[2023-06-17 03:26:38,870] [INFO] DFAST_QC pipeline started.
[2023-06-17 03:26:38,873] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 03:26:38,873] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf6538bb-1a2f-4eac-91f7-8d024e16db0e/dqc_reference
[2023-06-17 03:26:40,904] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 03:26:40,905] [INFO] Task started: Prodigal
[2023-06-17 03:26:40,905] [INFO] Running command: gunzip -c /var/lib/cwl/stga1cc37d1-a95c-4532-a485-2b351b0a5575/GCA_905207045.1_ERR1600733-mag-bin.40_genomic.fna.gz | prodigal -d GCA_905207045.1_ERR1600733-mag-bin.40_genomic.fna/cds.fna -a GCA_905207045.1_ERR1600733-mag-bin.40_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 03:26:44,389] [INFO] Task succeeded: Prodigal
[2023-06-17 03:26:44,390] [INFO] Task started: HMMsearch
[2023-06-17 03:26:44,390] [INFO] Running command: hmmsearch --tblout GCA_905207045.1_ERR1600733-mag-bin.40_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf6538bb-1a2f-4eac-91f7-8d024e16db0e/dqc_reference/reference_markers.hmm GCA_905207045.1_ERR1600733-mag-bin.40_genomic.fna/protein.faa > /dev/null
[2023-06-17 03:26:44,604] [INFO] Task succeeded: HMMsearch
[2023-06-17 03:26:44,605] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga1cc37d1-a95c-4532-a485-2b351b0a5575/GCA_905207045.1_ERR1600733-mag-bin.40_genomic.fna.gz]
[2023-06-17 03:26:44,626] [INFO] Query marker FASTA was written to GCA_905207045.1_ERR1600733-mag-bin.40_genomic.fna/markers.fasta
[2023-06-17 03:26:44,627] [INFO] Task started: Blastn
[2023-06-17 03:26:44,627] [INFO] Running command: blastn -query GCA_905207045.1_ERR1600733-mag-bin.40_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf6538bb-1a2f-4eac-91f7-8d024e16db0e/dqc_reference/reference_markers.fasta -out GCA_905207045.1_ERR1600733-mag-bin.40_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 03:26:45,568] [INFO] Task succeeded: Blastn
[2023-06-17 03:26:45,571] [INFO] Selected 15 target genomes.
[2023-06-17 03:26:45,572] [INFO] Target genome list was writen to GCA_905207045.1_ERR1600733-mag-bin.40_genomic.fna/target_genomes.txt
[2023-06-17 03:26:45,638] [INFO] Task started: fastANI
[2023-06-17 03:26:45,638] [INFO] Running command: fastANI --query /var/lib/cwl/stga1cc37d1-a95c-4532-a485-2b351b0a5575/GCA_905207045.1_ERR1600733-mag-bin.40_genomic.fna.gz --refList GCA_905207045.1_ERR1600733-mag-bin.40_genomic.fna/target_genomes.txt --output GCA_905207045.1_ERR1600733-mag-bin.40_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 03:26:52,403] [INFO] Task succeeded: fastANI
[2023-06-17 03:26:52,403] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf6538bb-1a2f-4eac-91f7-8d024e16db0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 03:26:52,404] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf6538bb-1a2f-4eac-91f7-8d024e16db0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 03:26:52,419] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 03:26:52,419] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 03:26:52,420] [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
Catenibacterium mitsuokai	strain=DSM 15897	GCA_025148785.1	100886	100886	suspected-type	True	94.0111	560	641	95	below_threshold
Sharpea porci	strain=CA-Schmier-601-WT-3	GCA_009695655.1	2652286	2652286	type	True	77.9705	118	641	95	below_threshold
Kandleria vitulina	strain=DSM 20405	GCA_000702065.1	1630	1630	type	True	77.9608	139	641	95	below_threshold
Kandleria vitulina	strain=DSM 20405	GCA_001436965.1	1630	1630	type	True	77.8501	138	641	95	below_threshold
Intestinibaculum porci	strain=SG0102	GCA_003925875.1	2487118	2487118	type	True	77.6991	94	641	95	below_threshold
Sharpea azabuensis	strain=DSM 18934	GCA_000702165.1	322505	322505	type	True	77.5888	128	641	95	below_threshold
Coprobacillus cateniformis	strain=RCA1-24	GCA_009767585.1	100884	100884	type	True	77.3229	83	641	95	below_threshold
Eggerthia catenaformis	strain=OT 569	GCA_000340375.1	31973	31973	type	True	77.0437	84	641	95	below_threshold
Eggerthia catenaformis	strain=DSM 20559	GCA_000422605.1	31973	31973	type	True	77.0027	86	641	95	below_threshold
Erysipelatoclostridium ramosum		GCA_900660185.1	1547	1547	type	True	76.7537	62	641	95	below_threshold
[Clostridium] cocleatum	strain=I50	GCA_010206155.1	69824	69824	type	True	76.3139	60	641	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 03:26:52,422] [INFO] DFAST Taxonomy check result was written to GCA_905207045.1_ERR1600733-mag-bin.40_genomic.fna/tc_result.tsv
[2023-06-17 03:26:52,422] [INFO] ===== Taxonomy check completed =====
[2023-06-17 03:26:52,422] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 03:26:52,423] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf6538bb-1a2f-4eac-91f7-8d024e16db0e/dqc_reference/checkm_data
[2023-06-17 03:26:52,424] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 03:26:52,453] [INFO] Task started: CheckM
[2023-06-17 03:26:52,453] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905207045.1_ERR1600733-mag-bin.40_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905207045.1_ERR1600733-mag-bin.40_genomic.fna/checkm_input GCA_905207045.1_ERR1600733-mag-bin.40_genomic.fna/checkm_result
[2023-06-17 03:27:11,327] [INFO] Task succeeded: CheckM
[2023-06-17 03:27:11,328] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 03:27:11,347] [INFO] ===== Completeness check finished =====
[2023-06-17 03:27:11,347] [INFO] ===== Start GTDB Search =====
[2023-06-17 03:27:11,348] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905207045.1_ERR1600733-mag-bin.40_genomic.fna/markers.fasta)
[2023-06-17 03:27:11,348] [INFO] Task started: Blastn
[2023-06-17 03:27:11,348] [INFO] Running command: blastn -query GCA_905207045.1_ERR1600733-mag-bin.40_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf6538bb-1a2f-4eac-91f7-8d024e16db0e/dqc_reference/reference_markers_gtdb.fasta -out GCA_905207045.1_ERR1600733-mag-bin.40_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 03:27:12,185] [INFO] Task succeeded: Blastn
[2023-06-17 03:27:12,190] [INFO] Selected 6 target genomes.
[2023-06-17 03:27:12,190] [INFO] Target genome list was writen to GCA_905207045.1_ERR1600733-mag-bin.40_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 03:27:12,195] [INFO] Task started: fastANI
[2023-06-17 03:27:12,195] [INFO] Running command: fastANI --query /var/lib/cwl/stga1cc37d1-a95c-4532-a485-2b351b0a5575/GCA_905207045.1_ERR1600733-mag-bin.40_genomic.fna.gz --refList GCA_905207045.1_ERR1600733-mag-bin.40_genomic.fna/target_genomes_gtdb.txt --output GCA_905207045.1_ERR1600733-mag-bin.40_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 03:27:15,739] [INFO] Task succeeded: fastANI
[2023-06-17 03:27:15,751] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 03:27:15,751] [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_900540665.1	s__Catenibacterium sp900540665	98.9289	536	641	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	99.03	99.03	0.84	0.84	2	conclusive
GCF_000173795.1	s__Catenibacterium mitsuokai	94.0602	517	641	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	92.7746	500	641	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	96.65	95.64	0.81	0.75	29	-
GCA_900764565.1	s__Catenibacterium sp900764565	92.3744	442	641	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	92.2323	508	641	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	99.87	99.87	0.90	0.90	2	-
GCA_900764725.1	s__Catenibacterium sp900764725	91.2368	456	641	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Catenibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 03:27:15,753] [INFO] GTDB search result was written to GCA_905207045.1_ERR1600733-mag-bin.40_genomic.fna/result_gtdb.tsv
[2023-06-17 03:27:15,754] [INFO] ===== GTDB Search completed =====
[2023-06-17 03:27:15,757] [INFO] DFAST_QC result json was written to GCA_905207045.1_ERR1600733-mag-bin.40_genomic.fna/dqc_result.json
[2023-06-17 03:27:15,757] [INFO] DFAST_QC completed!
[2023-06-17 03:27:15,757] [INFO] Total running time: 0h0m37s