[2023-06-29 13:57:23,485] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:57:23,487] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:57:23,487] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6a045dc-9810-4456-86da-598b593ed0fd/dqc_reference
[2023-06-29 13:57:24,718] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:57:24,719] [INFO] Task started: Prodigal
[2023-06-29 13:57:24,719] [INFO] Running command: gunzip -c /var/lib/cwl/stg03d9c20c-9846-42e4-8bd0-0da1ad52957c/GCA_021781795.1_ASM2178179v1_genomic.fna.gz | prodigal -d GCA_021781795.1_ASM2178179v1_genomic.fna/cds.fna -a GCA_021781795.1_ASM2178179v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:57:34,777] [INFO] Task succeeded: Prodigal
[2023-06-29 13:57:34,778] [INFO] Task started: HMMsearch
[2023-06-29 13:57:34,778] [INFO] Running command: hmmsearch --tblout GCA_021781795.1_ASM2178179v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6a045dc-9810-4456-86da-598b593ed0fd/dqc_reference/reference_markers.hmm GCA_021781795.1_ASM2178179v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:57:35,046] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:57:35,047] [INFO] Found 6/6 markers.
[2023-06-29 13:57:35,078] [INFO] Query marker FASTA was written to GCA_021781795.1_ASM2178179v1_genomic.fna/markers.fasta
[2023-06-29 13:57:35,079] [INFO] Task started: Blastn
[2023-06-29 13:57:35,079] [INFO] Running command: blastn -query GCA_021781795.1_ASM2178179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6a045dc-9810-4456-86da-598b593ed0fd/dqc_reference/reference_markers.fasta -out GCA_021781795.1_ASM2178179v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:57:35,742] [INFO] Task succeeded: Blastn
[2023-06-29 13:57:35,746] [INFO] Selected 16 target genomes.
[2023-06-29 13:57:35,746] [INFO] Target genome list was writen to GCA_021781795.1_ASM2178179v1_genomic.fna/target_genomes.txt
[2023-06-29 13:57:35,751] [INFO] Task started: fastANI
[2023-06-29 13:57:35,751] [INFO] Running command: fastANI --query /var/lib/cwl/stg03d9c20c-9846-42e4-8bd0-0da1ad52957c/GCA_021781795.1_ASM2178179v1_genomic.fna.gz --refList GCA_021781795.1_ASM2178179v1_genomic.fna/target_genomes.txt --output GCA_021781795.1_ASM2178179v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:57:50,000] [INFO] Task succeeded: fastANI
[2023-06-29 13:57:50,001] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6a045dc-9810-4456-86da-598b593ed0fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:57:50,002] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6a045dc-9810-4456-86da-598b593ed0fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:57:50,014] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 13:57:50,015] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 13:57:50,015] [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
Terracidiphilus gabretensis	strain=S55	GCA_001449115.1	1577687	1577687	type	True	77.7001	232	1089	95	below_threshold
Occallatibacter riparius	strain=DSM 25168	GCA_025264625.1	1002689	1002689	type	True	77.5259	289	1089	95	below_threshold
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	77.3622	168	1089	95	below_threshold
Silvibacterium dinghuense	strain=DHOF10	GCA_004123295.1	1560006	1560006	type	True	77.0806	165	1089	95	below_threshold
Acidobacterium capsulatum	strain=ATCC 51196	GCA_000022565.1	33075	33075	type	True	76.9834	162	1089	95	below_threshold
Silvibacterium bohemicum	strain=S15	GCA_001006305.1	1577686	1577686	type	True	76.6661	150	1089	95	below_threshold
Acidipila rosea	strain=DSM 103428	GCA_004339725.1	768535	768535	type	True	76.647	105	1089	95	below_threshold
Silvibacterium bohemicum	strain=DSM 103733	GCA_014201455.1	1577686	1577686	type	True	76.6439	150	1089	95	below_threshold
Granulicella tundricola	strain=MP5ACTX9	GCA_000178975.2	940615	940615	type	True	76.5561	97	1089	95	below_threshold
Bryocella elongata	strain=DSM 22489	GCA_900108185.1	863522	863522	type	True	76.5009	122	1089	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	76.3373	126	1089	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 13:57:50,018] [INFO] DFAST Taxonomy check result was written to GCA_021781795.1_ASM2178179v1_genomic.fna/tc_result.tsv
[2023-06-29 13:57:50,018] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:57:50,019] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:57:50,019] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6a045dc-9810-4456-86da-598b593ed0fd/dqc_reference/checkm_data
[2023-06-29 13:57:50,021] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:57:50,059] [INFO] Task started: CheckM
[2023-06-29 13:57:50,059] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021781795.1_ASM2178179v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021781795.1_ASM2178179v1_genomic.fna/checkm_input GCA_021781795.1_ASM2178179v1_genomic.fna/checkm_result
[2023-06-29 13:58:24,831] [INFO] Task succeeded: CheckM
[2023-06-29 13:58:24,832] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 13:58:24,858] [INFO] ===== Completeness check finished =====
[2023-06-29 13:58:24,859] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:58:24,859] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021781795.1_ASM2178179v1_genomic.fna/markers.fasta)
[2023-06-29 13:58:24,860] [INFO] Task started: Blastn
[2023-06-29 13:58:24,860] [INFO] Running command: blastn -query GCA_021781795.1_ASM2178179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6a045dc-9810-4456-86da-598b593ed0fd/dqc_reference/reference_markers_gtdb.fasta -out GCA_021781795.1_ASM2178179v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:58:25,846] [INFO] Task succeeded: Blastn
[2023-06-29 13:58:25,851] [INFO] Selected 20 target genomes.
[2023-06-29 13:58:25,852] [INFO] Target genome list was writen to GCA_021781795.1_ASM2178179v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:58:25,861] [INFO] Task started: fastANI
[2023-06-29 13:58:25,861] [INFO] Running command: fastANI --query /var/lib/cwl/stg03d9c20c-9846-42e4-8bd0-0da1ad52957c/GCA_021781795.1_ASM2178179v1_genomic.fna.gz --refList GCA_021781795.1_ASM2178179v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021781795.1_ASM2178179v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:58:41,732] [INFO] Task succeeded: fastANI
[2023-06-29 13:58:41,747] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 13:58:41,748] [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_002314435.1	s__Terracidiphilus sp002314435	78.1927	329	1089	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903849645.1	s__Terracidiphilus sp903849645	78.0808	343	1089	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.99	99.99	0.99	0.99	2	-
GCA_008682415.1	s__Terracidiphilus sp008682415	77.9896	280	1089	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003170825.1	s__Terracidiphilus sp003170825	77.9821	279	1089	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.88	99.70	0.95	0.95	8	-
GCA_003139795.1	s__Terracidiphilus sp003139795	77.8884	307	1089	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.74	99.71	0.89	0.87	5	-
GCA_000620725.1	s__Terracidiphilus sp000620725	77.7935	261	1089	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903842065.1	s__Terracidiphilus sp903842065	77.7875	210	1089	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003133425.1	s__Terracidiphilus sp003133425	77.5235	234	1089	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.36	99.32	0.83	0.80	3	-
GCA_903828675.1	s__Terracidiphilus sp903828675	77.4821	245	1089	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.87	99.75	0.95	0.93	4	-
GCA_015655195.1	s__Terracidiphilus sp015655195	77.3783	231	1089	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268915.1	s__Terracidiphilus sp018268915	77.3627	226	1089	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903904755.1	s__CAIVDV01 sp903904755	77.3485	201	1089	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAIVDV01	95.0	99.92	99.89	0.96	0.95	6	-
GCA_003138515.1	s__Terracidiphilus sp003138515	77.3409	229	1089	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.80	99.73	0.97	0.96	5	-
GCA_003165935.1	s__Terracidiphilus sp003165935	77.2403	206	1089	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003140785.1	s__Terracidiphilus sp003140785	77.0472	220	1089	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	98.14	96.92	0.80	0.78	3	-
GCA_003165095.1	s__Terracidiphilus sp003165095	77.03	207	1089	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003166055.1	s__Terracidiphilus sp003166055	77.0278	188	1089	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.24	99.18	0.83	0.82	3	-
GCA_903832055.1	s__CAIVDV01 sp903832055	76.9352	154	1089	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAIVDV01	95.0	100.00	100.00	0.99	0.99	4	-
GCA_903842845.1	s__CAIMNN01 sp903842845	76.7925	138	1089	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__CAIMNN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003164635.1	s__Terracidiphilus sp003164635	76.3448	132	1089	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 13:58:41,750] [INFO] GTDB search result was written to GCA_021781795.1_ASM2178179v1_genomic.fna/result_gtdb.tsv
[2023-06-29 13:58:41,750] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:58:41,755] [INFO] DFAST_QC result json was written to GCA_021781795.1_ASM2178179v1_genomic.fna/dqc_result.json
[2023-06-29 13:58:41,755] [INFO] DFAST_QC completed!
[2023-06-29 13:58:41,755] [INFO] Total running time: 0h1m18s