[2024-01-24 13:28:28,222] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:28,224] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:28,224] [INFO] DQC Reference Directory: /var/lib/cwl/stg1af59bf5-9923-4732-a574-02cd29b59d8b/dqc_reference
[2024-01-24 13:28:29,495] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:29,496] [INFO] Task started: Prodigal
[2024-01-24 13:28:29,496] [INFO] Running command: gunzip -c /var/lib/cwl/stg184da42e-9aff-472d-ad0e-aab9bb919778/GCF_009696175.1_ASM969617v1_genomic.fna.gz | prodigal -d GCF_009696175.1_ASM969617v1_genomic.fna/cds.fna -a GCF_009696175.1_ASM969617v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:33,529] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:33,530] [INFO] Task started: HMMsearch
[2024-01-24 13:28:33,530] [INFO] Running command: hmmsearch --tblout GCF_009696175.1_ASM969617v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1af59bf5-9923-4732-a574-02cd29b59d8b/dqc_reference/reference_markers.hmm GCF_009696175.1_ASM969617v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:33,750] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:33,751] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg184da42e-9aff-472d-ad0e-aab9bb919778/GCF_009696175.1_ASM969617v1_genomic.fna.gz]
[2024-01-24 13:28:33,776] [INFO] Query marker FASTA was written to GCF_009696175.1_ASM969617v1_genomic.fna/markers.fasta
[2024-01-24 13:28:33,777] [INFO] Task started: Blastn
[2024-01-24 13:28:33,777] [INFO] Running command: blastn -query GCF_009696175.1_ASM969617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1af59bf5-9923-4732-a574-02cd29b59d8b/dqc_reference/reference_markers.fasta -out GCF_009696175.1_ASM969617v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:34,339] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:34,342] [INFO] Selected 17 target genomes.
[2024-01-24 13:28:34,343] [INFO] Target genome list was writen to GCF_009696175.1_ASM969617v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:34,425] [INFO] Task started: fastANI
[2024-01-24 13:28:34,425] [INFO] Running command: fastANI --query /var/lib/cwl/stg184da42e-9aff-472d-ad0e-aab9bb919778/GCF_009696175.1_ASM969617v1_genomic.fna.gz --refList GCF_009696175.1_ASM969617v1_genomic.fna/target_genomes.txt --output GCF_009696175.1_ASM969617v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:39,844] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:39,845] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1af59bf5-9923-4732-a574-02cd29b59d8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:39,845] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1af59bf5-9923-4732-a574-02cd29b59d8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:39,856] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:39,856] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:39,856] [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
Floccifex porci	strain=LKV-178-WT-2G	GCA_009696175.1	2606629	2606629	type	True	100.0	650	651	95	conclusive
Holdemanella porci	strain=LKV-472-APC-3	GCA_009696075.1	2652276	2652276	suspected-type	True	78.7384	95	651	95	below_threshold
Faecalicoccus pleomorphus	strain=DSM 20574	GCA_000420345.1	1323	1323	type	True	77.787	62	651	95	below_threshold
Faecalicoccus pleomorphus	strain=NCTC11087	GCA_900459315.1	1323	1323	type	True	77.5951	66	651	95	below_threshold
Faecalitalea cylindroides	strain=ATCC 27803	GCA_000469305.1	39483	39483	type	True	77.3754	103	651	95	below_threshold
Absicoccus porci	strain=YH-panp20	GCA_003725415.1	2486576	2486576	type	True	77.3675	58	651	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:39,858] [INFO] DFAST Taxonomy check result was written to GCF_009696175.1_ASM969617v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:39,859] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:39,859] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:39,860] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1af59bf5-9923-4732-a574-02cd29b59d8b/dqc_reference/checkm_data
[2024-01-24 13:28:39,862] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:39,884] [INFO] Task started: CheckM
[2024-01-24 13:28:39,884] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009696175.1_ASM969617v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009696175.1_ASM969617v1_genomic.fna/checkm_input GCF_009696175.1_ASM969617v1_genomic.fna/checkm_result
[2024-01-24 13:28:59,843] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:59,845] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 3.12%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2024-01-24 13:28:59,865] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:59,866] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:59,867] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009696175.1_ASM969617v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:59,867] [INFO] Task started: Blastn
[2024-01-24 13:28:59,867] [INFO] Running command: blastn -query GCF_009696175.1_ASM969617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1af59bf5-9923-4732-a574-02cd29b59d8b/dqc_reference/reference_markers_gtdb.fasta -out GCF_009696175.1_ASM969617v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:00,668] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:00,671] [INFO] Selected 13 target genomes.
[2024-01-24 13:29:00,671] [INFO] Target genome list was writen to GCF_009696175.1_ASM969617v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:00,686] [INFO] Task started: fastANI
[2024-01-24 13:29:00,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg184da42e-9aff-472d-ad0e-aab9bb919778/GCF_009696175.1_ASM969617v1_genomic.fna.gz --refList GCF_009696175.1_ASM969617v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009696175.1_ASM969617v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:05,496] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:05,504] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:05,505] [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_009696175.1	s__Floccifex porci	100.0	650	651	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Floccifex	95.0	99.09	99.09	0.94	0.94	2	conclusive
GCF_009696075.1	s__Holdemanella porci	78.7168	96	651	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	96.44	95.01	0.80	0.66	21	-
GCF_003436425.1	s__Holdemanella sp003436425	78.5044	105	651	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	98.46	97.77	0.88	0.82	5	-
GCA_900556915.1	s__Holdemanella sp900556915	78.3165	54	651	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	96.25	96.18	0.85	0.83	3	-
GCA_900754615.1	s__Holdemanella sp900754615	77.9272	85	651	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725415.1	s__Absicoccus porci	77.3908	59	651	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Absicoccus	95.0	98.56	98.14	0.93	0.90	14	-
GCF_000469305.1	s__Faecalitalea cylindroides	77.3754	103	651	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalitalea	95.0	98.51	97.31	0.84	0.75	12	-
GCA_018065105.1	s__Floccifex sp018065105	77.1509	95	651	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Floccifex	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014337235.1	s__NSJ-61 sp003433845	76.9141	52	651	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__NSJ-61	95.0	99.54	98.10	0.85	0.77	12	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:05,507] [INFO] GTDB search result was written to GCF_009696175.1_ASM969617v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:05,508] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:05,513] [INFO] DFAST_QC result json was written to GCF_009696175.1_ASM969617v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:05,513] [INFO] DFAST_QC completed!
[2024-01-24 13:29:05,513] [INFO] Total running time: 0h0m37s