52fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:43,043] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:28:43,044] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:28:43,044] [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
Aminobacter aganoensis	strain=DSM 7051	GCA_014206975.1	83264	83264	type	True	78.9512	471	1422	95	below_threshold
Mesorhizobium zhangyense	strain=CGMCC 1.15528	GCA_011045115.1	1776730	1776730	type	True	78.8866	496	1422	95	below_threshold
Aminobacter niigataensis	strain=DSM 7050	GCA_014200015.1	83265	83265	type	True	78.8156	488	1422	95	below_threshold
Aminobacter aminovorans	strain=NCTC10684	GCA_900445235.1	83263	83263	type	True	78.8006	472	1422	95	below_threshold
Mesorhizobium jarvisii	strain=LMG 28313	GCA_003601985.1	1777867	1777867	type	True	78.7873	481	1422	95	below_threshold
Aminobacter aminovorans	strain=DSM 7048	GCA_004341645.1	83263	83263	type	True	78.6906	460	1422	95	below_threshold
Mesorhizobium jarvisii	strain=ATCC 33669	GCA_013170785.1	1777867	1777867	type	True	78.6882	489	1422	95	below_threshold
Aminobacter ciceronei	strain=DSM 17455	GCA_014138635.1	150723	150723	type	True	78.6767	489	1422	95	below_threshold
Aminobacter ciceronei	strain=DSM 15910	GCA_014138625.1	150723	150723	type	True	78.6519	491	1422	95	below_threshold
Mesorhizobium sangaii	strain=DSM 100039	GCA_014207355.1	505389	505389	type	True	78.6163	446	1422	95	below_threshold
Mesorhizobium sophorae	strain=ICMP 19535	GCA_002270415.1	1300294	1300294	type	True	78.6114	451	1422	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	78.5794	483	1422	95	below_threshold
Mesorhizobium intechi	strain=BD68	GCA_002879535.2	537601	537601	type	True	78.5281	454	1422	95	below_threshold
Mesorhizobium japonicum	strain=MAFF 303099	GCA_000009625.1	2066070	2066070	type	True	78.5192	519	1422	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	78.4938	435	1422	95	below_threshold
Mesorhizobium qingshengii	strain=CGMCC 1.12097	GCA_900103325.1	1165689	1165689	type	True	78.425	464	1422	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	78.404	462	1422	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	78.4004	494	1422	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	78.105	417	1422	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	78.0998	417	1422	95	below_threshold
Shinella kummerowiae	strain=CCBAU 25048	GCA_009827055.1	417745	417745	type	True	77.9722	368	1422	95	below_threshold
Nitratireductor arenosus	strain=CAU 1489	GCA_009742725.1	2682096	2682096	type	True	77.7807	348	1422	95	below_threshold
Rhizobium rhizolycopersici	strain=DBTS2	GCA_013378445.1	2746702	2746702	type	True	77.6289	325	1422	95	below_threshold
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	77.5706	287	1422	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	76.9091	162	1422	95	below_threshold
Bradyrhizobium oligotrophicum	strain=S58	GCA_000344805.1	44255	44255	type	True	76.7633	227	1422	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:43,045] [INFO] DFAST Taxonomy check result was written to GCF_014652875.1_ASM1465287v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:43,046] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:43,046] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:43,046] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3960240f-6218-4374-9c92-d209350d52fd/dqc_reference/checkm_data
[2024-01-24 13:28:43,048] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:43,109] [INFO] Task started: CheckM
[2024-01-24 13:28:43,110] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652875.1_ASM1465287v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652875.1_ASM1465287v1_genomic.fna/checkm_input GCF_014652875.1_ASM1465287v1_genomic.fna/checkm_result
[2024-01-24 13:29:25,275] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:25,276] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:25,291] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:25,291] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:25,292] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652875.1_ASM1465287v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:25,292] [INFO] Task started: Blastn
[2024-01-24 13:29:25,293] [INFO] Running command: blastn -query GCF_014652875.1_ASM1465287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3960240f-6218-4374-9c92-d209350d52fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652875.1_ASM1465287v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:27,211] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:27,216] [INFO] Selected 13 target genomes.
[2024-01-24 13:29:27,216] [INFO] Target genome list was writen to GCF_014652875.1_ASM1465287v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:27,242] [INFO] Task started: fastANI
[2024-01-24 13:29:27,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e20e3f4-2015-4976-be73-5b2e110e4866/GCF_014652875.1_ASM1465287v1_genomic.fna.gz --refList GCF_014652875.1_ASM1465287v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652875.1_ASM1465287v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:41,718] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:41,734] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:41,735] [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_014652875.1	s__Corticibacterium populi	100.0	1422	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Corticibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002316345.1	s__Corticibacterium sp002316345	93.4697	1070	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Corticibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018457165.1	s__Corticibacterium sp018457165	85.6948	989	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Corticibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017813335.1	s__Tianweitania sediminis	79.782	619	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Tianweitania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000372965.1	s__Aminobacter sp000372965	79.014	472	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590645.1	s__Pseudaminobacter sp900116595	79.0103	490	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	98.40	97.54	0.93	0.88	4	-
GCF_014200015.1	s__Aminobacter niigataensis	78.8031	490	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.01	98.00	0.90	0.90	3	-
GCF_001686985.1	s__Mesorhizobium amorphae_B	78.6052	510	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0866	99.99	99.99	1.00	1.00	2	-
GCF_006440675.1	s__Mesorhizobium sp006440675	78.5801	494	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	97.39	95.73	0.91	0.84	9	-
GCA_018823835.1	s__RCIZ01 sp018823835	78.4934	437	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIZ01	95.0	99.96	99.89	0.99	0.96	11	-
GCF_013170825.1	s__Mesorhizobium sp013170825	78.4359	491	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	95.36	95.35	0.82	0.81	3	-
GCA_017306585.1	s__Mesorhizobium sp017306585	78.3464	447	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006442685.1	s__Mesorhizobium sp006442685	78.2699	469	1422	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.73	95.49	0.95	0.85	44	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:41,736] [INFO] GTDB search result was written to GCF_014652875.1_ASM1465287v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:41,736] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:41,740] [INFO] DFAST_QC result json was written to GCF_014652875.1_ASM1465287v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:41,741] [INFO] DFAST_QC completed!
[2024-01-24 13:29:41,741] [INFO] Total running time: 0h1m43s