[2024-01-24 14:54:56,364] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:56,366] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:56,367] [INFO] DQC Reference Directory: /var/lib/cwl/stg94c35398-f500-44a3-84c1-5ded1b700764/dqc_reference
[2024-01-24 14:54:57,798] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:57,799] [INFO] Task started: Prodigal
[2024-01-24 14:54:57,799] [INFO] Running command: gunzip -c /var/lib/cwl/stg346bd462-ddf6-455e-b1cc-83ed9a5b3b33/GCF_002803405.1_ASM280340v1_genomic.fna.gz | prodigal -d GCF_002803405.1_ASM280340v1_genomic.fna/cds.fna -a GCF_002803405.1_ASM280340v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:02,405] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:02,406] [INFO] Task started: HMMsearch
[2024-01-24 14:55:02,406] [INFO] Running command: hmmsearch --tblout GCF_002803405.1_ASM280340v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg94c35398-f500-44a3-84c1-5ded1b700764/dqc_reference/reference_markers.hmm GCF_002803405.1_ASM280340v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:02,701] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:02,702] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg346bd462-ddf6-455e-b1cc-83ed9a5b3b33/GCF_002803405.1_ASM280340v1_genomic.fna.gz]
[2024-01-24 14:55:02,735] [INFO] Query marker FASTA was written to GCF_002803405.1_ASM280340v1_genomic.fna/markers.fasta
[2024-01-24 14:55:02,736] [INFO] Task started: Blastn
[2024-01-24 14:55:02,736] [INFO] Running command: blastn -query GCF_002803405.1_ASM280340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94c35398-f500-44a3-84c1-5ded1b700764/dqc_reference/reference_markers.fasta -out GCF_002803405.1_ASM280340v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:03,398] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:03,401] [INFO] Selected 11 target genomes.
[2024-01-24 14:55:03,401] [INFO] Target genome list was writen to GCF_002803405.1_ASM280340v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:03,408] [INFO] Task started: fastANI
[2024-01-24 14:55:03,408] [INFO] Running command: fastANI --query /var/lib/cwl/stg346bd462-ddf6-455e-b1cc-83ed9a5b3b33/GCF_002803405.1_ASM280340v1_genomic.fna.gz --refList GCF_002803405.1_ASM280340v1_genomic.fna/target_genomes.txt --output GCF_002803405.1_ASM280340v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:11,295] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:11,295] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg94c35398-f500-44a3-84c1-5ded1b700764/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:11,295] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg94c35398-f500-44a3-84c1-5ded1b700764/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:11,305] [INFO] Found 9 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 14:55:11,305] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:11,305] [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] cocleatum	strain=ATCC 29902	GCA_002803405.1	69824	69824	type	True	100.0	961	966	95	conclusive
[Clostridium] cocleatum	strain=DSM 1551	GCA_024622895.1	69824	69824	type	True	99.9449	929	966	95	conclusive
[Clostridium] cocleatum	strain=I50	GCA_010206155.1	69824	69824	type	True	99.9439	949	966	95	conclusive
[Clostridium] cocleatum	strain=DSM 1551	GCA_900102365.1	69824	69824	type	True	99.9171	926	966	95	conclusive
[Clostridium] saccharogumia	strain=DSM 17460	GCA_000686665.1	341225	341225	type	True	82.2672	577	966	95	below_threshold
[Clostridium] spiroforme	strain=DSM 1552	GCA_000154805.1	29348	29348	type	True	81.7919	469	966	95	below_threshold
[Clostridium] spiroforme	strain=DSM 1552	GCA_025149465.1	29348	29348	type	True	81.7591	473	966	95	below_threshold
Erysipelatoclostridium ramosum	strain=DSM 1402	GCA_014131695.1	1547	1547	type	True	81.1283	453	966	95	below_threshold
Coprobacillus cateniformis	strain=JCM 10604	GCA_001312445.1	100884	100884	type	True	77.5785	161	966	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:11,307] [INFO] DFAST Taxonomy check result was written to GCF_002803405.1_ASM280340v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:11,307] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:11,307] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:11,308] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg94c35398-f500-44a3-84c1-5ded1b700764/dqc_reference/checkm_data
[2024-01-24 14:55:11,309] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:11,339] [INFO] Task started: CheckM
[2024-01-24 14:55:11,340] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002803405.1_ASM280340v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002803405.1_ASM280340v1_genomic.fna/checkm_input GCF_002803405.1_ASM280340v1_genomic.fna/checkm_result
[2024-01-24 14:55:33,248] [INFO] Task succeeded: CheckM
[2024-01-24 14:55:33,249] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:55:33,283] [INFO] ===== Completeness check finished =====
[2024-01-24 14:55:33,284] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:55:33,284] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002803405.1_ASM280340v1_genomic.fna/markers.fasta)
[2024-01-24 14:55:33,285] [INFO] Task started: Blastn
[2024-01-24 14:55:33,285] [INFO] Running command: blastn -query GCF_002803405.1_ASM280340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94c35398-f500-44a3-84c1-5ded1b700764/dqc_reference/reference_markers_gtdb.fasta -out GCF_002803405.1_ASM280340v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:34,245] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:34,248] [INFO] Selected 12 target genomes.
[2024-01-24 14:55:34,248] [INFO] Target genome list was writen to GCF_002803405.1_ASM280340v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:55:34,261] [INFO] Task started: fastANI
[2024-01-24 14:55:34,261] [INFO] Running command: fastANI --query /var/lib/cwl/stg346bd462-ddf6-455e-b1cc-83ed9a5b3b33/GCF_002803405.1_ASM280340v1_genomic.fna.gz --refList GCF_002803405.1_ASM280340v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002803405.1_ASM280340v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:55:42,157] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:42,166] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:55:42,167] [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_900102365.1	s__Erysipelatoclostridium cocleatum	99.9171	926	966	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	99.07	98.04	0.92	0.85	5	conclusive
GCA_000508865.1	s__Erysipelatoclostridium sp000508865	82.7	553	966	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686665.1	s__Erysipelatoclostridium saccharogumia	82.2897	575	966	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	81.7961	468	966	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	81.2714	435	966	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014131695.1	s__Erysipelatoclostridium ramosum	81.1286	453	966	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	99.66	99.35	0.93	0.87	70	-
GCF_002160495.1	s__Erysipelatoclostridium merdavium	80.074	376	966	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	98.70	98.24	0.87	0.83	4	-
GCA_017889095.1	s__Erysipelatoclostridium sp017889095	79.067	309	966	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	78.5163	218	966	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	99.06	98.20	0.91	0.84	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:55:42,168] [INFO] GTDB search result was written to GCF_002803405.1_ASM280340v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:55:42,169] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:55:42,172] [INFO] DFAST_QC result json was written to GCF_002803405.1_ASM280340v1_genomic.fna/dqc_result.json
[2024-01-24 14:55:42,173] [INFO] DFAST_QC completed!
[2024-01-24 14:55:42,173] [INFO] Total running time: 0h0m46s