[2023-06-28 18:27:08,629] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:27:08,631] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:27:08,631] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e417797-b167-4eff-9c9a-049df702c525/dqc_reference
[2023-06-28 18:27:09,956] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:27:09,957] [INFO] Task started: Prodigal
[2023-06-28 18:27:09,957] [INFO] Running command: gunzip -c /var/lib/cwl/stgf01be406-a915-421c-b242-c21e3b3ce9d4/GCA_020844535.1_ASM2084453v1_genomic.fna.gz | prodigal -d GCA_020844535.1_ASM2084453v1_genomic.fna/cds.fna -a GCA_020844535.1_ASM2084453v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:27:15,168] [INFO] Task succeeded: Prodigal
[2023-06-28 18:27:15,168] [INFO] Task started: HMMsearch
[2023-06-28 18:27:15,168] [INFO] Running command: hmmsearch --tblout GCA_020844535.1_ASM2084453v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e417797-b167-4eff-9c9a-049df702c525/dqc_reference/reference_markers.hmm GCA_020844535.1_ASM2084453v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:27:15,445] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:27:15,447] [INFO] Found 6/6 markers.
[2023-06-28 18:27:15,469] [INFO] Query marker FASTA was written to GCA_020844535.1_ASM2084453v1_genomic.fna/markers.fasta
[2023-06-28 18:27:15,469] [INFO] Task started: Blastn
[2023-06-28 18:27:15,469] [INFO] Running command: blastn -query GCA_020844535.1_ASM2084453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e417797-b167-4eff-9c9a-049df702c525/dqc_reference/reference_markers.fasta -out GCA_020844535.1_ASM2084453v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:27:16,061] [INFO] Task succeeded: Blastn
[2023-06-28 18:27:16,065] [INFO] Selected 25 target genomes.
[2023-06-28 18:27:16,065] [INFO] Target genome list was writen to GCA_020844535.1_ASM2084453v1_genomic.fna/target_genomes.txt
[2023-06-28 18:27:16,072] [INFO] Task started: fastANI
[2023-06-28 18:27:16,072] [INFO] Running command: fastANI --query /var/lib/cwl/stgf01be406-a915-421c-b242-c21e3b3ce9d4/GCA_020844535.1_ASM2084453v1_genomic.fna.gz --refList GCA_020844535.1_ASM2084453v1_genomic.fna/target_genomes.txt --output GCA_020844535.1_ASM2084453v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:27:25,629] [INFO] Task succeeded: fastANI
[2023-06-28 18:27:25,630] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e417797-b167-4eff-9c9a-049df702c525/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:27:25,630] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e417797-b167-4eff-9c9a-049df702c525/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:27:25,646] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2023-06-28 18:27:25,646] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 18:27:25,646] [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
Limosilactobacillus mucosae	strain=DSM 13345	GCA_001436025.1	97478	97478	type	True	96.5148	575	655	95	conclusive
Limosilactobacillus fermentum	strain=B1 28	GCA_005341425.1	1613	1613	type	True	79.2073	79	655	95	below_threshold
Limosilactobacillus fermentum	strain=ATCC 14931	GCA_000159215.1	1613	1613	type	True	79.0206	78	655	95	below_threshold
Limosilactobacillus fermentum	strain=DSM 20052	GCA_013394085.1	1613	1613	type	True	79.0204	76	655	95	below_threshold
Limosilactobacillus portuensis	strain=c11Ua_112_M	GCA_014838735.1	2742601	2742601	type	True	78.4442	69	655	95	below_threshold
Limosilactobacillus secaliphilus	strain=DSM 17896	GCA_001437055.1	396268	396268	type	True	78.3881	92	655	95	below_threshold
Limosilactobacillus panis	strain=DSM 6035	GCA_001027985.1	47493	47493	type	True	78.2894	81	655	95	below_threshold
Limosilactobacillus panis	strain=DSM 6035	GCA_001435935.1	47493	47493	type	True	78.2451	83	655	95	below_threshold
Limosilactobacillus oris	strain=DSM 4864	GCA_001434465.1	1632	1632	type	True	78.012	87	655	95	below_threshold
[Lactobacillus] timonensis	strain=Marseille-P3825	GCA_900240275.1	1970790	1970790	type	True	77.7573	58	655	95	below_threshold
Limosilactobacillus gorillae	strain=KZ01	GCA_001293735.1	1450649	1450649	type	True	77.6919	67	655	95	below_threshold
Limosilactobacillus equigenerosi	strain=DSM 18793	GCA_001435245.1	417373	417373	type	True	77.4391	52	655	95	below_threshold
Limosilactobacillus equigenerosi	strain=JCM 14505	GCA_001311375.1	417373	417373	type	True	77.4006	53	655	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 18:27:25,648] [INFO] DFAST Taxonomy check result was written to GCA_020844535.1_ASM2084453v1_genomic.fna/tc_result.tsv
[2023-06-28 18:27:25,649] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:27:25,649] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:27:25,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e417797-b167-4eff-9c9a-049df702c525/dqc_reference/checkm_data
[2023-06-28 18:27:25,651] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:27:25,691] [INFO] Task started: CheckM
[2023-06-28 18:27:25,691] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020844535.1_ASM2084453v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020844535.1_ASM2084453v1_genomic.fna/checkm_input GCA_020844535.1_ASM2084453v1_genomic.fna/checkm_result
[2023-06-28 18:27:48,970] [INFO] Task succeeded: CheckM
[2023-06-28 18:27:48,971] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:27:48,993] [INFO] ===== Completeness check finished =====
[2023-06-28 18:27:48,994] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:27:48,994] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020844535.1_ASM2084453v1_genomic.fna/markers.fasta)
[2023-06-28 18:27:48,995] [INFO] Task started: Blastn
[2023-06-28 18:27:48,995] [INFO] Running command: blastn -query GCA_020844535.1_ASM2084453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e417797-b167-4eff-9c9a-049df702c525/dqc_reference/reference_markers_gtdb.fasta -out GCA_020844535.1_ASM2084453v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:27:49,750] [INFO] Task succeeded: Blastn
[2023-06-28 18:27:49,755] [INFO] Selected 19 target genomes.
[2023-06-28 18:27:49,755] [INFO] Target genome list was writen to GCA_020844535.1_ASM2084453v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:27:49,781] [INFO] Task started: fastANI
[2023-06-28 18:27:49,782] [INFO] Running command: fastANI --query /var/lib/cwl/stgf01be406-a915-421c-b242-c21e3b3ce9d4/GCA_020844535.1_ASM2084453v1_genomic.fna.gz --refList GCA_020844535.1_ASM2084453v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020844535.1_ASM2084453v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:27:55,995] [INFO] Task succeeded: fastANI
[2023-06-28 18:27:56,014] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 18:27:56,014] [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_001436025.1	s__Limosilactobacillus mucosae	96.4883	576	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.05	95.70	0.88	0.73	22	conclusive
GCF_012843675.1	s__Limosilactobacillus sp012843675	87.4229	523	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.07	98.07	0.86	0.86	2	-
GCF_013394085.1	s__Limosilactobacillus fermentum	79.0204	76	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.65	97.32	0.90	0.60	102	-
GCF_002940945.1	s__Limosilactobacillus pontis_A	78.7073	81	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019114515.1	s__Limosilactobacillus merdigallinarum	78.665	72	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435345.1	s__Limosilactobacillus pontis	78.6402	77	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.82	97.66	0.95	0.90	3	-
GCA_019117285.1	s__Limosilactobacillus intestinigallinarum	78.625	64	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.99	99.99	0.94	0.94	2	-
GCF_001437055.1	s__Limosilactobacillus secaliphilus	78.3954	91	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435935.1	s__Limosilactobacillus panis	78.2451	83	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.95	99.95	0.95	0.95	2	-
GCA_905214235.1	s__Limosilactobacillus sp905214235	78.2409	82	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014838745.1	s__Limosilactobacillus urinaemulieris	78.1028	65	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.61	97.61	0.86	0.86	2	-
GCF_001434465.1	s__Limosilactobacillus oris	77.9976	88	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.39	95.80	0.88	0.80	8	-
GCF_016900115.1	s__Limosilactobacillus alvi	77.7971	62	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.65	97.65	0.93	0.93	2	-
GCF_001293735.1	s__Limosilactobacillus gorillae	77.6919	67	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001311375.1	s__Limosilactobacillus equigenerosi	77.4006	53	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	99.90	99.89	0.99	0.98	3	-
GCA_019118405.1	s__Limosilactobacillus gallistercoris	77.3615	63	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.70	98.67	0.88	0.83	3	-
GCA_019113965.1	s__Limosilactobacillus merdipullorum	76.9931	57	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:27:56,017] [INFO] GTDB search result was written to GCA_020844535.1_ASM2084453v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:27:56,018] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:27:56,022] [INFO] DFAST_QC result json was written to GCA_020844535.1_ASM2084453v1_genomic.fna/dqc_result.json
[2023-06-28 18:27:56,022] [INFO] DFAST_QC completed!
[2023-06-28 18:27:56,023] [INFO] Total running time: 0h0m47s