[2024-01-24 14:07:31,191] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:07:31,193] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:07:31,193] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e02ee44-a813-482f-9e1b-301e862fbd13/dqc_reference
[2024-01-24 14:07:32,427] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:32,428] [INFO] Task started: Prodigal
[2024-01-24 14:07:32,428] [INFO] Running command: gunzip -c /var/lib/cwl/stg60d16dc3-0e6f-48ee-9645-cc91a74ba6ef/GCF_003725415.1_YH-panp20_genomic.fna.gz | prodigal -d GCF_003725415.1_YH-panp20_genomic.fna/cds.fna -a GCF_003725415.1_YH-panp20_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:38,337] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:38,338] [INFO] Task started: HMMsearch
[2024-01-24 14:07:38,338] [INFO] Running command: hmmsearch --tblout GCF_003725415.1_YH-panp20_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e02ee44-a813-482f-9e1b-301e862fbd13/dqc_reference/reference_markers.hmm GCF_003725415.1_YH-panp20_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:38,577] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:38,578] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg60d16dc3-0e6f-48ee-9645-cc91a74ba6ef/GCF_003725415.1_YH-panp20_genomic.fna.gz]
[2024-01-24 14:07:38,604] [INFO] Query marker FASTA was written to GCF_003725415.1_YH-panp20_genomic.fna/markers.fasta
[2024-01-24 14:07:38,605] [INFO] Task started: Blastn
[2024-01-24 14:07:38,605] [INFO] Running command: blastn -query GCF_003725415.1_YH-panp20_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e02ee44-a813-482f-9e1b-301e862fbd13/dqc_reference/reference_markers.fasta -out GCF_003725415.1_YH-panp20_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:39,175] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:39,183] [INFO] Selected 20 target genomes.
[2024-01-24 14:07:39,184] [INFO] Target genome list was writen to GCF_003725415.1_YH-panp20_genomic.fna/target_genomes.txt
[2024-01-24 14:07:39,194] [INFO] Task started: fastANI
[2024-01-24 14:07:39,194] [INFO] Running command: fastANI --query /var/lib/cwl/stg60d16dc3-0e6f-48ee-9645-cc91a74ba6ef/GCF_003725415.1_YH-panp20_genomic.fna.gz --refList GCF_003725415.1_YH-panp20_genomic.fna/target_genomes.txt --output GCF_003725415.1_YH-panp20_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:48,213] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:48,214] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e02ee44-a813-482f-9e1b-301e862fbd13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:48,214] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e02ee44-a813-482f-9e1b-301e862fbd13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:48,220] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:07:48,220] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:48,221] [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
Absicoccus porci	strain=YH-panp20	GCA_003725415.1	2486576	2486576	type	True	100.0	731	734	95	conclusive
Faecalicoccus acidiformans	strain=DSM 26963	GCA_014202635.1	915173	915173	type	True	78.103	59	734	95	below_threshold
Holdemanella biformis	strain=DSM 3989	GCA_000156655.1	1735	1735	suspected-type	True	77.9126	99	734	95	below_threshold
Floccifex porci	strain=LKV-178-WT-2G	GCA_009696175.1	2606629	2606629	type	True	77.4012	59	734	95	below_threshold
Catenisphaera adipataccumulans	strain=DSM 25799	GCA_014202755.1	700500	700500	type	True	76.9089	55	734	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:48,222] [INFO] DFAST Taxonomy check result was written to GCF_003725415.1_YH-panp20_genomic.fna/tc_result.tsv
[2024-01-24 14:07:48,223] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:48,223] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:48,223] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e02ee44-a813-482f-9e1b-301e862fbd13/dqc_reference/checkm_data
[2024-01-24 14:07:48,224] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:48,253] [INFO] Task started: CheckM
[2024-01-24 14:07:48,253] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003725415.1_YH-panp20_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003725415.1_YH-panp20_genomic.fna/checkm_input GCF_003725415.1_YH-panp20_genomic.fna/checkm_result
[2024-01-24 14:08:13,991] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:13,992] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 4.17%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:14,013] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:14,014] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:14,014] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003725415.1_YH-panp20_genomic.fna/markers.fasta)
[2024-01-24 14:08:14,014] [INFO] Task started: Blastn
[2024-01-24 14:08:14,015] [INFO] Running command: blastn -query GCF_003725415.1_YH-panp20_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e02ee44-a813-482f-9e1b-301e862fbd13/dqc_reference/reference_markers_gtdb.fasta -out GCF_003725415.1_YH-panp20_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:14,871] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:14,874] [INFO] Selected 18 target genomes.
[2024-01-24 14:08:14,874] [INFO] Target genome list was writen to GCF_003725415.1_YH-panp20_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:14,908] [INFO] Task started: fastANI
[2024-01-24 14:08:14,908] [INFO] Running command: fastANI --query /var/lib/cwl/stg60d16dc3-0e6f-48ee-9645-cc91a74ba6ef/GCF_003725415.1_YH-panp20_genomic.fna.gz --refList GCF_003725415.1_YH-panp20_genomic.fna/target_genomes_gtdb.txt --output GCF_003725415.1_YH-panp20_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:21,375] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:21,390] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:21,390] [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_003725415.1	s__Absicoccus porci	100.0	731	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Absicoccus	95.0	98.56	98.14	0.93	0.90	14	conclusive
GCA_902399855.1	s__Faecalicoccus sp900546545	78.7433	80	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalicoccus	95.0413	99.03	98.24	0.89	0.80	8	-
GCA_003480165.1	s__Absicoccus sp000434355	78.4326	179	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Absicoccus	95.0	99.44	99.16	0.95	0.93	5	-
GCF_000420345.1	s__Faecalicoccus pleomorphus	78.2693	73	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalicoccus	95.0413	97.06	96.03	0.88	0.84	9	-
GCF_014202635.1	s__Faecalicoccus acidiformans	78.1592	58	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalicoccus	95.0	98.13	97.66	0.90	0.87	3	-
GCF_000156655.1	s__Holdemanella biformis	77.9423	98	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	96.82	95.86	0.79	0.56	17	-
GCA_900754615.1	s__Holdemanella sp900754615	77.4018	88	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009696175.1	s__Floccifex porci	77.4012	59	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Floccifex	95.0	99.09	99.09	0.94	0.94	2	-
GCA_900556915.1	s__Holdemanella sp900556915	76.9811	58	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	96.25	96.18	0.85	0.83	3	-
GCF_014202755.1	s__Catenisphaera adipataccumulans	76.9472	54	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Catenisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000469305.1	s__Faecalitalea cylindroides	76.8013	61	734	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalitalea	95.0	98.51	97.31	0.84	0.75	12	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:21,395] [INFO] GTDB search result was written to GCF_003725415.1_YH-panp20_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:21,396] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:21,400] [INFO] DFAST_QC result json was written to GCF_003725415.1_YH-panp20_genomic.fna/dqc_result.json
[2024-01-24 14:08:21,400] [INFO] DFAST_QC completed!
[2024-01-24 14:08:21,400] [INFO] Total running time: 0h0m50s