[2023-06-18 12:30:43,822] [INFO] DFAST_QC pipeline started.
[2023-06-18 12:30:43,824] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 12:30:43,824] [INFO] DQC Reference Directory: /var/lib/cwl/stg38131399-3c12-4538-a5e9-eb851f29aeab/dqc_reference
[2023-06-18 12:30:45,068] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 12:30:45,069] [INFO] Task started: Prodigal
[2023-06-18 12:30:45,069] [INFO] Running command: gunzip -c /var/lib/cwl/stg2df55717-40fd-4a61-8813-d73e47c5f177/GCA_014848055.1_ASM1484805v1_genomic.fna.gz | prodigal -d GCA_014848055.1_ASM1484805v1_genomic.fna/cds.fna -a GCA_014848055.1_ASM1484805v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 12:30:49,753] [INFO] Task succeeded: Prodigal
[2023-06-18 12:30:49,754] [INFO] Task started: HMMsearch
[2023-06-18 12:30:49,754] [INFO] Running command: hmmsearch --tblout GCA_014848055.1_ASM1484805v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38131399-3c12-4538-a5e9-eb851f29aeab/dqc_reference/reference_markers.hmm GCA_014848055.1_ASM1484805v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 12:30:49,984] [INFO] Task succeeded: HMMsearch
[2023-06-18 12:30:49,986] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2df55717-40fd-4a61-8813-d73e47c5f177/GCA_014848055.1_ASM1484805v1_genomic.fna.gz]
[2023-06-18 12:30:50,015] [INFO] Query marker FASTA was written to GCA_014848055.1_ASM1484805v1_genomic.fna/markers.fasta
[2023-06-18 12:30:50,016] [INFO] Task started: Blastn
[2023-06-18 12:30:50,016] [INFO] Running command: blastn -query GCA_014848055.1_ASM1484805v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38131399-3c12-4538-a5e9-eb851f29aeab/dqc_reference/reference_markers.fasta -out GCA_014848055.1_ASM1484805v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 12:30:50,596] [INFO] Task succeeded: Blastn
[2023-06-18 12:30:50,603] [INFO] Selected 19 target genomes.
[2023-06-18 12:30:50,604] [INFO] Target genome list was writen to GCA_014848055.1_ASM1484805v1_genomic.fna/target_genomes.txt
[2023-06-18 12:30:50,632] [INFO] Task started: fastANI
[2023-06-18 12:30:50,633] [INFO] Running command: fastANI --query /var/lib/cwl/stg2df55717-40fd-4a61-8813-d73e47c5f177/GCA_014848055.1_ASM1484805v1_genomic.fna.gz --refList GCA_014848055.1_ASM1484805v1_genomic.fna/target_genomes.txt --output GCA_014848055.1_ASM1484805v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 12:30:58,100] [INFO] Task succeeded: fastANI
[2023-06-18 12:30:58,100] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38131399-3c12-4538-a5e9-eb851f29aeab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 12:30:58,101] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38131399-3c12-4538-a5e9-eb851f29aeab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 12:30:58,112] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2023-06-18 12:30:58,112] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-18 12:30:58,112] [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	95.8656	478	740	95	conclusive
Holdemanella biformis	strain=DSM 3989	GCA_000156655.1	1735	1735	suspected-type	True	90.6676	542	740	95	below_threshold
Floccifex porci	strain=LKV-178-WT-2G	GCA_009696175.1	2606629	2606629	type	True	78.0085	84	740	95	below_threshold
Faecalitalea cylindroides	strain=ATCC 27803	GCA_000469305.1	39483	39483	type	True	77.694	111	740	95	below_threshold
Faecalicoccus pleomorphus	strain=NCTC11087	GCA_900459315.1	1323	1323	type	True	76.9591	70	740	95	below_threshold
Faecalicoccus pleomorphus	strain=DSM 20574	GCA_000420345.1	1323	1323	type	True	76.9392	71	740	95	below_threshold
Absicoccus porci	strain=YH-panp20	GCA_003725415.1	2486576	2486576	type	True	76.9031	82	740	95	below_threshold
Amedibacterium intestinale	strain=9CBEGH2	GCA_010537335.1	2583452	2583452	type	True	76.7716	67	740	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 12:30:58,116] [INFO] DFAST Taxonomy check result was written to GCA_014848055.1_ASM1484805v1_genomic.fna/tc_result.tsv
[2023-06-18 12:30:58,117] [INFO] ===== Taxonomy check completed =====
[2023-06-18 12:30:58,117] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 12:30:58,117] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38131399-3c12-4538-a5e9-eb851f29aeab/dqc_reference/checkm_data
[2023-06-18 12:30:58,119] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 12:30:58,154] [INFO] Task started: CheckM
[2023-06-18 12:30:58,154] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014848055.1_ASM1484805v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014848055.1_ASM1484805v1_genomic.fna/checkm_input GCA_014848055.1_ASM1484805v1_genomic.fna/checkm_result
[2023-06-18 12:31:20,031] [INFO] Task succeeded: CheckM
[2023-06-18 12:31:20,032] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 12:31:20,063] [INFO] ===== Completeness check finished =====
[2023-06-18 12:31:20,063] [INFO] ===== Start GTDB Search =====
[2023-06-18 12:31:20,064] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014848055.1_ASM1484805v1_genomic.fna/markers.fasta)
[2023-06-18 12:31:20,064] [INFO] Task started: Blastn
[2023-06-18 12:31:20,064] [INFO] Running command: blastn -query GCA_014848055.1_ASM1484805v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38131399-3c12-4538-a5e9-eb851f29aeab/dqc_reference/reference_markers_gtdb.fasta -out GCA_014848055.1_ASM1484805v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 12:31:20,908] [INFO] Task succeeded: Blastn
[2023-06-18 12:31:20,918] [INFO] Selected 7 target genomes.
[2023-06-18 12:31:20,918] [INFO] Target genome list was writen to GCA_014848055.1_ASM1484805v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 12:31:20,922] [INFO] Task started: fastANI
[2023-06-18 12:31:20,923] [INFO] Running command: fastANI --query /var/lib/cwl/stg2df55717-40fd-4a61-8813-d73e47c5f177/GCA_014848055.1_ASM1484805v1_genomic.fna.gz --refList GCA_014848055.1_ASM1484805v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014848055.1_ASM1484805v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 12:31:24,538] [INFO] Task succeeded: fastANI
[2023-06-18 12:31:24,553] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-18 12:31:24,553] [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	95.8612	478	740	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	96.44	95.01	0.80	0.66	21	inconclusive
GCA_900556915.1	s__Holdemanella sp900556915	95.6979	324	740	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	96.25	96.18	0.85	0.83	3	inconclusive
GCF_003436425.1	s__Holdemanella sp003436425	93.5729	536	740	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	90.6383	543	740	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	89.9886	473	740	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	97.44	96.94	0.79	0.75	3	-
GCF_003458715.1	s__Holdemanella sp003458715	88.8197	518	740	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	97.81	97.17	0.85	0.77	7	-
GCA_900754615.1	s__Holdemanella sp900754615	88.3233	460	740	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 12:31:24,556] [INFO] GTDB search result was written to GCA_014848055.1_ASM1484805v1_genomic.fna/result_gtdb.tsv
[2023-06-18 12:31:24,558] [INFO] ===== GTDB Search completed =====
[2023-06-18 12:31:24,561] [INFO] DFAST_QC result json was written to GCA_014848055.1_ASM1484805v1_genomic.fna/dqc_result.json
[2023-06-18 12:31:24,562] [INFO] DFAST_QC completed!
[2023-06-18 12:31:24,562] [INFO] Total running time: 0h0m41s