[2024-01-24 12:00:36,718] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:00:36,722] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:00:36,722] [INFO] DQC Reference Directory: /var/lib/cwl/stgfdabe8d8-1819-4e3c-be32-ad88a9a93091/dqc_reference
[2024-01-24 12:00:39,377] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:00:39,379] [INFO] Task started: Prodigal
[2024-01-24 12:00:39,379] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4bf5caa-7f52-4347-9b76-eb36952dd733/GCF_014306155.1_ASM1430615v1_genomic.fna.gz | prodigal -d GCF_014306155.1_ASM1430615v1_genomic.fna/cds.fna -a GCF_014306155.1_ASM1430615v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:00:43,928] [INFO] Task succeeded: Prodigal
[2024-01-24 12:00:43,929] [INFO] Task started: HMMsearch
[2024-01-24 12:00:43,929] [INFO] Running command: hmmsearch --tblout GCF_014306155.1_ASM1430615v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfdabe8d8-1819-4e3c-be32-ad88a9a93091/dqc_reference/reference_markers.hmm GCF_014306155.1_ASM1430615v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:00:44,169] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:00:44,171] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb4bf5caa-7f52-4347-9b76-eb36952dd733/GCF_014306155.1_ASM1430615v1_genomic.fna.gz]
[2024-01-24 12:00:44,206] [INFO] Query marker FASTA was written to GCF_014306155.1_ASM1430615v1_genomic.fna/markers.fasta
[2024-01-24 12:00:44,206] [INFO] Task started: Blastn
[2024-01-24 12:00:44,207] [INFO] Running command: blastn -query GCF_014306155.1_ASM1430615v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdabe8d8-1819-4e3c-be32-ad88a9a93091/dqc_reference/reference_markers.fasta -out GCF_014306155.1_ASM1430615v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:45,175] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:45,179] [INFO] Selected 21 target genomes.
[2024-01-24 12:00:45,180] [INFO] Target genome list was writen to GCF_014306155.1_ASM1430615v1_genomic.fna/target_genomes.txt
[2024-01-24 12:00:45,267] [INFO] Task started: fastANI
[2024-01-24 12:00:45,267] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4bf5caa-7f52-4347-9b76-eb36952dd733/GCF_014306155.1_ASM1430615v1_genomic.fna.gz --refList GCF_014306155.1_ASM1430615v1_genomic.fna/target_genomes.txt --output GCF_014306155.1_ASM1430615v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:54,173] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:54,173] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfdabe8d8-1819-4e3c-be32-ad88a9a93091/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:54,174] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfdabe8d8-1819-4e3c-be32-ad88a9a93091/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:54,185] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:00:54,185] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:00:54,185] [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	95.4586	517	708	95	conclusive
Holdemanella biformis	strain=DSM 3989	GCA_000156655.1	1735	1735	suspected-type	True	90.2792	525	708	95	below_threshold
Floccifex porci	strain=LKV-178-WT-2G	GCA_009696175.1	2606629	2606629	type	True	78.1364	107	708	95	below_threshold
Amedibacterium intestinale	strain=9CBEGH2	GCA_010537335.1	2583452	2583452	type	True	77.6974	62	708	95	below_threshold
Faecalicoccus acidiformans	strain=DSM 26963	GCA_014202635.1	915173	915173	type	True	77.6267	72	708	95	below_threshold
Absicoccus porci	strain=YH-panp20	GCA_003725415.1	2486576	2486576	type	True	77.5673	91	708	95	below_threshold
Faecalitalea cylindroides	strain=ATCC 27803	GCA_000469305.1	39483	39483	type	True	77.5217	127	708	95	below_threshold
Faecalicoccus pleomorphus	strain=NCTC11087	GCA_900459315.1	1323	1323	type	True	77.1423	81	708	95	below_threshold
Faecalicoccus pleomorphus	strain=DSM 20574	GCA_000420345.1	1323	1323	type	True	77.0745	83	708	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:54,188] [INFO] DFAST Taxonomy check result was written to GCF_014306155.1_ASM1430615v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:54,188] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:54,188] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:54,189] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfdabe8d8-1819-4e3c-be32-ad88a9a93091/dqc_reference/checkm_data
[2024-01-24 12:00:54,189] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:54,214] [INFO] Task started: CheckM
[2024-01-24 12:00:54,214] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014306155.1_ASM1430615v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014306155.1_ASM1430615v1_genomic.fna/checkm_input GCF_014306155.1_ASM1430615v1_genomic.fna/checkm_result
[2024-01-24 12:01:15,156] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:15,157] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 4.17%
Strain heterogeneity: 60.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:15,178] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:15,179] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:15,179] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014306155.1_ASM1430615v1_genomic.fna/markers.fasta)
[2024-01-24 12:01:15,180] [INFO] Task started: Blastn
[2024-01-24 12:01:15,180] [INFO] Running command: blastn -query GCF_014306155.1_ASM1430615v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfdabe8d8-1819-4e3c-be32-ad88a9a93091/dqc_reference/reference_markers_gtdb.fasta -out GCF_014306155.1_ASM1430615v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:15,984] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:15,987] [INFO] Selected 7 target genomes.
[2024-01-24 12:01:15,987] [INFO] Target genome list was writen to GCF_014306155.1_ASM1430615v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:15,993] [INFO] Task started: fastANI
[2024-01-24 12:01:15,993] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4bf5caa-7f52-4347-9b76-eb36952dd733/GCF_014306155.1_ASM1430615v1_genomic.fna.gz --refList GCF_014306155.1_ASM1430615v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014306155.1_ASM1430615v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:01:19,597] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:19,611] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:01:19,612] [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_009696075.1	s__Holdemanella porci	95.4945	516	708	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	96.44	95.01	0.80	0.66	21	conclusive
GCA_900556915.1	s__Holdemanella sp900556915	93.7423	314	708	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	93.1833	542	708	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	90.2792	525	708	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	89.6951	455	708	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	97.44	96.94	0.79	0.75	3	-
GCA_900754615.1	s__Holdemanella sp900754615	88.3119	458	708	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003458715.1	s__Holdemanella sp003458715	88.229	514	708	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	97.81	97.17	0.85	0.77	7	-
--------------------------------------------------------------------------------
[2024-01-24 12:01:19,614] [INFO] GTDB search result was written to GCF_014306155.1_ASM1430615v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:01:19,614] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:01:19,617] [INFO] DFAST_QC result json was written to GCF_014306155.1_ASM1430615v1_genomic.fna/dqc_result.json
[2024-01-24 12:01:19,617] [INFO] DFAST_QC completed!
[2024-01-24 12:01:19,617] [INFO] Total running time: 0h0m43s