[2024-01-24 11:26:03,027] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:03,030] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:03,030] [INFO] DQC Reference Directory: /var/lib/cwl/stg282cd8e5-5513-4687-a140-ee11144f73b3/dqc_reference
[2024-01-24 11:26:04,161] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:04,162] [INFO] Task started: Prodigal
[2024-01-24 11:26:04,162] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8d70f23-fa02-4f99-b4f1-3e8f96f71b2d/GCF_014131695.1_ASM1413169v1_genomic.fna.gz | prodigal -d GCF_014131695.1_ASM1413169v1_genomic.fna/cds.fna -a GCF_014131695.1_ASM1413169v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:09,653] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:09,653] [INFO] Task started: HMMsearch
[2024-01-24 11:26:09,653] [INFO] Running command: hmmsearch --tblout GCF_014131695.1_ASM1413169v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg282cd8e5-5513-4687-a140-ee11144f73b3/dqc_reference/reference_markers.hmm GCF_014131695.1_ASM1413169v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:09,850] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:09,851] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf8d70f23-fa02-4f99-b4f1-3e8f96f71b2d/GCF_014131695.1_ASM1413169v1_genomic.fna.gz]
[2024-01-24 11:26:09,875] [INFO] Query marker FASTA was written to GCF_014131695.1_ASM1413169v1_genomic.fna/markers.fasta
[2024-01-24 11:26:09,876] [INFO] Task started: Blastn
[2024-01-24 11:26:09,876] [INFO] Running command: blastn -query GCF_014131695.1_ASM1413169v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg282cd8e5-5513-4687-a140-ee11144f73b3/dqc_reference/reference_markers.fasta -out GCF_014131695.1_ASM1413169v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:10,447] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:10,450] [INFO] Selected 11 target genomes.
[2024-01-24 11:26:10,451] [INFO] Target genome list was writen to GCF_014131695.1_ASM1413169v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:10,490] [INFO] Task started: fastANI
[2024-01-24 11:26:10,490] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8d70f23-fa02-4f99-b4f1-3e8f96f71b2d/GCF_014131695.1_ASM1413169v1_genomic.fna.gz --refList GCF_014131695.1_ASM1413169v1_genomic.fna/target_genomes.txt --output GCF_014131695.1_ASM1413169v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:17,140] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:17,140] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg282cd8e5-5513-4687-a140-ee11144f73b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:17,141] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg282cd8e5-5513-4687-a140-ee11144f73b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:17,149] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:26:17,149] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:17,149] [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
Erysipelatoclostridium ramosum	strain=DSM 1402	GCA_014131695.1	1547	1547	type	True	100.0	1079	1082	95	conclusive
Erysipelatoclostridium ramosum	strain=FDAARGOS_906	GCA_016027135.1	1547	1547	type	True	99.998	1076	1082	95	conclusive
Erysipelatoclostridium ramosum	strain=DSM 1402	GCA_000154485.1	1547	1547	type	True	99.993	1068	1082	95	conclusive
Erysipelatoclostridium ramosum		GCA_900660185.1	1547	1547	type	True	99.7388	1018	1082	95	conclusive
[Clostridium] cocleatum	strain=I50	GCA_010206155.1	69824	69824	type	True	81.165	455	1082	95	below_threshold
[Clostridium] spiroforme	strain=DSM 1552	GCA_025149465.1	29348	29348	type	True	80.327	393	1082	95	below_threshold
[Clostridium] spiroforme	strain=DSM 1552	GCA_000154805.1	29348	29348	type	True	80.2495	391	1082	95	below_threshold
Tannockella kyphosi	strain=BP52G	GCA_021054785.1	2899121	2899121	type	True	78.8974	153	1082	95	below_threshold
Longibaculum muris	strain=DSM 29487	GCA_004343035.1	1796628	1796628	type	True	78.1792	215	1082	95	below_threshold
Longibaculum muris	strain=DSM 29487	GCA_024622235.1	1796628	1796628	type	True	78.0732	217	1082	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:17,151] [INFO] DFAST Taxonomy check result was written to GCF_014131695.1_ASM1413169v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:17,151] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:17,151] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:17,152] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg282cd8e5-5513-4687-a140-ee11144f73b3/dqc_reference/checkm_data
[2024-01-24 11:26:17,152] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:17,184] [INFO] Task started: CheckM
[2024-01-24 11:26:17,184] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014131695.1_ASM1413169v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014131695.1_ASM1413169v1_genomic.fna/checkm_input GCF_014131695.1_ASM1413169v1_genomic.fna/checkm_result
[2024-01-24 11:26:39,394] [INFO] Task succeeded: CheckM
[2024-01-24 11:26:39,395] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:26:39,413] [INFO] ===== Completeness check finished =====
[2024-01-24 11:26:39,413] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:26:39,414] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014131695.1_ASM1413169v1_genomic.fna/markers.fasta)
[2024-01-24 11:26:39,414] [INFO] Task started: Blastn
[2024-01-24 11:26:39,414] [INFO] Running command: blastn -query GCF_014131695.1_ASM1413169v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg282cd8e5-5513-4687-a140-ee11144f73b3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014131695.1_ASM1413169v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:40,240] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:40,243] [INFO] Selected 13 target genomes.
[2024-01-24 11:26:40,243] [INFO] Target genome list was writen to GCF_014131695.1_ASM1413169v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:26:40,264] [INFO] Task started: fastANI
[2024-01-24 11:26:40,265] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8d70f23-fa02-4f99-b4f1-3e8f96f71b2d/GCF_014131695.1_ASM1413169v1_genomic.fna.gz --refList GCF_014131695.1_ASM1413169v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014131695.1_ASM1413169v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:26:47,330] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:47,338] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:26:47,339] [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_014131695.1	s__Erysipelatoclostridium ramosum	100.0	1078	1082	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	99.66	99.35	0.93	0.87	70	conclusive
GCF_900102365.1	s__Erysipelatoclostridium cocleatum	81.0601	449	1082	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	99.07	98.04	0.92	0.85	5	-
GCF_000686665.1	s__Erysipelatoclostridium saccharogumia	80.4254	443	1082	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	100.00	100.00	0.99	0.99	2	-
GCA_000508865.1	s__Erysipelatoclostridium sp000508865	80.2813	428	1082	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	80.2646	390	1082	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	97.13	96.38	0.84	0.79	13	-
GCA_018369555.1	s__Erysipelatoclostridium spiroforme_A	80.1546	362	1082	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002160495.1	s__Erysipelatoclostridium merdavium	79.9765	449	1082	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	98.70	98.24	0.87	0.83	4	-
GCF_003480255.1	s__Faecalibacillus sp003480255	78.5748	237	1082	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	99.06	98.20	0.91	0.84	5	-
GCA_900538465.1	s__Longibaculum sp900538465	78.0552	184	1082	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Longibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:26:47,340] [INFO] GTDB search result was written to GCF_014131695.1_ASM1413169v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:26:47,341] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:26:47,344] [INFO] DFAST_QC result json was written to GCF_014131695.1_ASM1413169v1_genomic.fna/dqc_result.json
[2024-01-24 11:26:47,344] [INFO] DFAST_QC completed!
[2024-01-24 11:26:47,344] [INFO] Total running time: 0h0m44s