[2023-06-05 02:26:31,832] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:26:31,837] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:26:31,837] [INFO] DQC Reference Directory: /var/lib/cwl/stga41242b0-469b-4490-b0eb-cd13a3531e4f/dqc_reference
[2023-06-05 02:26:33,525] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:26:33,547] [INFO] Task started: Prodigal
[2023-06-05 02:26:33,548] [INFO] Running command: gunzip -c /var/lib/cwl/stged544d98-740e-4153-9927-70b207ed1d93/GCA_934754535.1_ERR7738626_bin.238_genomic.fna.gz | prodigal -d GCA_934754535.1_ERR7738626_bin.238_genomic.fna/cds.fna -a GCA_934754535.1_ERR7738626_bin.238_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:26:36,619] [INFO] Task succeeded: Prodigal
[2023-06-05 02:26:36,619] [INFO] Task started: HMMsearch
[2023-06-05 02:26:36,619] [INFO] Running command: hmmsearch --tblout GCA_934754535.1_ERR7738626_bin.238_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga41242b0-469b-4490-b0eb-cd13a3531e4f/dqc_reference/reference_markers.hmm GCA_934754535.1_ERR7738626_bin.238_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:26:36,782] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:26:36,783] [WARNING] Found 5/6 markers. [/var/lib/cwl/stged544d98-740e-4153-9927-70b207ed1d93/GCA_934754535.1_ERR7738626_bin.238_genomic.fna.gz]
[2023-06-05 02:26:36,801] [INFO] Query marker FASTA was written to GCA_934754535.1_ERR7738626_bin.238_genomic.fna/markers.fasta
[2023-06-05 02:26:36,801] [INFO] Task started: Blastn
[2023-06-05 02:26:36,802] [INFO] Running command: blastn -query GCA_934754535.1_ERR7738626_bin.238_genomic.fna/markers.fasta -db /var/lib/cwl/stga41242b0-469b-4490-b0eb-cd13a3531e4f/dqc_reference/reference_markers.fasta -out GCA_934754535.1_ERR7738626_bin.238_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:26:38,251] [INFO] Task succeeded: Blastn
[2023-06-05 02:26:38,255] [INFO] Selected 16 target genomes.
[2023-06-05 02:26:38,255] [INFO] Target genome list was writen to GCA_934754535.1_ERR7738626_bin.238_genomic.fna/target_genomes.txt
[2023-06-05 02:26:38,259] [INFO] Task started: fastANI
[2023-06-05 02:26:38,259] [INFO] Running command: fastANI --query /var/lib/cwl/stged544d98-740e-4153-9927-70b207ed1d93/GCA_934754535.1_ERR7738626_bin.238_genomic.fna.gz --refList GCA_934754535.1_ERR7738626_bin.238_genomic.fna/target_genomes.txt --output GCA_934754535.1_ERR7738626_bin.238_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:26:44,034] [INFO] Task succeeded: fastANI
[2023-06-05 02:26:44,035] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga41242b0-469b-4490-b0eb-cd13a3531e4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:26:44,035] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga41242b0-469b-4490-b0eb-cd13a3531e4f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:26:44,042] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:26:44,043] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 02:26:44,043] [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
Holdemanella porci	strain=LKV-472-APC-3	GCA_009696075.1	2652276	2652276	suspected-type	True	87.3924	348	486	95	below_threshold
Holdemanella biformis	strain=DSM 3989	GCA_000156655.1	1735	1735	suspected-type	True	86.73	374	486	95	below_threshold
Floccifex porci	strain=LKV-178-WT-2G	GCA_009696175.1	2606629	2606629	type	True	77.1243	61	486	95	below_threshold
Faecalitalea cylindroides	strain=ATCC 27803	GCA_000469305.1	39483	39483	type	True	77.0466	77	486	95	below_threshold
Absicoccus porci	strain=YH-panp20	GCA_003725415.1	2486576	2486576	type	True	76.6861	61	486	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 02:26:44,045] [INFO] DFAST Taxonomy check result was written to GCA_934754535.1_ERR7738626_bin.238_genomic.fna/tc_result.tsv
[2023-06-05 02:26:44,046] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:26:44,046] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:26:44,046] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga41242b0-469b-4490-b0eb-cd13a3531e4f/dqc_reference/checkm_data
[2023-06-05 02:26:44,048] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:26:44,069] [INFO] Task started: CheckM
[2023-06-05 02:26:44,070] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934754535.1_ERR7738626_bin.238_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934754535.1_ERR7738626_bin.238_genomic.fna/checkm_input GCA_934754535.1_ERR7738626_bin.238_genomic.fna/checkm_result
[2023-06-05 02:27:00,372] [INFO] Task succeeded: CheckM
[2023-06-05 02:27:00,373] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 43.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 02:27:00,389] [INFO] ===== Completeness check finished =====
[2023-06-05 02:27:00,389] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:27:00,390] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934754535.1_ERR7738626_bin.238_genomic.fna/markers.fasta)
[2023-06-05 02:27:00,390] [INFO] Task started: Blastn
[2023-06-05 02:27:00,390] [INFO] Running command: blastn -query GCA_934754535.1_ERR7738626_bin.238_genomic.fna/markers.fasta -db /var/lib/cwl/stga41242b0-469b-4490-b0eb-cd13a3531e4f/dqc_reference/reference_markers_gtdb.fasta -out GCA_934754535.1_ERR7738626_bin.238_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:27:01,157] [INFO] Task succeeded: Blastn
[2023-06-05 02:27:01,160] [INFO] Selected 7 target genomes.
[2023-06-05 02:27:01,161] [INFO] Target genome list was writen to GCA_934754535.1_ERR7738626_bin.238_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:27:01,164] [INFO] Task started: fastANI
[2023-06-05 02:27:01,164] [INFO] Running command: fastANI --query /var/lib/cwl/stged544d98-740e-4153-9927-70b207ed1d93/GCA_934754535.1_ERR7738626_bin.238_genomic.fna.gz --refList GCA_934754535.1_ERR7738626_bin.238_genomic.fna/target_genomes_gtdb.txt --output GCA_934754535.1_ERR7738626_bin.238_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:27:04,074] [INFO] Task succeeded: fastANI
[2023-06-05 02:27:04,082] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 02:27:04,082] [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_900754615.1	s__Holdemanella sp900754615	97.6071	381	486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003458715.1	s__Holdemanella sp003458715	89.1262	374	486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	97.81	97.17	0.85	0.77	7	-
GCF_009696075.1	s__Holdemanella porci	87.3924	348	486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	96.44	95.01	0.80	0.66	21	-
GCA_900556915.1	s__Holdemanella sp900556915	87.0335	254	486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	96.25	96.18	0.85	0.83	3	-
GCF_003436425.1	s__Holdemanella sp003436425	86.9697	356	486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	98.46	97.77	0.88	0.82	5	-
GCF_000156655.1	s__Holdemanella biformis	86.73	374	486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	96.82	95.86	0.79	0.56	17	-
GCA_900547815.1	s__Holdemanella sp900547815	86.6602	338	486	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	97.44	96.94	0.79	0.75	3	-
--------------------------------------------------------------------------------
[2023-06-05 02:27:04,084] [INFO] GTDB search result was written to GCA_934754535.1_ERR7738626_bin.238_genomic.fna/result_gtdb.tsv
[2023-06-05 02:27:04,084] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:27:04,087] [INFO] DFAST_QC result json was written to GCA_934754535.1_ERR7738626_bin.238_genomic.fna/dqc_result.json
[2023-06-05 02:27:04,087] [INFO] DFAST_QC completed!
[2023-06-05 02:27:04,088] [INFO] Total running time: 0h0m32s