[2024-01-24 13:57:12,435] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:12,437] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:12,437] [INFO] DQC Reference Directory: /var/lib/cwl/stg77c86dab-1e76-4656-aa0d-55df82cad8c5/dqc_reference
[2024-01-24 13:57:13,820] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:13,821] [INFO] Task started: Prodigal
[2024-01-24 13:57:13,821] [INFO] Running command: gunzip -c /var/lib/cwl/stg07509c6c-2df1-468c-a020-fda06d51762e/GCF_021054785.1_ASM2105478v1_genomic.fna.gz | prodigal -d GCF_021054785.1_ASM2105478v1_genomic.fna/cds.fna -a GCF_021054785.1_ASM2105478v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:17,827] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:17,827] [INFO] Task started: HMMsearch
[2024-01-24 13:57:17,828] [INFO] Running command: hmmsearch --tblout GCF_021054785.1_ASM2105478v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77c86dab-1e76-4656-aa0d-55df82cad8c5/dqc_reference/reference_markers.hmm GCF_021054785.1_ASM2105478v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:18,068] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:18,069] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg07509c6c-2df1-468c-a020-fda06d51762e/GCF_021054785.1_ASM2105478v1_genomic.fna.gz]
[2024-01-24 13:57:18,094] [INFO] Query marker FASTA was written to GCF_021054785.1_ASM2105478v1_genomic.fna/markers.fasta
[2024-01-24 13:57:18,095] [INFO] Task started: Blastn
[2024-01-24 13:57:18,095] [INFO] Running command: blastn -query GCF_021054785.1_ASM2105478v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77c86dab-1e76-4656-aa0d-55df82cad8c5/dqc_reference/reference_markers.fasta -out GCF_021054785.1_ASM2105478v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:18,700] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:18,704] [INFO] Selected 21 target genomes.
[2024-01-24 13:57:18,704] [INFO] Target genome list was writen to GCF_021054785.1_ASM2105478v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:18,714] [INFO] Task started: fastANI
[2024-01-24 13:57:18,714] [INFO] Running command: fastANI --query /var/lib/cwl/stg07509c6c-2df1-468c-a020-fda06d51762e/GCF_021054785.1_ASM2105478v1_genomic.fna.gz --refList GCF_021054785.1_ASM2105478v1_genomic.fna/target_genomes.txt --output GCF_021054785.1_ASM2105478v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:27,925] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:27,926] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77c86dab-1e76-4656-aa0d-55df82cad8c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:27,926] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77c86dab-1e76-4656-aa0d-55df82cad8c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:27,936] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:27,936] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:27,936] [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
Tannockella kyphosi	strain=BP52G	GCA_021054785.1	2899121	2899121	type	True	100.0	753	753	95	conclusive
[Clostridium] spiroforme	strain=DSM 1552	GCA_025149465.1	29348	29348	type	True	78.3616	167	753	95	below_threshold
Faecalibacillus faecis	strain=SNUG30370	GCA_003024675.1	1982628	1982628	type	True	78.353	166	753	95	below_threshold
Faecalibacillus intestinalis	strain=SNUG30099	GCA_003024685.1	1982626	1982626	type	True	78.2895	173	753	95	below_threshold
Coprobacillus cateniformis	strain=RCA1-24	GCA_009767585.1	100884	100884	type	True	78.0391	122	753	95	below_threshold
Erysipelatoclostridium ramosum		GCA_900660185.1	1547	1547	type	True	78.0068	141	753	95	below_threshold
[Clostridium] cocleatum	strain=I50	GCA_010206155.1	69824	69824	type	True	77.8126	163	753	95	below_threshold
Longibaculum muris	strain=DSM 29487	GCA_004343035.1	1796628	1796628	type	True	77.8115	150	753	95	below_threshold
Longibaculum muris	strain=DSM 29487	GCA_024622235.1	1796628	1796628	type	True	77.6872	147	753	95	below_threshold
[Clostridium] cocleatum	strain=DSM 1551	GCA_024622895.1	69824	69824	type	True	77.6223	156	753	95	below_threshold
Coprobacillus cateniformis	strain=JCM 10604	GCA_001312445.1	100884	100884	type	True	77.509	115	753	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:27,938] [INFO] DFAST Taxonomy check result was written to GCF_021054785.1_ASM2105478v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:27,939] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:27,939] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:27,939] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77c86dab-1e76-4656-aa0d-55df82cad8c5/dqc_reference/checkm_data
[2024-01-24 13:57:27,940] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:27,965] [INFO] Task started: CheckM
[2024-01-24 13:57:27,965] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021054785.1_ASM2105478v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021054785.1_ASM2105478v1_genomic.fna/checkm_input GCF_021054785.1_ASM2105478v1_genomic.fna/checkm_result
[2024-01-24 13:57:47,807] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:47,808] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:47,827] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:47,827] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:47,828] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021054785.1_ASM2105478v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:47,828] [INFO] Task started: Blastn
[2024-01-24 13:57:47,828] [INFO] Running command: blastn -query GCF_021054785.1_ASM2105478v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77c86dab-1e76-4656-aa0d-55df82cad8c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_021054785.1_ASM2105478v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:48,695] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:48,699] [INFO] Selected 25 target genomes.
[2024-01-24 13:57:48,699] [INFO] Target genome list was writen to GCF_021054785.1_ASM2105478v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:48,715] [INFO] Task started: fastANI
[2024-01-24 13:57:48,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg07509c6c-2df1-468c-a020-fda06d51762e/GCF_021054785.1_ASM2105478v1_genomic.fna.gz --refList GCF_021054785.1_ASM2105478v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021054785.1_ASM2105478v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:01,950] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:01,973] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:58:01,973] [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
GCF_014131695.1	s__Erysipelatoclostridium ramosum	79.0861	151	753	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	99.66	99.35	0.93	0.87	70	-
GCF_003480255.1	s__Faecalibacillus sp003480255	78.6934	162	753	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	99.06	98.20	0.91	0.84	5	-
GCF_003024675.1	s__Faecalibacillus faecis	78.3393	166	753	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	97.99	96.95	0.86	0.80	14	-
GCF_001244545.1	s__Stoquefichus sp001244545	78.3148	135	753	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Stoquefichus	95.0	98.22	98.22	0.87	0.87	2	-
GCF_003024685.1	s__Faecalibacillus intestinalis	78.2887	172	753	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	97.94	96.13	0.85	0.76	51	-
GCA_900544435.1	s__Faecalibacillus sp900544435	78.2629	133	753	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	99.05	98.83	0.79	0.74	3	-
GCF_000154805.1	s__Erysipelatoclostridium spiroforme	78.2389	167	753	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	97.13	96.38	0.84	0.79	13	-
GCA_900538465.1	s__Longibaculum sp900538465	78.2386	128	753	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Longibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009767585.1	s__Coprobacillus cateniformis	78.1905	123	753	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Coprobacillus	95.0	99.28	99.05	0.92	0.87	12	-
GCF_002160495.1	s__Erysipelatoclostridium merdavium	77.9446	161	753	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	98.70	98.24	0.87	0.83	4	-
GCF_004343035.1	s__Longibaculum muris	77.833	149	753	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Longibaculum	95.0	98.90	96.51	0.88	0.82	7	-
GCA_018369555.1	s__Erysipelatoclostridium spiroforme_A	77.8093	151	753	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102365.1	s__Erysipelatoclostridium cocleatum	77.7009	158	753	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	99.07	98.04	0.92	0.85	5	-
GCA_018365815.1	s__Beduini sp018365815	77.6729	92	753	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Beduini	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586805.1	s__MGBC140090 sp910586805	77.508	94	753	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__MGBC140090	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588075.1	s__MGBC163490 sp910588075	77.254	130	753	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__MGBC163490	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579135.1	s__MGBC113645 sp910579135	77.0251	129	753	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__MGBC113645	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017889095.1	s__Erysipelatoclostridium sp017889095	76.6277	130	753	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:01,981] [INFO] GTDB search result was written to GCF_021054785.1_ASM2105478v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:01,982] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:01,988] [INFO] DFAST_QC result json was written to GCF_021054785.1_ASM2105478v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:01,989] [INFO] DFAST_QC completed!
[2024-01-24 13:58:01,989] [INFO] Total running time: 0h0m50s