[2024-01-24 13:50:26,854] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:50:26,858] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:50:26,859] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c23d699-eb79-44ed-b408-b78d9b1962d8/dqc_reference
[2024-01-24 13:50:28,440] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:50:28,441] [INFO] Task started: Prodigal
[2024-01-24 13:50:28,441] [INFO] Running command: gunzip -c /var/lib/cwl/stg79046ca1-be97-4d90-96fa-477c7a4b16a6/GCF_003925875.1_ASM392587v1_genomic.fna.gz | prodigal -d GCF_003925875.1_ASM392587v1_genomic.fna/cds.fna -a GCF_003925875.1_ASM392587v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:35,092] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:35,092] [INFO] Task started: HMMsearch
[2024-01-24 13:50:35,093] [INFO] Running command: hmmsearch --tblout GCF_003925875.1_ASM392587v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c23d699-eb79-44ed-b408-b78d9b1962d8/dqc_reference/reference_markers.hmm GCF_003925875.1_ASM392587v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:35,363] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:35,365] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg79046ca1-be97-4d90-96fa-477c7a4b16a6/GCF_003925875.1_ASM392587v1_genomic.fna.gz]
[2024-01-24 13:50:35,411] [INFO] Query marker FASTA was written to GCF_003925875.1_ASM392587v1_genomic.fna/markers.fasta
[2024-01-24 13:50:35,412] [INFO] Task started: Blastn
[2024-01-24 13:50:35,412] [INFO] Running command: blastn -query GCF_003925875.1_ASM392587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c23d699-eb79-44ed-b408-b78d9b1962d8/dqc_reference/reference_markers.fasta -out GCF_003925875.1_ASM392587v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:36,020] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:36,026] [INFO] Selected 22 target genomes.
[2024-01-24 13:50:36,027] [INFO] Target genome list was writen to GCF_003925875.1_ASM392587v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:36,040] [INFO] Task started: fastANI
[2024-01-24 13:50:36,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg79046ca1-be97-4d90-96fa-477c7a4b16a6/GCF_003925875.1_ASM392587v1_genomic.fna.gz --refList GCF_003925875.1_ASM392587v1_genomic.fna/target_genomes.txt --output GCF_003925875.1_ASM392587v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:45,784] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:45,784] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c23d699-eb79-44ed-b408-b78d9b1962d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:45,785] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c23d699-eb79-44ed-b408-b78d9b1962d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:45,797] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:45,797] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:45,797] [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
Intestinibaculum porci	strain=SG0102	GCA_003925875.1	2487118	2487118	type	True	100.0	1063	1070	95	conclusive
Catenibacterium mitsuokai	strain=DSM 15897	GCA_025148785.1	100886	100886	suspected-type	True	79.4161	111	1070	95	below_threshold
Kandleria vitulina	strain=DSM 20405	GCA_000702065.1	1630	1630	type	True	78.651	141	1070	95	below_threshold
Kandleria vitulina	strain=DSM 20405	GCA_001436965.1	1630	1630	type	True	78.6294	137	1070	95	below_threshold
Longibaculum muris	strain=DSM 29487	GCA_004343035.1	1796628	1796628	type	True	77.387	68	1070	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:45,800] [INFO] DFAST Taxonomy check result was written to GCF_003925875.1_ASM392587v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:45,801] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:45,801] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:45,802] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c23d699-eb79-44ed-b408-b78d9b1962d8/dqc_reference/checkm_data
[2024-01-24 13:50:45,804] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:45,853] [INFO] Task started: CheckM
[2024-01-24 13:50:45,853] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003925875.1_ASM392587v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003925875.1_ASM392587v1_genomic.fna/checkm_input GCF_003925875.1_ASM392587v1_genomic.fna/checkm_result
[2024-01-24 13:51:13,511] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:13,513] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:13,542] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:13,542] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:13,543] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003925875.1_ASM392587v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:13,544] [INFO] Task started: Blastn
[2024-01-24 13:51:13,544] [INFO] Running command: blastn -query GCF_003925875.1_ASM392587v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c23d699-eb79-44ed-b408-b78d9b1962d8/dqc_reference/reference_markers_gtdb.fasta -out GCF_003925875.1_ASM392587v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:14,375] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:14,378] [INFO] Selected 15 target genomes.
[2024-01-24 13:51:14,378] [INFO] Target genome list was writen to GCF_003925875.1_ASM392587v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:14,391] [INFO] Task started: fastANI
[2024-01-24 13:51:14,391] [INFO] Running command: fastANI --query /var/lib/cwl/stg79046ca1-be97-4d90-96fa-477c7a4b16a6/GCF_003925875.1_ASM392587v1_genomic.fna.gz --refList GCF_003925875.1_ASM392587v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003925875.1_ASM392587v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:21,888] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:21,904] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:21,904] [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_003925875.1	s__Intestinibaculum porci	100.0	1064	1070	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Intestinibaculum	95.0	97.71	97.29	0.92	0.84	24	conclusive
GCA_900317015.1	s__Intestinibaculum sp900317015	78.7457	268	1070	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Intestinibaculum	95.0	99.88	99.88	0.98	0.98	2	-
GCF_000702065.1	s__Kandleria vitulina	78.6499	141	1070	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Kandleria	95.0	98.93	98.27	0.93	0.86	20	-
GCF_000173795.1	s__Catenibacterium mitsuokai	78.0477	97	1070	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	97.03	96.27	0.82	0.73	7	-
GCF_004168205.1	s__Catenibacterium sp000437715	78.0359	90	1070	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	96.65	95.64	0.81	0.75	29	-
GCA_900764725.1	s__Catenibacterium sp900764725	77.3255	92	1070	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540685.1	s__Catenibacterium sp900540685	77.2779	108	1070	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	99.87	99.87	0.90	0.90	2	-
GCA_017633115.1	s__RGIG9341 sp017633115	76.975	69	1070	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__RGIG9341	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016901755.1	s__Faecalibacillus spiroforme_A	76.3678	51	1070	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	98.80	98.79	0.88	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:21,906] [INFO] GTDB search result was written to GCF_003925875.1_ASM392587v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:21,907] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:21,911] [INFO] DFAST_QC result json was written to GCF_003925875.1_ASM392587v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:21,912] [INFO] DFAST_QC completed!
[2024-01-24 13:51:21,912] [INFO] Total running time: 0h0m55s