[2024-01-24 12:06:11,174] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:11,177] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:11,177] [INFO] DQC Reference Directory: /var/lib/cwl/stgc93ef4fc-bb76-49ff-b368-53d75dd62721/dqc_reference
[2024-01-24 12:06:13,068] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:13,070] [INFO] Task started: Prodigal
[2024-01-24 12:06:13,070] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc4a9239-902e-4221-aa63-2f7f0603c084/GCF_014385195.1_ASM1438519v1_genomic.fna.gz | prodigal -d GCF_014385195.1_ASM1438519v1_genomic.fna/cds.fna -a GCF_014385195.1_ASM1438519v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:18,774] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:18,774] [INFO] Task started: HMMsearch
[2024-01-24 12:06:18,774] [INFO] Running command: hmmsearch --tblout GCF_014385195.1_ASM1438519v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc93ef4fc-bb76-49ff-b368-53d75dd62721/dqc_reference/reference_markers.hmm GCF_014385195.1_ASM1438519v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:19,139] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:19,140] [INFO] Found 6/6 markers.
[2024-01-24 12:06:19,170] [INFO] Query marker FASTA was written to GCF_014385195.1_ASM1438519v1_genomic.fna/markers.fasta
[2024-01-24 12:06:19,171] [INFO] Task started: Blastn
[2024-01-24 12:06:19,171] [INFO] Running command: blastn -query GCF_014385195.1_ASM1438519v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc93ef4fc-bb76-49ff-b368-53d75dd62721/dqc_reference/reference_markers.fasta -out GCF_014385195.1_ASM1438519v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:21,821] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:21,825] [INFO] Selected 18 target genomes.
[2024-01-24 12:06:21,825] [INFO] Target genome list was writen to GCF_014385195.1_ASM1438519v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:21,899] [INFO] Task started: fastANI
[2024-01-24 12:06:21,899] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc4a9239-902e-4221-aa63-2f7f0603c084/GCF_014385195.1_ASM1438519v1_genomic.fna.gz --refList GCF_014385195.1_ASM1438519v1_genomic.fna/target_genomes.txt --output GCF_014385195.1_ASM1438519v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:31,420] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:31,420] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc93ef4fc-bb76-49ff-b368-53d75dd62721/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:31,420] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc93ef4fc-bb76-49ff-b368-53d75dd62721/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:31,428] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:06:31,428] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:06:31,428] [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
Tissierella pigra	strain=WCA3-693-APC-4	GCA_009695605.1	2607614	2607614	type	True	76.8949	103	993	95	below_threshold
Tissierella praeacuta	strain=NCTC11158	GCA_900460335.1	43131	43131	type	True	76.796	109	993	95	below_threshold
Tissierella praeacuta	strain=DSM 18095	GCA_900128955.1	43131	43131	type	True	76.7152	105	993	95	below_threshold
Sporanaerobacter acetigenes	strain=DSM 13106	GCA_900130025.1	165813	165813	type	True	76.44	70	993	95	below_threshold
Tissierella creatinophila	strain=DSM 6911	GCA_001940565.1	79681	79681	type	True	76.3795	73	993	95	below_threshold
Keratinibaculum paraultunense	strain=DSM 26752	GCA_004343355.1	1278232	1278232	type	True	76.0999	55	993	95	below_threshold
Keratinibaculum paraultunense	strain=KD-1	GCA_016767175.1	1278232	1278232	type	True	76.0306	57	993	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:31,430] [INFO] DFAST Taxonomy check result was written to GCF_014385195.1_ASM1438519v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:31,431] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:31,431] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:31,432] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc93ef4fc-bb76-49ff-b368-53d75dd62721/dqc_reference/checkm_data
[2024-01-24 12:06:31,433] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:31,470] [INFO] Task started: CheckM
[2024-01-24 12:06:31,470] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014385195.1_ASM1438519v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014385195.1_ASM1438519v1_genomic.fna/checkm_input GCF_014385195.1_ASM1438519v1_genomic.fna/checkm_result
[2024-01-24 12:06:56,794] [INFO] Task succeeded: CheckM
[2024-01-24 12:06:56,799] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:06:56,850] [INFO] ===== Completeness check finished =====
[2024-01-24 12:06:56,850] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:06:56,851] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014385195.1_ASM1438519v1_genomic.fna/markers.fasta)
[2024-01-24 12:06:56,851] [INFO] Task started: Blastn
[2024-01-24 12:06:56,851] [INFO] Running command: blastn -query GCF_014385195.1_ASM1438519v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc93ef4fc-bb76-49ff-b368-53d75dd62721/dqc_reference/reference_markers_gtdb.fasta -out GCF_014385195.1_ASM1438519v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:57,788] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:57,792] [INFO] Selected 21 target genomes.
[2024-01-24 12:06:57,792] [INFO] Target genome list was writen to GCF_014385195.1_ASM1438519v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:06:57,836] [INFO] Task started: fastANI
[2024-01-24 12:06:57,837] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc4a9239-902e-4221-aa63-2f7f0603c084/GCF_014385195.1_ASM1438519v1_genomic.fna.gz --refList GCF_014385195.1_ASM1438519v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014385195.1_ASM1438519v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:08,637] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:08,648] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:08,649] [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_014385195.1	s__BX21 sp014385195	100.0	990	993	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__BX21	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009695605.1	s__DSM105185 sp009695605	76.8944	102	993	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__DSM105185	95.0	99.10	99.10	0.90	0.90	2	-
GCF_000511955.1	s__Schnuerera ultunensis	76.8515	73	993	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__Schnuerera	95.0	99.51	99.51	0.99	0.99	2	-
GCF_900155565.1	s__Anaerosalibacter_A sp900155565	76.7792	74	993	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sporanaerobacteraceae;g__Anaerosalibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128955.1	s__Tissierella praeacuta	76.7152	105	993	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__Tissierella	95.0	99.01	98.20	0.93	0.86	5	-
GCA_012735585.1	s__JAAYTL01 sp012735585	76.5033	91	993	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__JAAYTL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900130025.1	s__Sporanaerobacter acetigenes	76.44	70	993	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sporanaerobacteraceae;g__Sporanaerobacter	95.0	99.49	99.49	0.90	0.90	2	-
GCF_001940565.1	s__Tissierella_A creatinophila	76.3806	73	993	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__Tissierella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002266425.1	s__Tissierella carlieri	76.1825	111	993	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__Tissierella	95.0	97.51	96.78	0.86	0.84	3	-
GCA_012520755.1	s__UBA3583 sp012520755	76.182	65	993	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tissierellaceae;g__UBA3583	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016767175.1	s__Keratinibaculum paraultunense	76.0306	57	993	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Tepidimicrobiaceae;g__Keratinibaculum	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:08,650] [INFO] GTDB search result was written to GCF_014385195.1_ASM1438519v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:08,651] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:08,655] [INFO] DFAST_QC result json was written to GCF_014385195.1_ASM1438519v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:08,655] [INFO] DFAST_QC completed!
[2024-01-24 12:07:08,656] [INFO] Total running time: 0h0m57s