[2023-06-29 13:07:52,351] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:07:52,353] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:07:52,353] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6aae8da-7c1f-401a-a242-24c7d8c8ae98/dqc_reference
[2023-06-29 13:07:53,517] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:07:53,518] [INFO] Task started: Prodigal
[2023-06-29 13:07:53,518] [INFO] Running command: gunzip -c /var/lib/cwl/stg193234e6-17cb-47bc-a316-a870b13a8df4/GCA_021782655.1_ASM2178265v1_genomic.fna.gz | prodigal -d GCA_021782655.1_ASM2178265v1_genomic.fna/cds.fna -a GCA_021782655.1_ASM2178265v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:07:59,515] [INFO] Task succeeded: Prodigal
[2023-06-29 13:07:59,516] [INFO] Task started: HMMsearch
[2023-06-29 13:07:59,516] [INFO] Running command: hmmsearch --tblout GCA_021782655.1_ASM2178265v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6aae8da-7c1f-401a-a242-24c7d8c8ae98/dqc_reference/reference_markers.hmm GCA_021782655.1_ASM2178265v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:07:59,700] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:07:59,701] [INFO] Found 6/6 markers.
[2023-06-29 13:07:59,724] [INFO] Query marker FASTA was written to GCA_021782655.1_ASM2178265v1_genomic.fna/markers.fasta
[2023-06-29 13:07:59,724] [INFO] Task started: Blastn
[2023-06-29 13:07:59,724] [INFO] Running command: blastn -query GCA_021782655.1_ASM2178265v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6aae8da-7c1f-401a-a242-24c7d8c8ae98/dqc_reference/reference_markers.fasta -out GCA_021782655.1_ASM2178265v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:08:00,371] [INFO] Task succeeded: Blastn
[2023-06-29 13:08:00,376] [INFO] Selected 23 target genomes.
[2023-06-29 13:08:00,377] [INFO] Target genome list was writen to GCA_021782655.1_ASM2178265v1_genomic.fna/target_genomes.txt
[2023-06-29 13:08:00,383] [INFO] Task started: fastANI
[2023-06-29 13:08:00,383] [INFO] Running command: fastANI --query /var/lib/cwl/stg193234e6-17cb-47bc-a316-a870b13a8df4/GCA_021782655.1_ASM2178265v1_genomic.fna.gz --refList GCA_021782655.1_ASM2178265v1_genomic.fna/target_genomes.txt --output GCA_021782655.1_ASM2178265v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:08:15,318] [INFO] Task succeeded: fastANI
[2023-06-29 13:08:15,319] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6aae8da-7c1f-401a-a242-24c7d8c8ae98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:08:15,319] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6aae8da-7c1f-401a-a242-24c7d8c8ae98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:08:15,332] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 13:08:15,332] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 13:08:15,333] [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
Desulfobulbus elongatus	strain=DSM 2908	GCA_000621145.1	53332	53332	type	True	77.3626	128	728	95	below_threshold
Dissulfurirhabdus thermomarina	strain=DSM 100025	GCA_010499435.1	1765737	1765737	type	True	76.718	105	728	95	below_threshold
Desulfobulbus oralis	strain=HOT041/ORNL	GCA_002952055.1	1986146	1986146	type	True	76.6809	63	728	95	below_threshold
Dissulfurirhabdus thermomarina	strain=SH388	GCA_012979235.1	1765737	1765737	type	True	76.6783	107	728	95	below_threshold
Desulfoprunum benzoelyticum	strain=DSM 28570	GCA_014201505.1	1506996	1506996	type	True	76.5221	85	728	95	below_threshold
Desulfoprunum benzoelyticum	strain=DSM 28570	GCA_016918515.1	1506996	1506996	type	True	76.4957	85	728	95	below_threshold
Desulfogranum mediterraneum	strain=DSM 13871	GCA_000429965.1	160661	160661	type	True	76.384	98	728	95	below_threshold
Oryzomonas rubra	strain=Red88	GCA_008369015.1	2509454	2509454	type	True	76.2318	51	728	95	below_threshold
Oryzomonas sagensis	strain=Red100	GCA_008802355.1	2603857	2603857	type	True	76.2226	55	728	95	below_threshold
Geomonas azotofigens	strain=Red51	GCA_018919395.1	2843196	2843196	type	True	75.9383	68	728	95	below_threshold
Deferrisoma camini	strain=S3R1	GCA_000526155.1	1035120	1035120	type	True	75.8214	82	728	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_019397265.1	404386	404386	type	True	74.9988	56	728	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_000379885.1	404386	404386	type	True	74.8813	52	728	95	below_threshold
Nonomuraea wenchangensis	strain=CGMCC 4.5598	GCA_900111685.1	568860	568860	type	True	74.6759	58	728	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	74.6737	66	728	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 13:08:15,335] [INFO] DFAST Taxonomy check result was written to GCA_021782655.1_ASM2178265v1_genomic.fna/tc_result.tsv
[2023-06-29 13:08:15,335] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:08:15,335] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:08:15,336] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6aae8da-7c1f-401a-a242-24c7d8c8ae98/dqc_reference/checkm_data
[2023-06-29 13:08:15,337] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:08:15,361] [INFO] Task started: CheckM
[2023-06-29 13:08:15,361] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021782655.1_ASM2178265v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021782655.1_ASM2178265v1_genomic.fna/checkm_input GCA_021782655.1_ASM2178265v1_genomic.fna/checkm_result
[2023-06-29 13:08:37,853] [INFO] Task succeeded: CheckM
[2023-06-29 13:08:37,854] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.18%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 13:08:37,872] [INFO] ===== Completeness check finished =====
[2023-06-29 13:08:37,873] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:08:37,873] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021782655.1_ASM2178265v1_genomic.fna/markers.fasta)
[2023-06-29 13:08:37,873] [INFO] Task started: Blastn
[2023-06-29 13:08:37,874] [INFO] Running command: blastn -query GCA_021782655.1_ASM2178265v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6aae8da-7c1f-401a-a242-24c7d8c8ae98/dqc_reference/reference_markers_gtdb.fasta -out GCA_021782655.1_ASM2178265v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:08:38,935] [INFO] Task succeeded: Blastn
[2023-06-29 13:08:38,939] [INFO] Selected 22 target genomes.
[2023-06-29 13:08:38,939] [INFO] Target genome list was writen to GCA_021782655.1_ASM2178265v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:08:38,948] [INFO] Task started: fastANI
[2023-06-29 13:08:38,948] [INFO] Running command: fastANI --query /var/lib/cwl/stg193234e6-17cb-47bc-a316-a870b13a8df4/GCA_021782655.1_ASM2178265v1_genomic.fna.gz --refList GCA_021782655.1_ASM2178265v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021782655.1_ASM2178265v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:08:49,358] [INFO] Task succeeded: fastANI
[2023-06-29 13:08:49,373] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 13:08:49,373] [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_001873115.1	s__CG2-30-60-27 sp001873115	77.8574	149	728	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__CG2-30-60-27	95.0	99.49	99.49	0.83	0.83	2	-
GCA_011048585.1	s__Desulfurivibrio alkaliphilus_A	77.4714	111	728	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__Desulfurivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002414225.1	s__UBA5123 sp002414225	77.4637	216	728	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__UBA5123	95.0	99.93	99.93	0.96	0.96	2	-
GCA_003604995.1	s__UBA10518 sp003604995	77.3539	102	728	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__UBA10518	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015488275.1	s__S012-135 sp015488275	77.3287	140	728	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__S012-135;g__S012-135	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002347095.1	s__UBA2262 sp002347095	77.3091	145	728	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__UBA2262	95.0	98.22	98.22	0.94	0.94	2	-
GCA_002841785.1	s__UBA2262 sp002841785	77.2855	124	728	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__UBA2262	95.0	98.87	98.69	0.72	0.70	5	-
GCA_018830485.1	s__UBA2262 sp018830485	77.2265	144	728	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__UBA2262	95.0	99.86	99.86	0.95	0.94	3	-
GCA_002347185.1	s__UBA2262 sp002347185	77.225	147	728	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__UBA2262	95.0	99.47	99.47	0.90	0.90	2	-
GCA_002421565.1	s__UBA5628 sp002421565	77.1872	101	728	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__UBA5628	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001799285.1	s__UBA2262 sp001799285	77.1349	127	728	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__UBA2262	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015484845.1	s__DRKI01 sp015484845	77.1089	164	728	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__DRKI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002415465.1	s__UBA5123 sp002415465	76.9341	129	728	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__UBA5123	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903869265.1	s__UBA2262 sp903869265	76.9269	132	728	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__UBA2262	95.0	100.00	99.97	1.00	1.00	39	-
GCA_011051875.1	s__DRKI01 sp011051875	76.9112	122	728	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__DRKI01	95.0	99.14	99.09	0.93	0.90	3	-
GCA_003605035.1	s__SURF-16 sp003605035	76.7525	146	728	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__SURF-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016208225.1	s__SURF-16 sp016208225	76.585	98	728	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__SURF-16	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201505.1	s__Desulfoprunum benzoelyticum	76.5221	85	728	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfoprunum	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-06-29 13:08:49,375] [INFO] GTDB search result was written to GCA_021782655.1_ASM2178265v1_genomic.fna/result_gtdb.tsv
[2023-06-29 13:08:49,375] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:08:49,382] [INFO] DFAST_QC result json was written to GCA_021782655.1_ASM2178265v1_genomic.fna/dqc_result.json
[2023-06-29 13:08:49,383] [INFO] DFAST_QC completed!
[2023-06-29 13:08:49,383] [INFO] Total running time: 0h0m57s