[2023-06-29 15:27:05,461] [INFO] DFAST_QC pipeline started.
[2023-06-29 15:27:05,463] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 15:27:05,464] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0dc3b91-30c1-42d4-89cf-a3a33337f631/dqc_reference
[2023-06-29 15:27:06,786] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 15:27:06,787] [INFO] Task started: Prodigal
[2023-06-29 15:27:06,788] [INFO] Running command: gunzip -c /var/lib/cwl/stgbdc9d807-256c-4866-9b24-5b828bf2e35d/GCA_011526045.1_ASM1152604v1_genomic.fna.gz | prodigal -d GCA_011526045.1_ASM1152604v1_genomic.fna/cds.fna -a GCA_011526045.1_ASM1152604v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 15:27:17,790] [INFO] Task succeeded: Prodigal
[2023-06-29 15:27:17,790] [INFO] Task started: HMMsearch
[2023-06-29 15:27:17,791] [INFO] Running command: hmmsearch --tblout GCA_011526045.1_ASM1152604v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0dc3b91-30c1-42d4-89cf-a3a33337f631/dqc_reference/reference_markers.hmm GCA_011526045.1_ASM1152604v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 15:27:18,053] [INFO] Task succeeded: HMMsearch
[2023-06-29 15:27:18,055] [INFO] Found 6/6 markers.
[2023-06-29 15:27:18,103] [INFO] Query marker FASTA was written to GCA_011526045.1_ASM1152604v1_genomic.fna/markers.fasta
[2023-06-29 15:27:18,104] [INFO] Task started: Blastn
[2023-06-29 15:27:18,104] [INFO] Running command: blastn -query GCA_011526045.1_ASM1152604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0dc3b91-30c1-42d4-89cf-a3a33337f631/dqc_reference/reference_markers.fasta -out GCA_011526045.1_ASM1152604v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:27:19,074] [INFO] Task succeeded: Blastn
[2023-06-29 15:27:19,079] [INFO] Selected 33 target genomes.
[2023-06-29 15:27:19,080] [INFO] Target genome list was writen to GCA_011526045.1_ASM1152604v1_genomic.fna/target_genomes.txt
[2023-06-29 15:27:19,086] [INFO] Task started: fastANI
[2023-06-29 15:27:19,086] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdc9d807-256c-4866-9b24-5b828bf2e35d/GCA_011526045.1_ASM1152604v1_genomic.fna.gz --refList GCA_011526045.1_ASM1152604v1_genomic.fna/target_genomes.txt --output GCA_011526045.1_ASM1152604v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 15:27:43,926] [INFO] Task succeeded: fastANI
[2023-06-29 15:27:43,926] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0dc3b91-30c1-42d4-89cf-a3a33337f631/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 15:27:43,927] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0dc3b91-30c1-42d4-89cf-a3a33337f631/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 15:27:43,948] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 15:27:43,948] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 15:27:43,948] [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
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	76.3543	171	1178	95	below_threshold
Thioalkalivibrio paradoxus	strain=ARh 1	GCA_000227685.3	108010	108010	type	True	76.3419	83	1178	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.2895	85	1178	95	below_threshold
Steroidobacter agaridevorans	strain=SA29-B	GCA_009932555.1	2695856	2695856	type	True	76.126	101	1178	95	below_threshold
Steroidobacter gossypii	strain=S1-65	GCA_016801985.1	2805490	2805490	type	True	76.0427	119	1178	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.0059	114	1178	95	below_threshold
Povalibacter uvarum	strain=DSM 26723	GCA_014202975.1	732238	732238	type	True	75.967	113	1178	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	75.9185	84	1178	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	75.9017	91	1178	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	75.8829	79	1178	95	below_threshold
Steroidobacter cummioxidans	strain=35Y	GCA_003104955.1	1803913	1803913	type	True	75.8721	85	1178	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	75.8487	139	1178	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	75.7763	137	1178	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	75.7341	116	1178	95	below_threshold
Plasticicumulans acidivorans	strain=DSM 23606	GCA_003182095.1	886464	886464	type	True	75.6864	125	1178	95	below_threshold
Stenotrophomonas pavanii	strain=DSM 25135	GCA_001431565.1	487698	487698	type	True	75.679	86	1178	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	75.575	152	1178	95	below_threshold
Thermomonas carbonis	strain=KCTC 42013	GCA_014396975.1	1463158	1463158	type	True	75.5275	85	1178	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	75.4634	59	1178	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	75.4492	60	1178	95	below_threshold
Pseudomonas campi	strain=S1-A32-2	GCA_013200955.2	2731681	2731681	type	True	75.4454	53	1178	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	75.4361	61	1178	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	75.4326	61	1178	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	75.2515	65	1178	95	below_threshold
Bradyrhizobium cenepequi	strain=CNPSo 4026	GCA_020329485.1	2821403	2821403	type	True	75.0848	67	1178	95	below_threshold
Pseudomonas protegens	strain=CHA0	GCA_000397205.1	380021	380021	type	True	75.0571	68	1178	95	below_threshold
Pseudomonas protegens	strain=CHA0	GCA_900560965.1	380021	380021	type	True	75.047	69	1178	95	below_threshold
Pseudomonas inefficax	strain=JV551A3	GCA_900277125.1	2078786	2078786	type	True	75.0246	65	1178	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 15:27:43,950] [INFO] DFAST Taxonomy check result was written to GCA_011526045.1_ASM1152604v1_genomic.fna/tc_result.tsv
[2023-06-29 15:27:43,951] [INFO] ===== Taxonomy check completed =====
[2023-06-29 15:27:43,951] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 15:27:43,951] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0dc3b91-30c1-42d4-89cf-a3a33337f631/dqc_reference/checkm_data
[2023-06-29 15:27:43,953] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 15:27:43,994] [INFO] Task started: CheckM
[2023-06-29 15:27:43,995] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_011526045.1_ASM1152604v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_011526045.1_ASM1152604v1_genomic.fna/checkm_input GCA_011526045.1_ASM1152604v1_genomic.fna/checkm_result
[2023-06-29 15:28:19,848] [INFO] Task succeeded: CheckM
[2023-06-29 15:28:19,850] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 15:28:19,872] [INFO] ===== Completeness check finished =====
[2023-06-29 15:28:19,873] [INFO] ===== Start GTDB Search =====
[2023-06-29 15:28:19,873] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_011526045.1_ASM1152604v1_genomic.fna/markers.fasta)
[2023-06-29 15:28:19,874] [INFO] Task started: Blastn
[2023-06-29 15:28:19,874] [INFO] Running command: blastn -query GCA_011526045.1_ASM1152604v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0dc3b91-30c1-42d4-89cf-a3a33337f631/dqc_reference/reference_markers_gtdb.fasta -out GCA_011526045.1_ASM1152604v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:28:21,482] [INFO] Task succeeded: Blastn
[2023-06-29 15:28:21,487] [INFO] Selected 17 target genomes.
[2023-06-29 15:28:21,487] [INFO] Target genome list was writen to GCA_011526045.1_ASM1152604v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 15:28:21,494] [INFO] Task started: fastANI
[2023-06-29 15:28:21,494] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdc9d807-256c-4866-9b24-5b828bf2e35d/GCA_011526045.1_ASM1152604v1_genomic.fna.gz --refList GCA_011526045.1_ASM1152604v1_genomic.fna/target_genomes_gtdb.txt --output GCA_011526045.1_ASM1152604v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 15:28:31,272] [INFO] Task succeeded: fastANI
[2023-06-29 15:28:31,296] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 15:28:31,296] [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_011526045.1	s__QUBU01 sp011526045	100.0	1172	1178	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-2729495;f__GCA-2729495;g__QUBU01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014337915.1	s__QUBU01 sp014337915	79.1841	409	1178	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-2729495;f__GCA-2729495;g__QUBU01	95.0	99.72	99.56	0.97	0.95	4	-
GCA_015709695.1	s__QUBU01 sp015709695	78.9607	466	1178	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-2729495;f__GCA-2729495;g__QUBU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874095.1	s__QUBU01 sp016874095	77.8178	282	1178	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-2729495;f__GCA-2729495;g__QUBU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789885.1	s__SHZI01 sp016789885	77.7871	263	1178	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-2729495;f__GCA-2729495;g__SHZI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789845.1	s__SHZI01 sp016789845	77.2244	241	1178	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-2729495;f__GCA-2729495;g__SHZI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016882265.1	s__SCUD01 sp016882265	76.6494	160	1178	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__SCUD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017577365.1	s__ZC4RG20 sp017577365	76.3236	125	1178	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA6522;f__UBA6522;g__ZC4RG20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826635.1	s__CADEFQ01 sp902826635	76.1472	138	1178	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__CADEFQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016790635.1	s__JAEUOS01 sp016790635	75.8771	87	1178	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__JAEUOS01;g__JAEUOS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042375.1	s__UBA1847 sp013042375	75.7298	81	1178	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	99.79	99.73	0.92	0.88	6	-
GCA_011371455.1	s__DRQN01 sp011371455	75.6614	59	1178	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__DRQN01	95.0	97.38	97.35	0.90	0.88	5	-
GCA_018224485.1	s__Thioalkalivibrio_B sp018224485	75.6143	64	1178	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745005.1	s__Luteibacter sp000745005	75.4308	66	1178	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Luteibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 15:28:31,299] [INFO] GTDB search result was written to GCA_011526045.1_ASM1152604v1_genomic.fna/result_gtdb.tsv
[2023-06-29 15:28:31,299] [INFO] ===== GTDB Search completed =====
[2023-06-29 15:28:31,304] [INFO] DFAST_QC result json was written to GCA_011526045.1_ASM1152604v1_genomic.fna/dqc_result.json
[2023-06-29 15:28:31,304] [INFO] DFAST_QC completed!
[2023-06-29 15:28:31,304] [INFO] Total running time: 0h1m26s