[2023-06-28 00:41:07,023] [INFO] DFAST_QC pipeline started.
[2023-06-28 00:41:07,026] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 00:41:07,026] [INFO] DQC Reference Directory: /var/lib/cwl/stgcea22fe7-9158-4dce-bc22-50440d57c120/dqc_reference
[2023-06-28 00:41:08,469] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 00:41:08,470] [INFO] Task started: Prodigal
[2023-06-28 00:41:08,470] [INFO] Running command: gunzip -c /var/lib/cwl/stg135b0c07-e84f-42f8-86a0-433ac27525df/GCA_017889095.1_ASM1788909v1_genomic.fna.gz | prodigal -d GCA_017889095.1_ASM1788909v1_genomic.fna/cds.fna -a GCA_017889095.1_ASM1788909v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 00:41:12,947] [INFO] Task succeeded: Prodigal
[2023-06-28 00:41:12,948] [INFO] Task started: HMMsearch
[2023-06-28 00:41:12,948] [INFO] Running command: hmmsearch --tblout GCA_017889095.1_ASM1788909v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcea22fe7-9158-4dce-bc22-50440d57c120/dqc_reference/reference_markers.hmm GCA_017889095.1_ASM1788909v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 00:41:13,157] [INFO] Task succeeded: HMMsearch
[2023-06-28 00:41:13,158] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg135b0c07-e84f-42f8-86a0-433ac27525df/GCA_017889095.1_ASM1788909v1_genomic.fna.gz]
[2023-06-28 00:41:13,191] [INFO] Query marker FASTA was written to GCA_017889095.1_ASM1788909v1_genomic.fna/markers.fasta
[2023-06-28 00:41:13,192] [INFO] Task started: Blastn
[2023-06-28 00:41:13,192] [INFO] Running command: blastn -query GCA_017889095.1_ASM1788909v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcea22fe7-9158-4dce-bc22-50440d57c120/dqc_reference/reference_markers.fasta -out GCA_017889095.1_ASM1788909v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:41:13,757] [INFO] Task succeeded: Blastn
[2023-06-28 00:41:13,761] [INFO] Selected 15 target genomes.
[2023-06-28 00:41:13,761] [INFO] Target genome list was writen to GCA_017889095.1_ASM1788909v1_genomic.fna/target_genomes.txt
[2023-06-28 00:41:13,763] [INFO] Task started: fastANI
[2023-06-28 00:41:13,764] [INFO] Running command: fastANI --query /var/lib/cwl/stg135b0c07-e84f-42f8-86a0-433ac27525df/GCA_017889095.1_ASM1788909v1_genomic.fna.gz --refList GCA_017889095.1_ASM1788909v1_genomic.fna/target_genomes.txt --output GCA_017889095.1_ASM1788909v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 00:41:20,575] [INFO] Task succeeded: fastANI
[2023-06-28 00:41:20,576] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcea22fe7-9158-4dce-bc22-50440d57c120/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 00:41:20,576] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcea22fe7-9158-4dce-bc22-50440d57c120/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 00:41:20,586] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 00:41:20,586] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 00:41:20,586] [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
[Clostridium] saccharogumia	strain=DSM 17460	GCA_000686665.1	341225	341225	type	True	79.2581	326	860	95	below_threshold
Erysipelatoclostridium ramosum	strain=DSM 1402	GCA_014131695.1	1547	1547	type	True	79.179	343	860	95	below_threshold
[Clostridium] spiroforme	strain=DSM 1552	GCA_000154805.1	29348	29348	type	True	79.1626	287	860	95	below_threshold
[Clostridium] spiroforme	strain=DSM 1552	GCA_025149465.1	29348	29348	type	True	79.133	288	860	95	below_threshold
Erysipelatoclostridium ramosum		GCA_900660185.1	1547	1547	type	True	79.1315	339	860	95	below_threshold
[Clostridium] cocleatum	strain=DSM 1551	GCA_900102365.1	69824	69824	type	True	79.077	307	860	95	below_threshold
[Clostridium] cocleatum	strain=ATCC 29902	GCA_002803405.1	69824	69824	type	True	79.0654	307	860	95	below_threshold
[Clostridium] cocleatum	strain=I50	GCA_010206155.1	69824	69824	type	True	79.0274	310	860	95	below_threshold
[Clostridium] cocleatum	strain=DSM 1551	GCA_024622895.1	69824	69824	type	True	78.9945	309	860	95	below_threshold
Tannockella kyphosi	strain=BP52G	GCA_021054785.1	2899121	2899121	type	True	76.5875	120	860	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 00:41:20,588] [INFO] DFAST Taxonomy check result was written to GCA_017889095.1_ASM1788909v1_genomic.fna/tc_result.tsv
[2023-06-28 00:41:20,589] [INFO] ===== Taxonomy check completed =====
[2023-06-28 00:41:20,589] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 00:41:20,589] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcea22fe7-9158-4dce-bc22-50440d57c120/dqc_reference/checkm_data
[2023-06-28 00:41:20,590] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 00:41:20,624] [INFO] Task started: CheckM
[2023-06-28 00:41:20,624] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017889095.1_ASM1788909v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017889095.1_ASM1788909v1_genomic.fna/checkm_input GCA_017889095.1_ASM1788909v1_genomic.fna/checkm_result
[2023-06-28 00:41:40,403] [INFO] Task succeeded: CheckM
[2023-06-28 00:41:40,404] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.77%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 00:41:40,419] [INFO] ===== Completeness check finished =====
[2023-06-28 00:41:40,419] [INFO] ===== Start GTDB Search =====
[2023-06-28 00:41:40,420] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017889095.1_ASM1788909v1_genomic.fna/markers.fasta)
[2023-06-28 00:41:40,420] [INFO] Task started: Blastn
[2023-06-28 00:41:40,420] [INFO] Running command: blastn -query GCA_017889095.1_ASM1788909v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcea22fe7-9158-4dce-bc22-50440d57c120/dqc_reference/reference_markers_gtdb.fasta -out GCA_017889095.1_ASM1788909v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:41:41,201] [INFO] Task succeeded: Blastn
[2023-06-28 00:41:41,206] [INFO] Selected 11 target genomes.
[2023-06-28 00:41:41,206] [INFO] Target genome list was writen to GCA_017889095.1_ASM1788909v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 00:41:41,210] [INFO] Task started: fastANI
[2023-06-28 00:41:41,210] [INFO] Running command: fastANI --query /var/lib/cwl/stg135b0c07-e84f-42f8-86a0-433ac27525df/GCA_017889095.1_ASM1788909v1_genomic.fna.gz --refList GCA_017889095.1_ASM1788909v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017889095.1_ASM1788909v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 00:41:46,393] [INFO] Task succeeded: fastANI
[2023-06-28 00:41:46,401] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 00:41:46,401] [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_017889095.1	s__Erysipelatoclostridium sp017889095	100.0	845	860	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002160495.1	s__Erysipelatoclostridium merdavium	81.6808	452	860	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	98.70	98.24	0.87	0.83	4	-
GCF_000686665.1	s__Erysipelatoclostridium saccharogumia	79.2581	326	860	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014131695.1	s__Erysipelatoclostridium ramosum	79.1729	343	860	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	99.66	99.35	0.93	0.87	70	-
GCA_018369555.1	s__Erysipelatoclostridium spiroforme_A	79.1614	254	860	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154805.1	s__Erysipelatoclostridium spiroforme	79.1467	288	860	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	97.13	96.38	0.84	0.79	13	-
GCF_900102365.1	s__Erysipelatoclostridium cocleatum	79.0787	306	860	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	99.07	98.04	0.92	0.85	5	-
GCA_910588075.1	s__MGBC163490 sp910588075	76.9982	126	860	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__MGBC163490	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 00:41:46,402] [INFO] GTDB search result was written to GCA_017889095.1_ASM1788909v1_genomic.fna/result_gtdb.tsv
[2023-06-28 00:41:46,403] [INFO] ===== GTDB Search completed =====
[2023-06-28 00:41:46,406] [INFO] DFAST_QC result json was written to GCA_017889095.1_ASM1788909v1_genomic.fna/dqc_result.json
[2023-06-28 00:41:46,406] [INFO] DFAST_QC completed!
[2023-06-28 00:41:46,406] [INFO] Total running time: 0h0m39s