[2023-06-30 12:42:04,662] [INFO] DFAST_QC pipeline started.
[2023-06-30 12:42:04,665] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 12:42:04,666] [INFO] DQC Reference Directory: /var/lib/cwl/stg0c7e1892-f393-4fda-a68a-5b6707cabe45/dqc_reference
[2023-06-30 12:42:06,695] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 12:42:06,696] [INFO] Task started: Prodigal
[2023-06-30 12:42:06,697] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b53d930-b75f-4f22-88d4-9256d7b2fc2b/GCA_025355995.1_ASM2535599v1_genomic.fna.gz | prodigal -d GCA_025355995.1_ASM2535599v1_genomic.fna/cds.fna -a GCA_025355995.1_ASM2535599v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 12:42:16,584] [INFO] Task succeeded: Prodigal
[2023-06-30 12:42:16,585] [INFO] Task started: HMMsearch
[2023-06-30 12:42:16,585] [INFO] Running command: hmmsearch --tblout GCA_025355995.1_ASM2535599v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0c7e1892-f393-4fda-a68a-5b6707cabe45/dqc_reference/reference_markers.hmm GCA_025355995.1_ASM2535599v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 12:42:16,876] [INFO] Task succeeded: HMMsearch
[2023-06-30 12:42:16,877] [INFO] Found 6/6 markers.
[2023-06-30 12:42:16,916] [INFO] Query marker FASTA was written to GCA_025355995.1_ASM2535599v1_genomic.fna/markers.fasta
[2023-06-30 12:42:16,917] [INFO] Task started: Blastn
[2023-06-30 12:42:16,917] [INFO] Running command: blastn -query GCA_025355995.1_ASM2535599v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c7e1892-f393-4fda-a68a-5b6707cabe45/dqc_reference/reference_markers.fasta -out GCA_025355995.1_ASM2535599v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:42:17,533] [INFO] Task succeeded: Blastn
[2023-06-30 12:42:17,538] [INFO] Selected 25 target genomes.
[2023-06-30 12:42:17,538] [INFO] Target genome list was writen to GCA_025355995.1_ASM2535599v1_genomic.fna/target_genomes.txt
[2023-06-30 12:42:17,546] [INFO] Task started: fastANI
[2023-06-30 12:42:17,546] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b53d930-b75f-4f22-88d4-9256d7b2fc2b/GCA_025355995.1_ASM2535599v1_genomic.fna.gz --refList GCA_025355995.1_ASM2535599v1_genomic.fna/target_genomes.txt --output GCA_025355995.1_ASM2535599v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 12:42:33,688] [INFO] Task succeeded: fastANI
[2023-06-30 12:42:33,689] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0c7e1892-f393-4fda-a68a-5b6707cabe45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 12:42:33,690] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0c7e1892-f393-4fda-a68a-5b6707cabe45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 12:42:33,702] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 12:42:33,702] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 12:42:33,702] [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
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	74.9671	54	1429	95	below_threshold
Bosea thiooxidans	strain=DSM 9653	GCA_900168195.1	53254	53254	type	True	74.7233	71	1429	95	below_threshold
Methylorubrum extorquens	strain=TK 0001	GCA_900234795.1	408	408	type	True	74.7214	89	1429	95	below_threshold
Methylorubrum rhodinum	strain=DSM 2163	GCA_014199935.1	29428	29428	type	True	74.7206	84	1429	95	below_threshold
Methylorubrum salsuginis	strain=CGMCC 1.6474	GCA_900114375.1	414703	414703	type	True	74.7151	78	1429	95	below_threshold
Methylobacterium jeotgali	strain=LMG 23639	GCA_022179345.1	381630	381630	type	True	74.6616	78	1429	95	below_threshold
Mobilicoccus massiliensis	strain=SIT2	GCA_000826525.2	1522310	1522310	type	True	74.6336	54	1429	95	below_threshold
Microvirga thermotolerans	strain=HR1	GCA_009363855.1	2651334	2651334	type	True	74.6319	63	1429	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	74.6264	113	1429	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 12:42:33,704] [INFO] DFAST Taxonomy check result was written to GCA_025355995.1_ASM2535599v1_genomic.fna/tc_result.tsv
[2023-06-30 12:42:33,705] [INFO] ===== Taxonomy check completed =====
[2023-06-30 12:42:33,705] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 12:42:33,705] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0c7e1892-f393-4fda-a68a-5b6707cabe45/dqc_reference/checkm_data
[2023-06-30 12:42:33,706] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 12:42:33,748] [INFO] Task started: CheckM
[2023-06-30 12:42:33,748] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025355995.1_ASM2535599v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025355995.1_ASM2535599v1_genomic.fna/checkm_input GCA_025355995.1_ASM2535599v1_genomic.fna/checkm_result
[2023-06-30 12:43:05,773] [INFO] Task succeeded: CheckM
[2023-06-30 12:43:05,775] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 12:43:05,797] [INFO] ===== Completeness check finished =====
[2023-06-30 12:43:05,798] [INFO] ===== Start GTDB Search =====
[2023-06-30 12:43:05,798] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025355995.1_ASM2535599v1_genomic.fna/markers.fasta)
[2023-06-30 12:43:05,798] [INFO] Task started: Blastn
[2023-06-30 12:43:05,799] [INFO] Running command: blastn -query GCA_025355995.1_ASM2535599v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0c7e1892-f393-4fda-a68a-5b6707cabe45/dqc_reference/reference_markers_gtdb.fasta -out GCA_025355995.1_ASM2535599v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:43:06,713] [INFO] Task succeeded: Blastn
[2023-06-30 12:43:06,718] [INFO] Selected 23 target genomes.
[2023-06-30 12:43:06,718] [INFO] Target genome list was writen to GCA_025355995.1_ASM2535599v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 12:43:06,734] [INFO] Task started: fastANI
[2023-06-30 12:43:06,734] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b53d930-b75f-4f22-88d4-9256d7b2fc2b/GCA_025355995.1_ASM2535599v1_genomic.fna.gz --refList GCA_025355995.1_ASM2535599v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025355995.1_ASM2535599v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 12:43:19,619] [INFO] Task succeeded: fastANI
[2023-06-30 12:43:19,634] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 12:43:19,634] [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_002307245.1	s__UBA1306 sp002307245	79.9099	593	1429	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA8932;g__UBA1306	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794765.1	s__JAEUJG01 sp016794765	78.4169	298	1429	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA8932;g__JAEUJG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262985.1	s__JAFGNN01 sp018262985	77.4692	269	1429	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA12059;g__JAFGNN01	95.0	98.32	98.32	0.96	0.96	2	-
GCA_016926955.1	s__JAFGNN01 sp016926955	77.1656	207	1429	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA12059;g__JAFGNN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003247225.1	s__SZUA-370 sp003247225	77.0567	214	1429	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA12059;g__SZUA-370	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903821875.1	s__CAIJMU01 sp903821875	77.0304	206	1429	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA8932;g__CAIJMU01	95.0	99.44	98.70	0.93	0.88	8	-
GCA_012517645.1	s__JAAYUR01 sp012517645	76.8468	114	1429	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA12059;g__JAAYUR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002839315.1	s__SZUA-370 sp002839315	76.6926	149	1429	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA12059;g__SZUA-370	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003245635.1	s__SZUA-426 sp003245635	76.5396	93	1429	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Termitinemataceae;g__SZUA-426	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002839245.1	s__SZUA-370 sp002839245	76.492	107	1429	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__UBA12059;g__SZUA-370	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003527485.1	s__UBA12037 sp003527485	76.4317	125	1429	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Termitinemataceae;g__UBA12037	95.0	99.92	99.92	0.93	0.93	2	-
GCF_001469165.1	s__Thiohalocapsa sp001469165	74.7688	63	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiohalocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903828235.1	s__Rubrivivax sp903828235	74.6978	60	1429	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.94	99.91	0.96	0.96	5	-
--------------------------------------------------------------------------------
[2023-06-30 12:43:19,636] [INFO] GTDB search result was written to GCA_025355995.1_ASM2535599v1_genomic.fna/result_gtdb.tsv
[2023-06-30 12:43:19,637] [INFO] ===== GTDB Search completed =====
[2023-06-30 12:43:19,640] [INFO] DFAST_QC result json was written to GCA_025355995.1_ASM2535599v1_genomic.fna/dqc_result.json
[2023-06-30 12:43:19,641] [INFO] DFAST_QC completed!
[2023-06-30 12:43:19,641] [INFO] Total running time: 0h1m15s