[2023-06-27 04:40:51,898] [INFO] DFAST_QC pipeline started.
[2023-06-27 04:40:51,963] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 04:40:51,964] [INFO] DQC Reference Directory: /var/lib/cwl/stg3906fa65-f46d-4df7-aae0-49a26c72cd1c/dqc_reference
[2023-06-27 04:40:54,902] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 04:40:54,903] [INFO] Task started: Prodigal
[2023-06-27 04:40:54,904] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6d35114-8eb0-4c9e-91c0-4cbab9909775/GCA_002449795.1_ASM244979v1_genomic.fna.gz | prodigal -d GCA_002449795.1_ASM244979v1_genomic.fna/cds.fna -a GCA_002449795.1_ASM244979v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 04:40:57,796] [INFO] Task succeeded: Prodigal
[2023-06-27 04:40:57,797] [INFO] Task started: HMMsearch
[2023-06-27 04:40:57,797] [INFO] Running command: hmmsearch --tblout GCA_002449795.1_ASM244979v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3906fa65-f46d-4df7-aae0-49a26c72cd1c/dqc_reference/reference_markers.hmm GCA_002449795.1_ASM244979v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 04:40:57,957] [INFO] Task succeeded: HMMsearch
[2023-06-27 04:40:57,958] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc6d35114-8eb0-4c9e-91c0-4cbab9909775/GCA_002449795.1_ASM244979v1_genomic.fna.gz]
[2023-06-27 04:40:57,979] [INFO] Query marker FASTA was written to GCA_002449795.1_ASM244979v1_genomic.fna/markers.fasta
[2023-06-27 04:40:57,979] [INFO] Task started: Blastn
[2023-06-27 04:40:57,979] [INFO] Running command: blastn -query GCA_002449795.1_ASM244979v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3906fa65-f46d-4df7-aae0-49a26c72cd1c/dqc_reference/reference_markers.fasta -out GCA_002449795.1_ASM244979v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 04:40:58,944] [INFO] Task succeeded: Blastn
[2023-06-27 04:40:58,947] [INFO] Selected 14 target genomes.
[2023-06-27 04:40:58,948] [INFO] Target genome list was writen to GCA_002449795.1_ASM244979v1_genomic.fna/target_genomes.txt
[2023-06-27 04:40:58,974] [INFO] Task started: fastANI
[2023-06-27 04:40:58,974] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6d35114-8eb0-4c9e-91c0-4cbab9909775/GCA_002449795.1_ASM244979v1_genomic.fna.gz --refList GCA_002449795.1_ASM244979v1_genomic.fna/target_genomes.txt --output GCA_002449795.1_ASM244979v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 04:41:05,974] [INFO] Task succeeded: fastANI
[2023-06-27 04:41:05,975] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3906fa65-f46d-4df7-aae0-49a26c72cd1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 04:41:05,975] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3906fa65-f46d-4df7-aae0-49a26c72cd1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 04:41:05,983] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2023-06-27 04:41:05,983] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-27 04:41:05,983] [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
Kandleria vitulina	strain=DSM 20405	GCA_001436965.1	1630	1630	type	True	99.1255	432	459	95	conclusive
Kandleria vitulina	strain=DSM 20405	GCA_000702065.1	1630	1630	type	True	99.1242	435	459	95	conclusive
Intestinibaculum porci	strain=SG0102	GCA_003925875.1	2487118	2487118	type	True	78.5137	119	459	95	below_threshold
Sharpea azabuensis	strain=DSM 18934	GCA_000702165.1	322505	322505	type	True	78.0933	119	459	95	below_threshold
Catenibacterium mitsuokai	strain=DSM 15897	GCA_025148785.1	100886	100886	suspected-type	True	77.6549	126	459	95	below_threshold
Longibaculum muris	strain=DSM 29487	GCA_024622235.1	1796628	1796628	type	True	77.0699	84	459	95	below_threshold
Longibaculum muris	strain=DSM 29487	GCA_004343035.1	1796628	1796628	type	True	77.0145	84	459	95	below_threshold
Coprobacillus cateniformis	strain=RCA1-24	GCA_009767585.1	100884	100884	type	True	76.5735	69	459	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 04:41:05,986] [INFO] DFAST Taxonomy check result was written to GCA_002449795.1_ASM244979v1_genomic.fna/tc_result.tsv
[2023-06-27 04:41:05,986] [INFO] ===== Taxonomy check completed =====
[2023-06-27 04:41:05,986] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 04:41:05,986] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3906fa65-f46d-4df7-aae0-49a26c72cd1c/dqc_reference/checkm_data
[2023-06-27 04:41:05,987] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 04:41:06,008] [INFO] Task started: CheckM
[2023-06-27 04:41:06,008] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002449795.1_ASM244979v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002449795.1_ASM244979v1_genomic.fna/checkm_input GCA_002449795.1_ASM244979v1_genomic.fna/checkm_result
[2023-06-27 04:41:22,041] [INFO] Task succeeded: CheckM
[2023-06-27 04:41:22,042] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.57%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 04:41:22,059] [INFO] ===== Completeness check finished =====
[2023-06-27 04:41:22,059] [INFO] ===== Start GTDB Search =====
[2023-06-27 04:41:22,060] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002449795.1_ASM244979v1_genomic.fna/markers.fasta)
[2023-06-27 04:41:22,060] [INFO] Task started: Blastn
[2023-06-27 04:41:22,060] [INFO] Running command: blastn -query GCA_002449795.1_ASM244979v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3906fa65-f46d-4df7-aae0-49a26c72cd1c/dqc_reference/reference_markers_gtdb.fasta -out GCA_002449795.1_ASM244979v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 04:41:22,879] [INFO] Task succeeded: Blastn
[2023-06-27 04:41:22,893] [INFO] Selected 11 target genomes.
[2023-06-27 04:41:22,893] [INFO] Target genome list was writen to GCA_002449795.1_ASM244979v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 04:41:22,927] [INFO] Task started: fastANI
[2023-06-27 04:41:22,928] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6d35114-8eb0-4c9e-91c0-4cbab9909775/GCA_002449795.1_ASM244979v1_genomic.fna.gz --refList GCA_002449795.1_ASM244979v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002449795.1_ASM244979v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 04:41:27,801] [INFO] Task succeeded: fastANI
[2023-06-27 04:41:27,810] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 04:41:27,811] [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_000702065.1	s__Kandleria vitulina	99.1242	435	459	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Kandleria	95.0	98.93	98.27	0.93	0.86	20	conclusive
GCF_003925875.1	s__Intestinibaculum porci	78.5341	119	459	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Intestinibaculum	95.0	97.71	97.29	0.92	0.84	24	-
GCF_004168205.1	s__Catenibacterium sp000437715	78.0902	123	459	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	96.65	95.64	0.81	0.75	29	-
GCA_900540665.1	s__Catenibacterium sp900540665	78.0388	105	459	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	99.03	99.03	0.84	0.84	2	-
GCA_900540685.1	s__Catenibacterium sp900540685	77.9781	119	459	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	99.87	99.87	0.90	0.90	2	-
GCF_000173795.1	s__Catenibacterium mitsuokai	77.8586	122	459	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	97.03	96.27	0.82	0.73	7	-
GCA_900764725.1	s__Catenibacterium sp900764725	77.796	112	459	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900764565.1	s__Catenibacterium sp900764565	77.7184	109	459	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317015.1	s__Intestinibaculum sp900317015	77.6083	101	459	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Intestinibaculum	95.0	99.88	99.88	0.98	0.98	2	-
GCA_910579135.1	s__MGBC113645 sp910579135	76.8078	65	459	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__MGBC113645	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 04:41:27,812] [INFO] GTDB search result was written to GCA_002449795.1_ASM244979v1_genomic.fna/result_gtdb.tsv
[2023-06-27 04:41:27,814] [INFO] ===== GTDB Search completed =====
[2023-06-27 04:41:27,824] [INFO] DFAST_QC result json was written to GCA_002449795.1_ASM244979v1_genomic.fna/dqc_result.json
[2023-06-27 04:41:27,825] [INFO] DFAST_QC completed!
[2023-06-27 04:41:27,825] [INFO] Total running time: 0h0m36s