[2023-06-27 23:46:47,203] [INFO] DFAST_QC pipeline started.
[2023-06-27 23:46:47,212] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 23:46:47,212] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f786da6-6b1f-4fee-8a7a-0c0ff9bd8f21/dqc_reference
[2023-06-27 23:46:48,383] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 23:46:48,384] [INFO] Task started: Prodigal
[2023-06-27 23:46:48,384] [INFO] Running command: gunzip -c /var/lib/cwl/stg4e5f9c8e-135c-41a1-8d21-fb129da33dc9/GCA_027394125.1_ASM2739412v1_genomic.fna.gz | prodigal -d GCA_027394125.1_ASM2739412v1_genomic.fna/cds.fna -a GCA_027394125.1_ASM2739412v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 23:46:57,254] [INFO] Task succeeded: Prodigal
[2023-06-27 23:46:57,254] [INFO] Task started: HMMsearch
[2023-06-27 23:46:57,254] [INFO] Running command: hmmsearch --tblout GCA_027394125.1_ASM2739412v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f786da6-6b1f-4fee-8a7a-0c0ff9bd8f21/dqc_reference/reference_markers.hmm GCA_027394125.1_ASM2739412v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 23:46:57,423] [INFO] Task succeeded: HMMsearch
[2023-06-27 23:46:57,424] [INFO] Found 6/6 markers.
[2023-06-27 23:46:57,446] [INFO] Query marker FASTA was written to GCA_027394125.1_ASM2739412v1_genomic.fna/markers.fasta
[2023-06-27 23:46:57,447] [INFO] Task started: Blastn
[2023-06-27 23:46:57,447] [INFO] Running command: blastn -query GCA_027394125.1_ASM2739412v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f786da6-6b1f-4fee-8a7a-0c0ff9bd8f21/dqc_reference/reference_markers.fasta -out GCA_027394125.1_ASM2739412v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 23:46:58,211] [INFO] Task succeeded: Blastn
[2023-06-27 23:46:58,216] [INFO] Selected 32 target genomes.
[2023-06-27 23:46:58,216] [INFO] Target genome list was writen to GCA_027394125.1_ASM2739412v1_genomic.fna/target_genomes.txt
[2023-06-27 23:46:58,220] [INFO] Task started: fastANI
[2023-06-27 23:46:58,221] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e5f9c8e-135c-41a1-8d21-fb129da33dc9/GCA_027394125.1_ASM2739412v1_genomic.fna.gz --refList GCA_027394125.1_ASM2739412v1_genomic.fna/target_genomes.txt --output GCA_027394125.1_ASM2739412v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 23:47:19,029] [INFO] Task succeeded: fastANI
[2023-06-27 23:47:19,030] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f786da6-6b1f-4fee-8a7a-0c0ff9bd8f21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 23:47:19,030] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f786da6-6b1f-4fee-8a7a-0c0ff9bd8f21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 23:47:19,050] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 23:47:19,050] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 23:47:19,050] [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
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.3733	83	480	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.2603	118	480	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.14	133	480	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	75.7054	88	480	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.6945	127	480	95	below_threshold
Nocardioides currus	strain=IB-3	GCA_003057875.1	2133958	2133958	type	True	75.6818	105	480	95	below_threshold
Motilibacter peucedani	strain=RP-AC37	GCA_003634695.1	598650	598650	type	True	75.6691	105	480	95	below_threshold
Phycicoccus endophyticus	strain=IP6SC6	GCA_011326735.1	1690220	1690220	type	True	75.606	107	480	95	below_threshold
Phycicoccus endophyticus	strain=CGMCC 4.7300	GCA_014646175.1	1690220	1690220	type	True	75.5731	110	480	95	below_threshold
Cellulomonas citrea	strain=Ao-9	GCA_009829685.1	1909423	1909423	type	True	75.5721	60	480	95	below_threshold
Protaetiibacter larvae	strain=KACC 19322	GCA_008365275.1	2592654	2592654	type	True	75.5363	52	480	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	75.4918	118	480	95	below_threshold
Micromonospora maris	strain=NRRL B-24793	GCA_001507315.1	1003110	1003110	type	True	75.4096	81	480	95	below_threshold
Micromonospora maris	strain=AB-18-032	GCA_000204155.1	1003110	1003110	type	True	75.406	84	480	95	below_threshold
Streptomyces mobaraensis	strain=DSM 40847	GCA_000342125.1	35621	35621	type	True	75.3258	102	480	95	below_threshold
Micromonospora marina	strain=DSM 45555	GCA_900091565.1	307120	307120	type	True	75.2369	100	480	95	below_threshold
Williamsia serinedens	strain=DSM 45037	GCA_024171725.1	391736	391736	type	True	75.1839	93	480	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.1652	67	480	95	below_threshold
Jiangella alkaliphila	strain=DSM 45079	GCA_900105925.1	419479	419479	type	True	75.1168	127	480	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	75.1115	87	480	95	below_threshold
Jiangella alkaliphila	strain=KCTC 19222	GCA_001005145.1	419479	419479	type	True	75.0855	130	480	95	below_threshold
Promicromonospora citrea	strain=ATCC 15908	GCA_013004695.1	43677	43677	type	True	75.0618	99	480	95	below_threshold
Micromonospora nigra	strain=DSM 43818	GCA_900091585.1	145857	145857	type	True	75.0617	89	480	95	below_threshold
Promicromonospora citrea	strain=JCM 3051	GCA_014647735.1	43677	43677	type	True	75.0383	104	480	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	75.0209	110	480	95	below_threshold
Cellulomonas hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	74.9825	107	480	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 23:47:19,053] [INFO] DFAST Taxonomy check result was written to GCA_027394125.1_ASM2739412v1_genomic.fna/tc_result.tsv
[2023-06-27 23:47:19,053] [INFO] ===== Taxonomy check completed =====
[2023-06-27 23:47:19,053] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 23:47:19,054] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f786da6-6b1f-4fee-8a7a-0c0ff9bd8f21/dqc_reference/checkm_data
[2023-06-27 23:47:19,055] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 23:47:19,078] [INFO] Task started: CheckM
[2023-06-27 23:47:19,079] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027394125.1_ASM2739412v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027394125.1_ASM2739412v1_genomic.fna/checkm_input GCA_027394125.1_ASM2739412v1_genomic.fna/checkm_result
[2023-06-27 23:47:41,553] [INFO] Task succeeded: CheckM
[2023-06-27 23:47:41,555] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.85%
Contamintation: 7.64%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2023-06-27 23:47:41,576] [INFO] ===== Completeness check finished =====
[2023-06-27 23:47:41,576] [INFO] ===== Start GTDB Search =====
[2023-06-27 23:47:41,577] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027394125.1_ASM2739412v1_genomic.fna/markers.fasta)
[2023-06-27 23:47:41,577] [INFO] Task started: Blastn
[2023-06-27 23:47:41,577] [INFO] Running command: blastn -query GCA_027394125.1_ASM2739412v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f786da6-6b1f-4fee-8a7a-0c0ff9bd8f21/dqc_reference/reference_markers_gtdb.fasta -out GCA_027394125.1_ASM2739412v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 23:47:42,875] [INFO] Task succeeded: Blastn
[2023-06-27 23:47:42,879] [INFO] Selected 19 target genomes.
[2023-06-27 23:47:42,879] [INFO] Target genome list was writen to GCA_027394125.1_ASM2739412v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 23:47:42,881] [INFO] Task started: fastANI
[2023-06-27 23:47:42,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e5f9c8e-135c-41a1-8d21-fb129da33dc9/GCA_027394125.1_ASM2739412v1_genomic.fna.gz --refList GCA_027394125.1_ASM2739412v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027394125.1_ASM2739412v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 23:47:51,000] [INFO] Task succeeded: fastANI
[2023-06-27 23:47:51,016] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 23:47:51,016] [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_002255565.1	s__RAAP-2 sp002255565	89.2051	377	480	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903860745.1	s__RAAP-2 sp903860745	79.3582	213	480	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	99.88	99.81	0.92	0.91	5	-
GCA_017883045.1	s__RAAP-2 sp017883045	79.3296	226	480	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003138815.1	s__RAAP-2 sp003138815	78.8702	225	480	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	99.85	99.69	0.94	0.86	28	-
GCA_018971185.1	s__RAAP-2 sp018971185	78.6036	204	480	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001443545.1	s__RAAP-2 sp001443545	78.2361	182	480	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003132205.1	s__RAAP-2 sp003132205	78.1504	185	480	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003133075.1	s__RAAP-2 sp003133075	77.9177	152	480	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	99.28	99.10	0.84	0.81	8	-
GCA_003162475.1	s__RAAP-2 sp003162475	77.763	154	480	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003155915.1	s__RAAP-2 sp003155915	77.63	166	480	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	99.91	99.78	0.97	0.95	27	-
GCA_003160115.1	s__RAAP-2 sp003160115	77.6095	140	480	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	99.36	95.42	0.89	0.81	14	-
GCA_003133125.1	s__RAAP-2 sp003133125	77.5114	145	480	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	99.58	99.35	0.91	0.88	7	-
GCA_003133405.1	s__RAAP-2 sp003133405	77.4764	139	480	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	99.62	99.62	0.92	0.92	2	-
GCA_003142095.1	s__RAAP-2 sp003142095	77.4539	134	480	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	99.96	99.96	0.97	0.97	2	-
GCA_003134515.1	s__RAAP-2 sp003134515	77.4248	132	480	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003151555.1	s__RAAP-2 sp003151555	77.0071	111	480	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003155135.1	s__Bog-515 sp003155135	76.8647	141	480	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-515	95.0	99.89	99.76	0.97	0.95	17	-
GCA_003164095.1	s__Bog-756 sp003164095	76.5644	113	480	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-756	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003453695.1	s__UBA8190 sp003453695	76.099	100	480	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA8190;g__UBA8190	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 23:47:51,019] [INFO] GTDB search result was written to GCA_027394125.1_ASM2739412v1_genomic.fna/result_gtdb.tsv
[2023-06-27 23:47:51,020] [INFO] ===== GTDB Search completed =====
[2023-06-27 23:47:51,025] [INFO] DFAST_QC result json was written to GCA_027394125.1_ASM2739412v1_genomic.fna/dqc_result.json
[2023-06-27 23:47:51,025] [INFO] DFAST_QC completed!
[2023-06-27 23:47:51,025] [INFO] Total running time: 0h1m4s