[2023-06-27 11:40:17,712] [INFO] DFAST_QC pipeline started.
[2023-06-27 11:40:17,715] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 11:40:17,715] [INFO] DQC Reference Directory: /var/lib/cwl/stg9544b616-3f89-481f-aef6-d0c240a69076/dqc_reference
[2023-06-27 11:40:19,067] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 11:40:19,068] [INFO] Task started: Prodigal
[2023-06-27 11:40:19,069] [INFO] Running command: gunzip -c /var/lib/cwl/stgc371dfc1-0895-41e4-a9e4-22c19362ba4b/GCA_026399895.1_ASM2639989v1_genomic.fna.gz | prodigal -d GCA_026399895.1_ASM2639989v1_genomic.fna/cds.fna -a GCA_026399895.1_ASM2639989v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 11:40:27,310] [INFO] Task succeeded: Prodigal
[2023-06-27 11:40:27,310] [INFO] Task started: HMMsearch
[2023-06-27 11:40:27,310] [INFO] Running command: hmmsearch --tblout GCA_026399895.1_ASM2639989v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9544b616-3f89-481f-aef6-d0c240a69076/dqc_reference/reference_markers.hmm GCA_026399895.1_ASM2639989v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 11:40:27,590] [INFO] Task succeeded: HMMsearch
[2023-06-27 11:40:27,592] [INFO] Found 6/6 markers.
[2023-06-27 11:40:27,653] [INFO] Query marker FASTA was written to GCA_026399895.1_ASM2639989v1_genomic.fna/markers.fasta
[2023-06-27 11:40:27,653] [INFO] Task started: Blastn
[2023-06-27 11:40:27,654] [INFO] Running command: blastn -query GCA_026399895.1_ASM2639989v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9544b616-3f89-481f-aef6-d0c240a69076/dqc_reference/reference_markers.fasta -out GCA_026399895.1_ASM2639989v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:40:28,464] [INFO] Task succeeded: Blastn
[2023-06-27 11:40:28,469] [INFO] Selected 27 target genomes.
[2023-06-27 11:40:28,469] [INFO] Target genome list was writen to GCA_026399895.1_ASM2639989v1_genomic.fna/target_genomes.txt
[2023-06-27 11:40:28,473] [INFO] Task started: fastANI
[2023-06-27 11:40:28,473] [INFO] Running command: fastANI --query /var/lib/cwl/stgc371dfc1-0895-41e4-a9e4-22c19362ba4b/GCA_026399895.1_ASM2639989v1_genomic.fna.gz --refList GCA_026399895.1_ASM2639989v1_genomic.fna/target_genomes.txt --output GCA_026399895.1_ASM2639989v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 11:40:52,243] [INFO] Task succeeded: fastANI
[2023-06-27 11:40:52,243] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9544b616-3f89-481f-aef6-d0c240a69076/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 11:40:52,244] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9544b616-3f89-481f-aef6-d0c240a69076/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 11:40:52,263] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 11:40:52,264] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 11:40:52,264] [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
Oxalicibacterium flavum	strain=CCM 7086	GCA_014635065.1	179467	179467	type	True	77.3194	123	877	95	below_threshold
Oxalicibacterium solurbis	strain=CCM 7664	GCA_014635845.1	69280	69280	type	True	77.1974	122	877	95	below_threshold
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	77.0842	136	877	95	below_threshold
Herbaspirillum hiltneri	strain=N3	GCA_001267925.1	341045	341045	type	True	77.0387	123	877	95	below_threshold
Herbaspirillum rhizosphaerae	strain=UMS-37	GCA_001189965.1	346179	346179	type	True	77.0333	114	877	95	below_threshold
Noviherbaspirillum humi	strain=U15	GCA_900188095.1	1688639	1688639	type	True	77.022	123	877	95	below_threshold
Noviherbaspirillum massiliense	strain=JC206	GCA_000312045.1	1465823	1465823	type	True	77.0103	113	877	95	below_threshold
Noviherbaspirillum autotrophicum	strain=TSA66	GCA_000818395.1	709839	709839	type	True	76.9579	121	877	95	below_threshold
Massilia polaris	strain=RP-1-19	GCA_012927275.1	2728846	2728846	type	True	76.9383	97	877	95	below_threshold
Collimonas humicola	strain=RLT1W51	GCA_018304945.1	2825886	2825886	type	True	76.9342	111	877	95	below_threshold
Collimonas fungivorans	strain=Ter6	GCA_001584145.1	158899	158899	type	True	76.9324	114	877	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	76.9119	109	877	95	below_threshold
Collimonas pratensis	strain=Ter91	GCA_001584185.1	279113	279113	type	True	76.9114	109	877	95	below_threshold
Massilia arenosa	strain=MC02	GCA_004614185.1	2561931	2561931	type	True	76.8745	90	877	95	below_threshold
Pseudoduganella plicata	strain=DSM 17505	GCA_004421005.1	321984	321984	type	True	76.8465	88	877	95	below_threshold
Massilia yuzhufengensis	strain=CGMCC 1.12041	GCA_900112225.1	1164594	1164594	type	True	76.8223	99	877	95	below_threshold
Collimonas silvisoli	strain=RXD178	GCA_018305005.1	2825884	2825884	type	True	76.7757	94	877	95	below_threshold
Pseudoduganella armeniaca	strain=ZMN-3	GCA_003028855.1	2072590	2072590	type	True	76.7334	98	877	95	below_threshold
Pseudoduganella violacea	strain=CECT 8897	GCA_014191875.1	1715466	1715466	type	True	76.7215	85	877	95	below_threshold
Pseudoduganella guangdongensis	strain=DS3	GCA_009857475.1	2692179	2692179	type	True	76.6929	87	877	95	below_threshold
Herbaspirillum autotrophicum	strain=IAM 14942	GCA_001189915.1	180195	180195	type	True	76.6319	111	877	95	below_threshold
Pseudoduganella plicata	strain=KCTC 12344	GCA_014651435.1	321984	321984	type	True	76.6208	88	877	95	below_threshold
Undibacterium terreum	strain=CGMCC 1.10998	GCA_014636315.1	1224302	1224302	type	True	76.4633	70	877	95	below_threshold
Herminiimonas fonticola	strain=DSM 18555	GCA_004361795.1	303380	303380	type	True	76.4527	87	877	95	below_threshold
Undibacterium hunanense	strain=CY18W	GCA_014284335.1	2762292	2762292	type	True	76.1982	60	877	95	below_threshold
Burkholderia anthina	strain=DSM 16086	GCA_016836725.1	179879	179879	suspected-type	True	76.1427	72	877	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 11:40:52,266] [INFO] DFAST Taxonomy check result was written to GCA_026399895.1_ASM2639989v1_genomic.fna/tc_result.tsv
[2023-06-27 11:40:52,267] [INFO] ===== Taxonomy check completed =====
[2023-06-27 11:40:52,267] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 11:40:52,267] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9544b616-3f89-481f-aef6-d0c240a69076/dqc_reference/checkm_data
[2023-06-27 11:40:52,268] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 11:40:52,304] [INFO] Task started: CheckM
[2023-06-27 11:40:52,304] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026399895.1_ASM2639989v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026399895.1_ASM2639989v1_genomic.fna/checkm_input GCA_026399895.1_ASM2639989v1_genomic.fna/checkm_result
[2023-06-27 11:41:21,930] [INFO] Task succeeded: CheckM
[2023-06-27 11:41:21,931] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 11:41:21,954] [INFO] ===== Completeness check finished =====
[2023-06-27 11:41:21,954] [INFO] ===== Start GTDB Search =====
[2023-06-27 11:41:21,955] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026399895.1_ASM2639989v1_genomic.fna/markers.fasta)
[2023-06-27 11:41:21,955] [INFO] Task started: Blastn
[2023-06-27 11:41:21,955] [INFO] Running command: blastn -query GCA_026399895.1_ASM2639989v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9544b616-3f89-481f-aef6-d0c240a69076/dqc_reference/reference_markers_gtdb.fasta -out GCA_026399895.1_ASM2639989v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 11:41:23,233] [INFO] Task succeeded: Blastn
[2023-06-27 11:41:23,238] [INFO] Selected 23 target genomes.
[2023-06-27 11:41:23,238] [INFO] Target genome list was writen to GCA_026399895.1_ASM2639989v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 11:41:23,275] [INFO] Task started: fastANI
[2023-06-27 11:41:23,275] [INFO] Running command: fastANI --query /var/lib/cwl/stgc371dfc1-0895-41e4-a9e4-22c19362ba4b/GCA_026399895.1_ASM2639989v1_genomic.fna.gz --refList GCA_026399895.1_ASM2639989v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026399895.1_ASM2639989v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 11:41:38,765] [INFO] Task succeeded: fastANI
[2023-06-27 11:41:38,782] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 11:41:38,782] [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_018882935.1	s__SYFN01 sp018882935	81.7229	527	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SYFN01	95.0	98.35	98.35	0.89	0.89	2	-
GCA_016868055.1	s__SYFN01 sp016868055	81.627	498	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SYFN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010024875.1	s__SYFN01 sp010024875	77.4683	183	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SYFN01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017814915.1	s__Herbaspirillum sp017814915	77.3986	125	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903846425.1	s__SYFN01 sp903846425	77.3181	84	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SYFN01	95.0	98.24	98.19	0.76	0.73	3	-
GCA_016467405.1	s__Lacisediminimonas sp016467405	77.2639	131	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lacisediminimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590835.1	s__Paucimonas sp003590835	77.1985	135	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900299005.1	s__SYFN01 sp900299005	77.0664	166	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SYFN01	95.0	99.47	99.47	0.89	0.89	2	-
GCA_903872555.1	s__SYFN01 sp903872555	77.0598	148	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SYFN01	95.0	98.62	98.25	0.82	0.81	3	-
GCF_001267925.1	s__Herbaspirillum hiltneri	77.0387	123	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	97.60	97.60	0.89	0.89	2	-
GCF_900188095.1	s__Noviherbaspirillum humi	77.0197	124	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000312045.1	s__Noviherbaspirillum massiliense	77.0103	113	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCA_005800405.1	s__SYFN01 sp005800405	76.9595	94	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SYFN01	95.0	99.76	99.76	0.86	0.86	2	-
GCF_002564105.1	s__Collimonas sp002564105	76.9428	108	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001770855.1	s__MESE01 sp001770855	76.9322	88	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__MESE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192645.1	s__Herbaspirillum sp014192645	76.9256	82	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018305005.1	s__Collimonas sp018305005	76.7757	94	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013376005.1	s__Duganella sp013376005	76.7456	104	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014284335.1	s__Undibacterium sp014284335	76.1982	60	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Undibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002735705.1	s__Janthinobacterium sp002735705	76.1975	92	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012927625.1	s__AVCC01 sp012927625	76.1194	65	877	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__AVCC01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 11:41:38,785] [INFO] GTDB search result was written to GCA_026399895.1_ASM2639989v1_genomic.fna/result_gtdb.tsv
[2023-06-27 11:41:38,786] [INFO] ===== GTDB Search completed =====
[2023-06-27 11:41:38,836] [INFO] DFAST_QC result json was written to GCA_026399895.1_ASM2639989v1_genomic.fna/dqc_result.json
[2023-06-27 11:41:38,836] [INFO] DFAST_QC completed!
[2023-06-27 11:41:38,836] [INFO] Total running time: 0h1m21s