[2024-01-24 11:20:34,040] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:34,042] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:34,042] [INFO] DQC Reference Directory: /var/lib/cwl/stg92af83ad-e825-4263-9c82-b848e79e01fb/dqc_reference
[2024-01-24 11:20:35,222] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:35,223] [INFO] Task started: Prodigal
[2024-01-24 11:20:35,223] [INFO] Running command: gunzip -c /var/lib/cwl/stg33643c7d-5514-4323-ad85-8adbe0a8e7c1/GCF_006742065.1_ASM674206v1_genomic.fna.gz | prodigal -d GCF_006742065.1_ASM674206v1_genomic.fna/cds.fna -a GCF_006742065.1_ASM674206v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:42,861] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:42,862] [INFO] Task started: HMMsearch
[2024-01-24 11:20:42,862] [INFO] Running command: hmmsearch --tblout GCF_006742065.1_ASM674206v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92af83ad-e825-4263-9c82-b848e79e01fb/dqc_reference/reference_markers.hmm GCF_006742065.1_ASM674206v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:43,176] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:43,177] [INFO] Found 6/6 markers.
[2024-01-24 11:20:43,219] [INFO] Query marker FASTA was written to GCF_006742065.1_ASM674206v1_genomic.fna/markers.fasta
[2024-01-24 11:20:43,220] [INFO] Task started: Blastn
[2024-01-24 11:20:43,220] [INFO] Running command: blastn -query GCF_006742065.1_ASM674206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92af83ad-e825-4263-9c82-b848e79e01fb/dqc_reference/reference_markers.fasta -out GCF_006742065.1_ASM674206v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:43,816] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:43,821] [INFO] Selected 24 target genomes.
[2024-01-24 11:20:43,821] [INFO] Target genome list was writen to GCF_006742065.1_ASM674206v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:43,850] [INFO] Task started: fastANI
[2024-01-24 11:20:43,850] [INFO] Running command: fastANI --query /var/lib/cwl/stg33643c7d-5514-4323-ad85-8adbe0a8e7c1/GCF_006742065.1_ASM674206v1_genomic.fna.gz --refList GCF_006742065.1_ASM674206v1_genomic.fna/target_genomes.txt --output GCF_006742065.1_ASM674206v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:03,308] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:03,309] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92af83ad-e825-4263-9c82-b848e79e01fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:03,309] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92af83ad-e825-4263-9c82-b848e79e01fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:03,331] [INFO] Found 20 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:21:03,332] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:21:03,332] [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 butyricum	strain=NBRC 13949	GCA_006742065.1	1492	1492	type	True	100.0	1559	1566	95	conclusive
Clostridium butyricum	strain=DSM 10702	GCA_014131795.1	1492	1492	type	True	99.9937	1558	1566	95	conclusive
Clostridium butyricum	strain=DSM 10702	GCA_000409755.1	1492	1492	type	True	99.9378	1449	1566	95	conclusive
Clostridium butyricum	strain=NBRC 13949	GCA_007992895.1	1492	1492	type	True	99.9299	1475	1566	95	conclusive
Clostridium saccharobutylicum	strain=DSM 13864	GCA_000473995.1	169679	169679	type	True	79.9233	538	1566	95	below_threshold
Clostridium neonatale	strain=LCDC 99A005	GCA_002553615.1	137838	137838	type	True	79.4798	541	1566	95	below_threshold
Clostridium beijerinckii	strain=DSM 791	GCA_018223745.1	1520	1520	suspected-type	True	79.4502	477	1566	95	below_threshold
Clostridium saccharobutylicum	strain=DSM 13864	GCA_001657435.1	169679	169679	type	True	79.4067	482	1566	95	below_threshold
Clostridium gelidum	strain=C5S11	GCA_019977655.1	704125	704125	type	True	79.2096	546	1566	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=N1-4(HMT)	GCA_000340885.1	36745	36745	type	True	79.1575	502	1566	95	below_threshold
Clostridium puniceum	strain=DSM 2619	GCA_002006345.1	29367	29367	type	True	78.9496	509	1566	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=ATCC 27021	GCA_000334435.1	36745	36745	type	True	78.7883	482	1566	95	below_threshold
Clostridium cagae	strain=Marseille-P4344	GCA_900290265.1	2080751	2080751	type	True	78.5126	425	1566	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	77.4211	240	1566	95	below_threshold
Hathewaya histolytica	strain=NCTC503	GCA_901482605.1	1498	1498	type	True	77.3434	108	1566	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	77.1691	209	1566	95	below_threshold
Clostridium simiarum	strain=MSJ-4	GCA_018919175.1	2841506	2841506	type	True	76.33	125	1566	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	76.2207	173	1566	95	below_threshold
Halarcobacter bivalviorum	strain=LMG 26154	GCA_003346815.1	663364	663364	type	True	75.3456	52	1566	95	below_threshold
Malaciobacter halophilus	strain=DSM 18005	GCA_002837275.1	197482	197482	type	True	74.6726	52	1566	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:03,335] [INFO] DFAST Taxonomy check result was written to GCF_006742065.1_ASM674206v1_genomic.fna/tc_result.tsv
[2024-01-24 11:21:03,335] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:03,335] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:03,336] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92af83ad-e825-4263-9c82-b848e79e01fb/dqc_reference/checkm_data
[2024-01-24 11:21:03,337] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:03,385] [INFO] Task started: CheckM
[2024-01-24 11:21:03,385] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006742065.1_ASM674206v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006742065.1_ASM674206v1_genomic.fna/checkm_input GCF_006742065.1_ASM674206v1_genomic.fna/checkm_result
[2024-01-24 11:21:31,934] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:31,936] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:31,958] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:31,958] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:31,959] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006742065.1_ASM674206v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:31,960] [INFO] Task started: Blastn
[2024-01-24 11:21:31,960] [INFO] Running command: blastn -query GCF_006742065.1_ASM674206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92af83ad-e825-4263-9c82-b848e79e01fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_006742065.1_ASM674206v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:32,812] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:32,816] [INFO] Selected 21 target genomes.
[2024-01-24 11:21:32,817] [INFO] Target genome list was writen to GCF_006742065.1_ASM674206v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:32,860] [INFO] Task started: fastANI
[2024-01-24 11:21:32,861] [INFO] Running command: fastANI --query /var/lib/cwl/stg33643c7d-5514-4323-ad85-8adbe0a8e7c1/GCF_006742065.1_ASM674206v1_genomic.fna.gz --refList GCF_006742065.1_ASM674206v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006742065.1_ASM674206v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:47,174] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:47,190] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:47,191] [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_006742065.1	s__Clostridium butyricum	100.0	1560	1566	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.58	97.46	0.89	0.80	64	conclusive
GCA_900769625.1	s__Clostridium sp900769625	83.0954	689	1566	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015058525.1	s__Clostridium butyricum_A	80.262	393	1566	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012843905.1	s__Clostridium sp012843905	80.1322	517	1566	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473995.1	s__Clostridium saccharobutylicum	79.8175	540	1566	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.89	95.82	0.99	0.83	65	-
GCA_003539755.1	s__Clostridium sp003539755	79.6274	393	1566	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018223745.1	s__Clostridium beijerinckii	79.4491	484	1566	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.01	95.18	0.85	0.79	244	-
GCF_001458595.1	s__Clostridium neonatale	79.3678	530	1566	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.07	98.42	0.91	0.80	11	-
GCF_000340885.1	s__Clostridium saccharoperbutylacetonicum	79.1865	502	1566	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.35	98.00	0.96	0.89	7	-
GCF_001735765.2	s__Clostridium taeniosporum	79.0796	397	1566	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002006345.1	s__Clostridium puniceum	78.9416	511	1566	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000827935.1	s__Clostridium botulinum_A	78.9278	427	1566	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.05	97.92	0.91	0.85	31	-
GCF_900290265.1	s__Clostridium cagae	78.5141	426	1566	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.09	97.56	0.90	0.85	15	-
GCF_901482605.1	s__Hathewaya histolytica	77.6096	107	1566	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Hathewaya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003346815.1	s__Halarcobacter bivalviorum	75.3738	52	1566	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	98.23	96.46	0.96	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:47,192] [INFO] GTDB search result was written to GCF_006742065.1_ASM674206v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:47,193] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:47,196] [INFO] DFAST_QC result json was written to GCF_006742065.1_ASM674206v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:47,197] [INFO] DFAST_QC completed!
[2024-01-24 11:21:47,197] [INFO] Total running time: 0h1m13s