[2023-06-12 22:44:21,164] [INFO] DFAST_QC pipeline started.
[2023-06-12 22:44:21,166] [INFO] DFAST_QC version: 0.5.7
[2023-06-12 22:44:21,166] [INFO] DQC Reference Directory: /var/lib/cwl/stg7becfd57-37fb-4f20-a170-8cb68c9e7e4b/dqc_reference
[2023-06-12 22:44:22,478] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-12 22:44:22,479] [INFO] Task started: Prodigal
[2023-06-12 22:44:22,479] [INFO] Running command: gunzip -c /var/lib/cwl/stg8bfbd2a0-f73c-4edb-a468-f267a4a7bbd4/GCA_022072095.1_ASM2207209v1_genomic.fna.gz | prodigal -d GCA_022072095.1_ASM2207209v1_genomic.fna/cds.fna -a GCA_022072095.1_ASM2207209v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-12 22:44:31,041] [INFO] Task succeeded: Prodigal
[2023-06-12 22:44:31,041] [INFO] Task started: HMMsearch
[2023-06-12 22:44:31,042] [INFO] Running command: hmmsearch --tblout GCA_022072095.1_ASM2207209v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7becfd57-37fb-4f20-a170-8cb68c9e7e4b/dqc_reference/reference_markers.hmm GCA_022072095.1_ASM2207209v1_genomic.fna/protein.faa > /dev/null
[2023-06-12 22:44:31,289] [INFO] Task succeeded: HMMsearch
[2023-06-12 22:44:31,293] [INFO] Found 6/6 markers.
[2023-06-12 22:44:31,321] [INFO] Query marker FASTA was written to GCA_022072095.1_ASM2207209v1_genomic.fna/markers.fasta
[2023-06-12 22:44:31,321] [INFO] Task started: Blastn
[2023-06-12 22:44:31,321] [INFO] Running command: blastn -query GCA_022072095.1_ASM2207209v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7becfd57-37fb-4f20-a170-8cb68c9e7e4b/dqc_reference/reference_markers.fasta -out GCA_022072095.1_ASM2207209v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 22:44:32,077] [INFO] Task succeeded: Blastn
[2023-06-12 22:44:32,081] [INFO] Selected 25 target genomes.
[2023-06-12 22:44:32,081] [INFO] Target genome list was writen to GCA_022072095.1_ASM2207209v1_genomic.fna/target_genomes.txt
[2023-06-12 22:44:32,089] [INFO] Task started: fastANI
[2023-06-12 22:44:32,090] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bfbd2a0-f73c-4edb-a468-f267a4a7bbd4/GCA_022072095.1_ASM2207209v1_genomic.fna.gz --refList GCA_022072095.1_ASM2207209v1_genomic.fna/target_genomes.txt --output GCA_022072095.1_ASM2207209v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-12 22:44:48,864] [INFO] Task succeeded: fastANI
[2023-06-12 22:44:48,864] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7becfd57-37fb-4f20-a170-8cb68c9e7e4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-12 22:44:48,865] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7becfd57-37fb-4f20-a170-8cb68c9e7e4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-12 22:44:48,883] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-12 22:44:48,883] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-12 22:44:48,884] [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
Thauera aromatica	strain=K172	GCA_003030465.1	59405	59405	type	True	76.8042	154	905	95	below_threshold
Thauera propionica	strain=KNDSS-Mac4	GCA_002245655.1	2019431	2019431	type	True	76.6249	144	905	95	below_threshold
Thauera butanivorans	strain=NBRC 103042	GCA_001591165.1	86174	86174	type	True	76.6197	169	905	95	below_threshold
Thauera phenolivorans	strain=ZV1C	GCA_001696715.1	1792543	1792543	type	True	76.5681	154	905	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	76.5644	151	905	95	below_threshold
Sulfurisoma sediminicola	strain=DSM 26916	GCA_003663955.1	1381557	1381557	type	True	76.5619	150	905	95	below_threshold
Aromatoleum tolulyticum	strain=ATCC 51758	GCA_900156155.1	34027	34027	type	True	76.5062	152	905	95	below_threshold
Thauera linaloolentis	strain=DSM 12138	GCA_000621305.1	76112	76112	type	True	76.4008	145	905	95	below_threshold
Thauera linaloolentis	strain=47Lol = DSM 12138	GCA_000310205.1	76112	76112	type	True	76.3516	149	905	95	below_threshold
Aromatoleum evansii	strain=KB740	GCA_012910805.1	59406	59406	type	True	76.3454	154	905	95	below_threshold
Aromatoleum aromaticum	strain=EbN1	GCA_000025965.1	551760	551760	type	True	76.3126	143	905	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	76.2163	156	905	95	below_threshold
Thauera terpenica	strain=58Eu	GCA_000443165.1	76113	76113	type	True	76.0353	138	905	95	below_threshold
Jeongeupia naejangsanensis	strain=DSM 24253	GCA_016865585.1	613195	613195	type	True	75.8852	79	905	95	below_threshold
Propionivibrio dicarboxylicus	strain=DSM 5885	GCA_900099695.1	83767	83767	type	True	75.7221	96	905	95	below_threshold
Thiocystis violascens	strain=DSM 198	GCA_000227745.3	73141	73141	type	True	75.611	53	905	95	below_threshold
Thiorhodococcus minor	strain=DSM 11518	GCA_010820565.1	57489	57489	type	True	75.5719	55	905	95	below_threshold
Pandoraea apista	strain=DSM 16535	GCA_001465595.2	93218	93218	type	True	75.4892	60	905	95	below_threshold
Pandoraea apista	strain=LMG16407	GCA_001049515.1	93218	93218	type	True	75.4723	61	905	95	below_threshold
Oleiagrimonas soli	strain=DSM 107085	GCA_014201555.1	1543381	1543381	type	True	75.416	58	905	95	below_threshold
Oleiagrimonas soli	strain=3.5X	GCA_000761445.1	1543381	1543381	type	True	75.416	58	905	95	below_threshold
Luteimonas abyssi	strain=XH031	GCA_001482195.1	1247514	1247514	type	True	75.3029	73	905	95	below_threshold
Lysobacter soli	strain=KCTC 22011	GCA_003382285.1	453783	453783	type	True	75.3009	75	905	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-12 22:44:48,886] [INFO] DFAST Taxonomy check result was written to GCA_022072095.1_ASM2207209v1_genomic.fna/tc_result.tsv
[2023-06-12 22:44:48,886] [INFO] ===== Taxonomy check completed =====
[2023-06-12 22:44:48,886] [INFO] ===== Start completeness check using CheckM =====
[2023-06-12 22:44:48,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7becfd57-37fb-4f20-a170-8cb68c9e7e4b/dqc_reference/checkm_data
[2023-06-12 22:44:48,888] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-12 22:44:48,923] [INFO] Task started: CheckM
[2023-06-12 22:44:48,924] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022072095.1_ASM2207209v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022072095.1_ASM2207209v1_genomic.fna/checkm_input GCA_022072095.1_ASM2207209v1_genomic.fna/checkm_result
[2023-06-12 22:45:20,323] [INFO] Task succeeded: CheckM
[2023-06-12 22:45:20,324] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-12 22:45:20,347] [INFO] ===== Completeness check finished =====
[2023-06-12 22:45:20,347] [INFO] ===== Start GTDB Search =====
[2023-06-12 22:45:20,348] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022072095.1_ASM2207209v1_genomic.fna/markers.fasta)
[2023-06-12 22:45:20,348] [INFO] Task started: Blastn
[2023-06-12 22:45:20,348] [INFO] Running command: blastn -query GCA_022072095.1_ASM2207209v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7becfd57-37fb-4f20-a170-8cb68c9e7e4b/dqc_reference/reference_markers_gtdb.fasta -out GCA_022072095.1_ASM2207209v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 22:45:21,585] [INFO] Task succeeded: Blastn
[2023-06-12 22:45:21,589] [INFO] Selected 27 target genomes.
[2023-06-12 22:45:21,589] [INFO] Target genome list was writen to GCA_022072095.1_ASM2207209v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-12 22:45:21,607] [INFO] Task started: fastANI
[2023-06-12 22:45:21,608] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bfbd2a0-f73c-4edb-a468-f267a4a7bbd4/GCA_022072095.1_ASM2207209v1_genomic.fna.gz --refList GCA_022072095.1_ASM2207209v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022072095.1_ASM2207209v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-12 22:45:35,985] [INFO] Task succeeded: fastANI
[2023-06-12 22:45:36,008] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-12 22:45:36,009] [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_011330945.1	s__UBA2250 sp011330945	76.7905	161	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__UBA2250	95.0	99.90	99.90	0.95	0.95	2	-
GCA_008933825.1	s__Desulfobacillus sp008933825	76.7772	140	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	99.14	98.51	0.86	0.84	3	-
GCA_016711925.1	s__JAEUNL01 sp016711925	76.7712	155	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JAEUNL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003105015.1	s__Desulfobacillus sp003105015	76.7611	163	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	97.07	97.07	0.88	0.88	2	-
GCA_002347285.1	s__UBA2250 sp002347285	76.74	157	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__UBA2250	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591165.1	s__Thauera butanivorans	76.633	168	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016208415.1	s__JACQYB01 sp016208415	76.6238	148	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__JACQYB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001872285.1	s__CG2-30-68-42 sp001872285	76.6091	135	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__CG2-30-68-42	95.0	99.75	99.70	0.94	0.93	3	-
GCA_016868295.1	s__Desulfobacillus sp016868295	76.6067	159	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001696715.1	s__Thauera phenolivorans	76.5974	152	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	99.27	99.27	0.98	0.98	2	-
GCA_002840845.1	s__Desulfobacillus sp002840845	76.4546	123	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Desulfobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900174485.1	s__Sterolibacterium denitrificans	76.4036	131	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sterolibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018825305.1	s__Sulfurisoma sp018825305	76.3918	130	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Sulfurisoma	95.0	100.00	99.99	1.00	1.00	3	-
GCF_000310205.1	s__Thauera linaloolentis	76.3509	149	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003963015.1	s__Thauera sp003963015	76.2517	178	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377645.1	s__Thiomonas sp000377645	76.1265	117	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Thiomonas	95.0	96.94	96.87	0.91	0.90	3	-
GCA_003510325.1	s__Thiobacillus sp003510325	75.979	59	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Thiobacillaceae;g__Thiobacillus	95.0	99.33	99.33	0.73	0.73	2	-
GCA_903904605.1	s__CAIYYX01 sp903904605	75.8928	104	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__CAIYYX01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900099695.1	s__Propionivibrio dicarboxylicus	75.726	94	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Propionivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721185.1	s__Azonexus sp016721185	75.7251	52	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	98.23	97.74	0.89	0.86	3	-
GCA_903828235.1	s__Rubrivivax sp903828235	75.6451	123	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.94	99.91	0.96	0.96	5	-
GCF_003382285.1	s__Lysobacter soli	75.3023	75	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	96.84	96.81	0.94	0.93	3	-
GCF_014202825.1	s__Chiayiivirga flava	75.077	73	905	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Chiayiivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-12 22:45:36,011] [INFO] GTDB search result was written to GCA_022072095.1_ASM2207209v1_genomic.fna/result_gtdb.tsv
[2023-06-12 22:45:36,011] [INFO] ===== GTDB Search completed =====
[2023-06-12 22:45:36,016] [INFO] DFAST_QC result json was written to GCA_022072095.1_ASM2207209v1_genomic.fna/dqc_result.json
[2023-06-12 22:45:36,016] [INFO] DFAST_QC completed!
[2023-06-12 22:45:36,016] [INFO] Total running time: 0h1m15s