[2024-01-25 19:42:05,646] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:42:05,648] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:42:05,648] [INFO] DQC Reference Directory: /var/lib/cwl/stg57527465-d099-4e1c-87c4-ded833727ab7/dqc_reference
[2024-01-25 19:42:06,798] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:42:06,799] [INFO] Task started: Prodigal
[2024-01-25 19:42:06,799] [INFO] Running command: gunzip -c /var/lib/cwl/stgc592b0b6-89de-4814-bb7a-97351fc3b386/GCF_014202635.1_ASM1420263v1_genomic.fna.gz | prodigal -d GCF_014202635.1_ASM1420263v1_genomic.fna/cds.fna -a GCF_014202635.1_ASM1420263v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:42:10,573] [INFO] Task succeeded: Prodigal
[2024-01-25 19:42:10,573] [INFO] Task started: HMMsearch
[2024-01-25 19:42:10,573] [INFO] Running command: hmmsearch --tblout GCF_014202635.1_ASM1420263v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57527465-d099-4e1c-87c4-ded833727ab7/dqc_reference/reference_markers.hmm GCF_014202635.1_ASM1420263v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:42:10,745] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:42:10,746] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc592b0b6-89de-4814-bb7a-97351fc3b386/GCF_014202635.1_ASM1420263v1_genomic.fna.gz]
[2024-01-25 19:42:10,764] [INFO] Query marker FASTA was written to GCF_014202635.1_ASM1420263v1_genomic.fna/markers.fasta
[2024-01-25 19:42:10,764] [INFO] Task started: Blastn
[2024-01-25 19:42:10,764] [INFO] Running command: blastn -query GCF_014202635.1_ASM1420263v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57527465-d099-4e1c-87c4-ded833727ab7/dqc_reference/reference_markers.fasta -out GCF_014202635.1_ASM1420263v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:11,301] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:11,304] [INFO] Selected 16 target genomes.
[2024-01-25 19:42:11,304] [INFO] Target genome list was writen to GCF_014202635.1_ASM1420263v1_genomic.fna/target_genomes.txt
[2024-01-25 19:42:11,343] [INFO] Task started: fastANI
[2024-01-25 19:42:11,343] [INFO] Running command: fastANI --query /var/lib/cwl/stgc592b0b6-89de-4814-bb7a-97351fc3b386/GCF_014202635.1_ASM1420263v1_genomic.fna.gz --refList GCF_014202635.1_ASM1420263v1_genomic.fna/target_genomes.txt --output GCF_014202635.1_ASM1420263v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:42:17,080] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:17,080] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57527465-d099-4e1c-87c4-ded833727ab7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:42:17,080] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57527465-d099-4e1c-87c4-ded833727ab7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:42:17,086] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:42:17,087] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:42:17,087] [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
Faecalicoccus acidiformans	strain=DSM 26963	GCA_014202635.1	915173	915173	type	True	100.0	574	574	95	conclusive
Faecalicoccus pleomorphus	strain=NCTC11087	GCA_900459315.1	1323	1323	type	True	79.8451	191	574	95	below_threshold
Faecalicoccus pleomorphus	strain=DSM 20574	GCA_000420345.1	1323	1323	type	True	79.6292	193	574	95	below_threshold
Faecalitalea cylindroides	strain=ATCC 27803	GCA_000469305.1	39483	39483	type	True	77.8946	95	574	95	below_threshold
Holdemanella porci	strain=LKV-472-APC-3	GCA_009696075.1	2652276	2652276	suspected-type	True	77.7046	69	574	95	below_threshold
Holdemanella biformis	strain=DSM 3989	GCA_000156655.1	1735	1735	suspected-type	True	77.7013	68	574	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:42:17,088] [INFO] DFAST Taxonomy check result was written to GCF_014202635.1_ASM1420263v1_genomic.fna/tc_result.tsv
[2024-01-25 19:42:17,089] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:42:17,089] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:42:17,089] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57527465-d099-4e1c-87c4-ded833727ab7/dqc_reference/checkm_data
[2024-01-25 19:42:17,090] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:42:17,110] [INFO] Task started: CheckM
[2024-01-25 19:42:17,110] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014202635.1_ASM1420263v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014202635.1_ASM1420263v1_genomic.fna/checkm_input GCF_014202635.1_ASM1420263v1_genomic.fna/checkm_result
[2024-01-25 19:42:35,375] [INFO] Task succeeded: CheckM
[2024-01-25 19:42:35,375] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:42:35,402] [INFO] ===== Completeness check finished =====
[2024-01-25 19:42:35,403] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:42:35,403] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014202635.1_ASM1420263v1_genomic.fna/markers.fasta)
[2024-01-25 19:42:35,403] [INFO] Task started: Blastn
[2024-01-25 19:42:35,403] [INFO] Running command: blastn -query GCF_014202635.1_ASM1420263v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57527465-d099-4e1c-87c4-ded833727ab7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014202635.1_ASM1420263v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:36,153] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:36,156] [INFO] Selected 21 target genomes.
[2024-01-25 19:42:36,156] [INFO] Target genome list was writen to GCF_014202635.1_ASM1420263v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:42:36,173] [INFO] Task started: fastANI
[2024-01-25 19:42:36,174] [INFO] Running command: fastANI --query /var/lib/cwl/stgc592b0b6-89de-4814-bb7a-97351fc3b386/GCF_014202635.1_ASM1420263v1_genomic.fna.gz --refList GCF_014202635.1_ASM1420263v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014202635.1_ASM1420263v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:42:43,776] [INFO] Task succeeded: fastANI
[2024-01-25 19:42:43,782] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:42:43,782] [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_014202635.1	s__Faecalicoccus acidiformans	100.0	574	574	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalicoccus	95.0	98.13	97.66	0.90	0.87	3	conclusive
GCF_000420345.1	s__Faecalicoccus pleomorphus	79.6292	193	574	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalicoccus	95.0413	97.06	96.03	0.88	0.84	9	-
GCA_902399855.1	s__Faecalicoccus sp900546545	79.308	200	574	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalicoccus	95.0413	99.03	98.24	0.89	0.80	8	-
GCF_000469305.1	s__Faecalitalea cylindroides	77.9033	94	574	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Faecalitalea	95.0	98.51	97.31	0.84	0.75	12	-
GCF_003458715.1	s__Holdemanella sp003458715	77.8357	60	574	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	97.81	97.17	0.85	0.77	7	-
GCF_003436425.1	s__Holdemanella sp003436425	77.7462	68	574	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	77.6555	69	574	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Holdemanella	95.0	96.82	95.86	0.79	0.56	17	-
--------------------------------------------------------------------------------
[2024-01-25 19:42:43,784] [INFO] GTDB search result was written to GCF_014202635.1_ASM1420263v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:42:43,784] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:42:43,786] [INFO] DFAST_QC result json was written to GCF_014202635.1_ASM1420263v1_genomic.fna/dqc_result.json
[2024-01-25 19:42:43,787] [INFO] DFAST_QC completed!
[2024-01-25 19:42:43,787] [INFO] Total running time: 0h0m38s