[2023-06-30 16:14:52,173] [INFO] DFAST_QC pipeline started.
[2023-06-30 16:14:52,175] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 16:14:52,175] [INFO] DQC Reference Directory: /var/lib/cwl/stg360cdd76-e9b3-42ce-bf1c-231680201d6a/dqc_reference
[2023-06-30 16:14:53,458] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 16:14:53,459] [INFO] Task started: Prodigal
[2023-06-30 16:14:53,459] [INFO] Running command: gunzip -c /var/lib/cwl/stgf604dd39-cb56-4b90-964a-aab6d4814e38/GCA_900758025.1_ERS608477_44_genomic.fna.gz | prodigal -d GCA_900758025.1_ERS608477_44_genomic.fna/cds.fna -a GCA_900758025.1_ERS608477_44_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 16:14:57,443] [INFO] Task succeeded: Prodigal
[2023-06-30 16:14:57,443] [INFO] Task started: HMMsearch
[2023-06-30 16:14:57,443] [INFO] Running command: hmmsearch --tblout GCA_900758025.1_ERS608477_44_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg360cdd76-e9b3-42ce-bf1c-231680201d6a/dqc_reference/reference_markers.hmm GCA_900758025.1_ERS608477_44_genomic.fna/protein.faa > /dev/null
[2023-06-30 16:14:57,645] [INFO] Task succeeded: HMMsearch
[2023-06-30 16:14:57,647] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf604dd39-cb56-4b90-964a-aab6d4814e38/GCA_900758025.1_ERS608477_44_genomic.fna.gz]
[2023-06-30 16:14:57,674] [INFO] Query marker FASTA was written to GCA_900758025.1_ERS608477_44_genomic.fna/markers.fasta
[2023-06-30 16:14:57,674] [INFO] Task started: Blastn
[2023-06-30 16:14:57,674] [INFO] Running command: blastn -query GCA_900758025.1_ERS608477_44_genomic.fna/markers.fasta -db /var/lib/cwl/stg360cdd76-e9b3-42ce-bf1c-231680201d6a/dqc_reference/reference_markers.fasta -out GCA_900758025.1_ERS608477_44_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:14:58,224] [INFO] Task succeeded: Blastn
[2023-06-30 16:14:58,228] [INFO] Selected 13 target genomes.
[2023-06-30 16:14:58,228] [INFO] Target genome list was writen to GCA_900758025.1_ERS608477_44_genomic.fna/target_genomes.txt
[2023-06-30 16:14:58,230] [INFO] Task started: fastANI
[2023-06-30 16:14:58,230] [INFO] Running command: fastANI --query /var/lib/cwl/stgf604dd39-cb56-4b90-964a-aab6d4814e38/GCA_900758025.1_ERS608477_44_genomic.fna.gz --refList GCA_900758025.1_ERS608477_44_genomic.fna/target_genomes.txt --output GCA_900758025.1_ERS608477_44_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 16:15:04,365] [INFO] Task succeeded: fastANI
[2023-06-30 16:15:04,366] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg360cdd76-e9b3-42ce-bf1c-231680201d6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 16:15:04,366] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg360cdd76-e9b3-42ce-bf1c-231680201d6a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 16:15:04,374] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 16:15:04,374] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 16:15:04,374] [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
Faecalibacillus intestinalis	strain=SNUG30099	GCA_003024685.1	1982626	1982626	type	True	92.2557	582	785	95	below_threshold
Faecalibacillus faecis	strain=SNUG30370	GCA_003024675.1	1982628	1982628	type	True	88.5063	530	785	95	below_threshold
Erysipelatoclostridium ramosum	strain=DSM 1402	GCA_014131695.1	1547	1547	type	True	78.4684	210	785	95	below_threshold
[Clostridium] cocleatum	strain=I50	GCA_010206155.1	69824	69824	type	True	78.3674	203	785	95	below_threshold
[Clostridium] spiroforme	strain=DSM 1552	GCA_000154805.1	29348	29348	type	True	78.323	210	785	95	below_threshold
[Clostridium] spiroforme	strain=DSM 1552	GCA_025149465.1	29348	29348	type	True	78.2866	215	785	95	below_threshold
Coprobacillus cateniformis	strain=RCA1-24	GCA_009767585.1	100884	100884	type	True	77.4982	187	785	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 16:15:04,376] [INFO] DFAST Taxonomy check result was written to GCA_900758025.1_ERS608477_44_genomic.fna/tc_result.tsv
[2023-06-30 16:15:04,377] [INFO] ===== Taxonomy check completed =====
[2023-06-30 16:15:04,377] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 16:15:04,377] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg360cdd76-e9b3-42ce-bf1c-231680201d6a/dqc_reference/checkm_data
[2023-06-30 16:15:04,378] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 16:15:04,407] [INFO] Task started: CheckM
[2023-06-30 16:15:04,407] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900758025.1_ERS608477_44_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900758025.1_ERS608477_44_genomic.fna/checkm_input GCA_900758025.1_ERS608477_44_genomic.fna/checkm_result
[2023-06-30 16:15:23,513] [INFO] Task succeeded: CheckM
[2023-06-30 16:15:23,514] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.06%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-30 16:15:23,535] [INFO] ===== Completeness check finished =====
[2023-06-30 16:15:23,535] [INFO] ===== Start GTDB Search =====
[2023-06-30 16:15:23,536] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900758025.1_ERS608477_44_genomic.fna/markers.fasta)
[2023-06-30 16:15:23,536] [INFO] Task started: Blastn
[2023-06-30 16:15:23,536] [INFO] Running command: blastn -query GCA_900758025.1_ERS608477_44_genomic.fna/markers.fasta -db /var/lib/cwl/stg360cdd76-e9b3-42ce-bf1c-231680201d6a/dqc_reference/reference_markers_gtdb.fasta -out GCA_900758025.1_ERS608477_44_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 16:15:24,269] [INFO] Task succeeded: Blastn
[2023-06-30 16:15:24,273] [INFO] Selected 9 target genomes.
[2023-06-30 16:15:24,273] [INFO] Target genome list was writen to GCA_900758025.1_ERS608477_44_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 16:15:24,277] [INFO] Task started: fastANI
[2023-06-30 16:15:24,277] [INFO] Running command: fastANI --query /var/lib/cwl/stgf604dd39-cb56-4b90-964a-aab6d4814e38/GCA_900758025.1_ERS608477_44_genomic.fna.gz --refList GCA_900758025.1_ERS608477_44_genomic.fna/target_genomes_gtdb.txt --output GCA_900758025.1_ERS608477_44_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 16:15:28,828] [INFO] Task succeeded: fastANI
[2023-06-30 16:15:28,836] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 16:15:28,837] [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_900544435.1	s__Faecalibacillus sp900544435	98.5196	487	785	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	99.05	98.83	0.79	0.74	3	conclusive
GCF_003024685.1	s__Faecalibacillus intestinalis	92.2481	582	785	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	97.94	96.13	0.85	0.76	51	-
GCF_003024675.1	s__Faecalibacillus faecis	88.459	533	785	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	97.99	96.95	0.86	0.80	14	-
GCF_003480255.1	s__Faecalibacillus sp003480255	81.0883	332	785	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	99.06	98.20	0.91	0.84	5	-
GCF_016901755.1	s__Faecalibacillus spiroforme_A	78.9466	231	785	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	98.80	98.79	0.88	0.87	3	-
GCF_000154805.1	s__Erysipelatoclostridium spiroforme	78.3218	210	785	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	97.13	96.38	0.84	0.79	13	-
GCF_002160495.1	s__Erysipelatoclostridium merdavium	78.2999	262	785	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Erysipelatoclostridium	95.0	98.70	98.24	0.87	0.83	4	-
GCA_002359025.1	s__UBA3379 sp002359025	77.8756	132	785	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__UBA3379	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 16:15:28,839] [INFO] GTDB search result was written to GCA_900758025.1_ERS608477_44_genomic.fna/result_gtdb.tsv
[2023-06-30 16:15:28,839] [INFO] ===== GTDB Search completed =====
[2023-06-30 16:15:28,842] [INFO] DFAST_QC result json was written to GCA_900758025.1_ERS608477_44_genomic.fna/dqc_result.json
[2023-06-30 16:15:28,843] [INFO] DFAST_QC completed!
[2023-06-30 16:15:28,843] [INFO] Total running time: 0h0m37s