[2023-06-18 23:43:27,545] [INFO] DFAST_QC pipeline started.
[2023-06-18 23:43:27,549] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 23:43:27,549] [INFO] DQC Reference Directory: /var/lib/cwl/stgd10bf1d7-6dc5-430c-a0dc-0aad7aee0ffc/dqc_reference
[2023-06-18 23:43:30,625] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 23:43:30,627] [INFO] Task started: Prodigal
[2023-06-18 23:43:30,627] [INFO] Running command: gunzip -c /var/lib/cwl/stg0d70b7cf-fdfb-4031-b399-c29db3257134/GCA_018369555.1_ASM1836955v1_genomic.fna.gz | prodigal -d GCA_018369555.1_ASM1836955v1_genomic.fna/cds.fna -a GCA_018369555.1_ASM1836955v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 23:43:34,086] [INFO] Task succeeded: Prodigal
[2023-06-18 23:43:34,087] [INFO] Task started: HMMsearch
[2023-06-18 23:43:34,087] [INFO] Running command: hmmsearch --tblout GCA_018369555.1_ASM1836955v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd10bf1d7-6dc5-430c-a0dc-0aad7aee0ffc/dqc_reference/reference_markers.hmm GCA_018369555.1_ASM1836955v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 23:43:34,370] [INFO] Task succeeded: HMMsearch
[2023-06-18 23:43:34,371] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0d70b7cf-fdfb-4031-b399-c29db3257134/GCA_018369555.1_ASM1836955v1_genomic.fna.gz]
[2023-06-18 23:43:34,410] [INFO] Query marker FASTA was written to GCA_018369555.1_ASM1836955v1_genomic.fna/markers.fasta
[2023-06-18 23:43:34,411] [INFO] Task started: Blastn
[2023-06-18 23:43:34,411] [INFO] Running command: blastn -query GCA_018369555.1_ASM1836955v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd10bf1d7-6dc5-430c-a0dc-0aad7aee0ffc/dqc_reference/reference_markers.fasta -out GCA_018369555.1_ASM1836955v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:43:36,470] [INFO] Task succeeded: Blastn
[2023-06-18 23:43:36,475] [INFO] Selected 13 target genomes.
[2023-06-18 23:43:36,475] [INFO] Target genome list was writen to GCA_018369555.1_ASM1836955v1_genomic.fna/target_genomes.txt
[2023-06-18 23:43:36,490] [INFO] Task started: fastANI
[2023-06-18 23:43:36,491] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d70b7cf-fdfb-4031-b399-c29db3257134/GCA_018369555.1_ASM1836955v1_genomic.fna.gz --refList GCA_018369555.1_ASM1836955v1_genomic.fna/target_genomes.txt --output GCA_018369555.1_ASM1836955v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 23:43:43,492] [INFO] Task succeeded: fastANI
[2023-06-18 23:43:43,493] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd10bf1d7-6dc5-430c-a0dc-0aad7aee0ffc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 23:43:43,494] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd10bf1d7-6dc5-430c-a0dc-0aad7aee0ffc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 23:43:43,508] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 23:43:43,508] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 23:43:43,508] [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] spiroforme	strain=DSM 1552	GCA_000154805.1	29348	29348	type	True	91.3701	595	708	95	below_threshold
[Clostridium] spiroforme	strain=DSM 1552	GCA_025149465.1	29348	29348	type	True	91.3552	598	708	95	below_threshold
[Clostridium] cocleatum	strain=DSM 1551	GCA_024622895.1	69824	69824	type	True	81.3678	422	708	95	below_threshold
[Clostridium] cocleatum	strain=DSM 1551	GCA_900102365.1	69824	69824	type	True	81.3558	425	708	95	below_threshold
[Clostridium] cocleatum	strain=I50	GCA_010206155.1	69824	69824	type	True	81.3381	424	708	95	below_threshold
[Clostridium] cocleatum	strain=ATCC 29902	GCA_002803405.1	69824	69824	type	True	81.3016	430	708	95	below_threshold
[Clostridium] saccharogumia	strain=DSM 17460	GCA_000686665.1	341225	341225	type	True	81.0829	410	708	95	below_threshold
Erysipelatoclostridium ramosum		GCA_900660185.1	1547	1547	type	True	80.307	343	708	95	below_threshold
Erysipelatoclostridium ramosum	strain=FDAARGOS_906	GCA_016027135.1	1547	1547	type	True	80.2985	355	708	95	below_threshold
Erysipelatoclostridium ramosum	strain=DSM 1402	GCA_014131695.1	1547	1547	type	True	80.2383	344	708	95	below_threshold
Tannockella kyphosi	strain=BP52G	GCA_021054785.1	2899121	2899121	type	True	77.8041	140	708	95	below_threshold
Longibaculum muris	strain=DSM 29487	GCA_024622235.1	1796628	1796628	type	True	77.6741	176	708	95	below_threshold
Longibaculum muris	strain=DSM 29487	GCA_004343035.1	1796628	1796628	type	True	77.6525	178	708	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 23:43:43,510] [INFO] DFAST Taxonomy check result was written to GCA_018369555.1_ASM1836955v1_genomic.fna/tc_result.tsv
[2023-06-18 23:43:43,511] [INFO] ===== Taxonomy check completed =====
[2023-06-18 23:43:43,512] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 23:43:43,512] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd10bf1d7-6dc5-430c-a0dc-0aad7aee0ffc/dqc_reference/checkm_data
[2023-06-18 23:43:43,514] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 23:43:43,548] [INFO] Task started: CheckM
[2023-06-18 23:43:43,548] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018369555.1_ASM1836955v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018369555.1_ASM1836955v1_genomic.fna/checkm_input GCA_018369555.1_ASM1836955v1_genomic.fna/checkm_result
[2023-06-18 23:44:03,007] [INFO] Task succeeded: CheckM
[2023-06-18 23:44:03,009] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 23:44:03,038] [INFO] ===== Completeness check finished =====
[2023-06-18 23:44:03,038] [INFO] ===== Start GTDB Search =====
[2023-06-18 23:44:03,038] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018369555.1_ASM1836955v1_genomic.fna/markers.fasta)
[2023-06-18 23:44:03,039] [INFO] Task started: Blastn
[2023-06-18 23:44:03,039] [INFO] Running command: blastn -query GCA_018369555.1_ASM1836955v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd10bf1d7-6dc5-430c-a0dc-0aad7aee0ffc/dqc_reference/reference_markers_gtdb.fasta -out GCA_018369555.1_ASM1836955v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:44:03,915] [INFO] Task succeeded: Blastn
[2023-06-18 23:44:03,918] [INFO] Selected 12 target genomes.
[2023-06-18 23:44:03,918] [INFO] Target genome list was writen to GCA_018369555.1_ASM1836955v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 23:44:03,943] [INFO] Task started: fastANI
[2023-06-18 23:44:03,943] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d70b7cf-fdfb-4031-b399-c29db3257134/GCA_018369555.1_ASM1836955v1_genomic.fna.gz --refList GCA_018369555.1_ASM1836955v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018369555.1_ASM1836955v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 23:44:09,969] [INFO] Task succeeded: fastANI
[2023-06-18 23:44:09,982] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 23:44:09,982] [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_018369555.1	s__Erysipelatoclostridium spiroforme_A	100.0	697	708	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_000154805.1	s__Erysipelatoclostridium spiroforme	91.376	594	708	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	81.3658	424	708	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	81.159	405	708	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	80.8694	412	708	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	80.2475	343	708	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	80.2341	341	708	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	78.9623	261	708	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	78.9015	197	708	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	99.06	98.20	0.91	0.84	5	-
GCA_900544435.1	s__Faecalibacillus sp900544435	78.0611	176	708	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Coprobacillaceae;g__Faecalibacillus	95.0	99.05	98.83	0.79	0.74	3	-
--------------------------------------------------------------------------------
[2023-06-18 23:44:09,984] [INFO] GTDB search result was written to GCA_018369555.1_ASM1836955v1_genomic.fna/result_gtdb.tsv
[2023-06-18 23:44:09,985] [INFO] ===== GTDB Search completed =====
[2023-06-18 23:44:09,990] [INFO] DFAST_QC result json was written to GCA_018369555.1_ASM1836955v1_genomic.fna/dqc_result.json
[2023-06-18 23:44:09,990] [INFO] DFAST_QC completed!
[2023-06-18 23:44:09,990] [INFO] Total running time: 0h0m42s