[2024-01-24 11:58:54,307] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:54,309] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:54,309] [INFO] DQC Reference Directory: /var/lib/cwl/stg33f89046-a59e-4344-829b-d91f14ccd417/dqc_reference
[2024-01-24 11:58:57,420] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:57,421] [INFO] Task started: Prodigal
[2024-01-24 11:58:57,422] [INFO] Running command: gunzip -c /var/lib/cwl/stg8936446b-3c90-415b-8195-cb13e7817e1c/GCF_016027135.1_ASM1602713v1_genomic.fna.gz | prodigal -d GCF_016027135.1_ASM1602713v1_genomic.fna/cds.fna -a GCF_016027135.1_ASM1602713v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:03,070] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:03,071] [INFO] Task started: HMMsearch
[2024-01-24 11:59:03,071] [INFO] Running command: hmmsearch --tblout GCF_016027135.1_ASM1602713v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33f89046-a59e-4344-829b-d91f14ccd417/dqc_reference/reference_markers.hmm GCF_016027135.1_ASM1602713v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:03,435] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:03,436] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8936446b-3c90-415b-8195-cb13e7817e1c/GCF_016027135.1_ASM1602713v1_genomic.fna.gz]
[2024-01-24 11:59:03,467] [INFO] Query marker FASTA was written to GCF_016027135.1_ASM1602713v1_genomic.fna/markers.fasta
[2024-01-24 11:59:03,469] [INFO] Task started: Blastn
[2024-01-24 11:59:03,469] [INFO] Running command: blastn -query GCF_016027135.1_ASM1602713v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33f89046-a59e-4344-829b-d91f14ccd417/dqc_reference/reference_markers.fasta -out GCF_016027135.1_ASM1602713v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:06,026] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:06,030] [INFO] Selected 11 target genomes.
[2024-01-24 11:59:06,031] [INFO] Target genome list was writen to GCF_016027135.1_ASM1602713v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:06,063] [INFO] Task started: fastANI
[2024-01-24 11:59:06,063] [INFO] Running command: fastANI --query /var/lib/cwl/stg8936446b-3c90-415b-8195-cb13e7817e1c/GCF_016027135.1_ASM1602713v1_genomic.fna.gz --refList GCF_016027135.1_ASM1602713v1_genomic.fna/target_genomes.txt --output GCF_016027135.1_ASM1602713v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:12,669] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:12,669] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33f89046-a59e-4344-829b-d91f14ccd417/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:12,670] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33f89046-a59e-4344-829b-d91f14ccd417/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:12,684] [INFO] Found 10 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:59:12,684] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:12,685] [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=FDAARGOS_906	GCA_016027135.1	1547	1547	type	True	100.0	1079	1081	95	conclusive
Erysipelatoclostridium ramosum	strain=DSM 1402	GCA_014131695.1	1547	1547	type	True	99.995	1077	1081	95	conclusive
Erysipelatoclostridium ramosum	strain=DSM 1402	GCA_000154485.1	1547	1547	type	True	99.9929	1066	1081	95	conclusive
Erysipelatoclostridium ramosum		GCA_900660185.1	1547	1547	type	True	99.7329	1016	1081	95	conclusive
[Clostridium] cocleatum	strain=I50	GCA_010206155.1	69824	69824	type	True	81.2083	454	1081	95	below_threshold
[Clostridium] spiroforme	strain=DSM 1552	GCA_025149465.1	29348	29348	type	True	80.4154	395	1081	95	below_threshold
[Clostridium] spiroforme	strain=DSM 1552	GCA_000154805.1	29348	29348	type	True	80.3242	386	1081	95	below_threshold
Tannockella kyphosi	strain=BP52G	GCA_021054785.1	2899121	2899121	type	True	78.4408	159	1081	95	below_threshold
Longibaculum muris	strain=DSM 29487	GCA_024622235.1	1796628	1796628	type	True	77.9404	224	1081	95	below_threshold
Longibaculum muris	strain=DSM 29487	GCA_004343035.1	1796628	1796628	type	True	77.9295	226	1081	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:12,686] [INFO] DFAST Taxonomy check result was written to GCF_016027135.1_ASM1602713v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:12,687] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:12,687] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:12,687] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33f89046-a59e-4344-829b-d91f14ccd417/dqc_reference/checkm_data
[2024-01-24 11:59:12,688] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:12,726] [INFO] Task started: CheckM
[2024-01-24 11:59:12,727] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016027135.1_ASM1602713v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016027135.1_ASM1602713v1_genomic.fna/checkm_input GCF_016027135.1_ASM1602713v1_genomic.fna/checkm_result
[2024-01-24 11:59:39,944] [INFO] Task succeeded: CheckM
[2024-01-24 11:59:39,945] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:59:39,966] [INFO] ===== Completeness check finished =====
[2024-01-24 11:59:39,967] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:59:39,967] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016027135.1_ASM1602713v1_genomic.fna/markers.fasta)
[2024-01-24 11:59:39,968] [INFO] Task started: Blastn
[2024-01-24 11:59:39,968] [INFO] Running command: blastn -query GCF_016027135.1_ASM1602713v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33f89046-a59e-4344-829b-d91f14ccd417/dqc_reference/reference_markers_gtdb.fasta -out GCF_016027135.1_ASM1602713v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:40,795] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:40,800] [INFO] Selected 13 target genomes.
[2024-01-24 11:59:40,800] [INFO] Target genome list was writen to GCF_016027135.1_ASM1602713v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:59:40,821] [INFO] Task started: fastANI
[2024-01-24 11:59:40,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg8936446b-3c90-415b-8195-cb13e7817e1c/GCF_016027135.1_ASM1602713v1_genomic.fna.gz --refList GCF_016027135.1_ASM1602713v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016027135.1_ASM1602713v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:59:47,260] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:47,275] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:59:47,276] [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	99.995	1078	1081	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	81.087	443	1081	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	80.4796	433	1081	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000154805.1	s__Erysipelatoclostridium spiroforme	80.3093	387	1081	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	97.13	96.38	0.84	0.79	13	-
GCA_000508865.1	s__Erysipelatoclostridium sp000508865	80.2561	429	1081	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	80.1278	437	1081	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	98.70	98.24	0.87	0.83	4	-
GCA_018369555.1	s__Erysipelatoclostridium spiroforme_A	80.0379	368	1081	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003480255.1	s__Faecalibacillus sp003480255	78.6811	231	1081	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	78.18	175	1081	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 11:59:47,278] [INFO] GTDB search result was written to GCF_016027135.1_ASM1602713v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:59:47,278] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:59:47,282] [INFO] DFAST_QC result json was written to GCF_016027135.1_ASM1602713v1_genomic.fna/dqc_result.json
[2024-01-24 11:59:47,283] [INFO] DFAST_QC completed!
[2024-01-24 11:59:47,283] [INFO] Total running time: 0h0m53s