[2024-01-24 13:57:43,011] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:43,013] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:43,013] [INFO] DQC Reference Directory: /var/lib/cwl/stg2db051f8-2b9e-48fb-bd26-8a14a85f7f3d/dqc_reference
[2024-01-24 13:57:44,328] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:44,329] [INFO] Task started: Prodigal
[2024-01-24 13:57:44,329] [INFO] Running command: gunzip -c /var/lib/cwl/stg47b123af-00b2-4f33-b012-8429ec78df82/GCF_017874425.1_ASM1787442v1_genomic.fna.gz | prodigal -d GCF_017874425.1_ASM1787442v1_genomic.fna/cds.fna -a GCF_017874425.1_ASM1787442v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:51,608] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:51,608] [INFO] Task started: HMMsearch
[2024-01-24 13:57:51,609] [INFO] Running command: hmmsearch --tblout GCF_017874425.1_ASM1787442v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2db051f8-2b9e-48fb-bd26-8a14a85f7f3d/dqc_reference/reference_markers.hmm GCF_017874425.1_ASM1787442v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:51,978] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:51,979] [INFO] Found 6/6 markers.
[2024-01-24 13:57:52,021] [INFO] Query marker FASTA was written to GCF_017874425.1_ASM1787442v1_genomic.fna/markers.fasta
[2024-01-24 13:57:52,022] [INFO] Task started: Blastn
[2024-01-24 13:57:52,022] [INFO] Running command: blastn -query GCF_017874425.1_ASM1787442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2db051f8-2b9e-48fb-bd26-8a14a85f7f3d/dqc_reference/reference_markers.fasta -out GCF_017874425.1_ASM1787442v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:52,684] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:52,690] [INFO] Selected 27 target genomes.
[2024-01-24 13:57:52,691] [INFO] Target genome list was writen to GCF_017874425.1_ASM1787442v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:52,701] [INFO] Task started: fastANI
[2024-01-24 13:57:52,701] [INFO] Running command: fastANI --query /var/lib/cwl/stg47b123af-00b2-4f33-b012-8429ec78df82/GCF_017874425.1_ASM1787442v1_genomic.fna.gz --refList GCF_017874425.1_ASM1787442v1_genomic.fna/target_genomes.txt --output GCF_017874425.1_ASM1787442v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:13,055] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:13,056] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2db051f8-2b9e-48fb-bd26-8a14a85f7f3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:13,056] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2db051f8-2b9e-48fb-bd26-8a14a85f7f3d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:13,075] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:13,075] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:13,075] [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 punense	strain=DSM 28650	GCA_017874425.1	1054297	1054297	type	True	100.0	1522	1525	95	conclusive
Clostridium senegalense	strain=type strain: JC122	GCA_000285575.1	1465809	1465809	type	True	77.6775	194	1525	95	below_threshold
Clostridium ihumii	strain=AP5	GCA_000612845.1	1470356	1470356	type	True	77.2869	225	1525	95	below_threshold
Clostridium faecium	strain=N37	GCA_014836835.1	2762223	2762223	type	True	77.2432	243	1525	95	below_threshold
Clostridium tagluense	strain=A121	GCA_003865095.1	360422	360422	type	True	76.7866	168	1525	95	below_threshold
Clostridium bowmanii	strain=DSM 14206	GCA_018861315.1	132925	132925	type	True	76.5571	141	1525	95	below_threshold
Clostridium estertheticum subsp. estertheticum	strain=DSM 8809	GCA_001877035.1	1552	238834	type	True	76.479	108	1525	95	below_threshold
Clostridium algoriphilum	strain=DSM 16153	GCA_020443705.1	198347	198347	type	True	76.3706	117	1525	95	below_threshold
Clostridium celatum	strain=DSM 1785	GCA_000320405.1	36834	36834	type	True	76.3577	104	1525	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	76.3505	132	1525	95	below_threshold
Clostridium nigeriense	strain=Marseille-P2414	GCA_900086595.1	1805470	1805470	type	True	76.3407	116	1525	95	below_threshold
Clostridium septicum	strain=FDAARGOS_1551	GCA_020736665.1	1504	1504	type	True	76.3065	117	1525	95	below_threshold
Clostridium septicum	strain=DSM 7534	GCA_003606265.1	1504	1504	type	True	76.2648	119	1525	95	below_threshold
Clostridium fungisolvens	strain=TW1	GCA_014193895.1	1604897	1604897	type	True	76.2589	122	1525	95	below_threshold
Clostridium niameyense	strain=MT5	GCA_001243045.1	1622073	1622073	type	True	76.246	121	1525	95	below_threshold
Clostridium carboxidivorans	strain=P7	GCA_001038625.1	217159	217159	type	True	76.2065	148	1525	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	76.1806	97	1525	95	below_threshold
Clostridium carboxidivorans	strain=P7	GCA_000175595.1	217159	217159	type	True	76.1319	140	1525	95	below_threshold
Clostridium isatidis	strain=DSM 15098	GCA_002285495.1	182773	182773	type	True	75.9837	110	1525	95	below_threshold
Clostridium felsineum	strain=DSM 793	GCA_002006235.2	36839	36839	type	True	75.9494	123	1525	95	below_threshold
Clostridium felsineum	strain=DSM 794	GCA_002006355.2	36839	36839	type	True	75.894	114	1525	95	below_threshold
Clostridium felsineum	strain=DSM 7320	GCA_002006215.2	36839	36839	type	True	75.8565	122	1525	95	below_threshold
Clostridium gelidum	strain=C5S11	GCA_019977655.1	704125	704125	type	True	75.8456	129	1525	95	below_threshold
Clostridium neonatale	strain=LCDC 99A005	GCA_002553615.1	137838	137838	type	True	75.843	101	1525	95	below_threshold
Clostridium neonatale	strain=LCDC no.99-A-005	GCA_001458595.1	137838	137838	type	True	75.8194	101	1525	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:13,077] [INFO] DFAST Taxonomy check result was written to GCF_017874425.1_ASM1787442v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:13,078] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:13,078] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:13,078] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2db051f8-2b9e-48fb-bd26-8a14a85f7f3d/dqc_reference/checkm_data
[2024-01-24 13:58:13,079] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:13,126] [INFO] Task started: CheckM
[2024-01-24 13:58:13,127] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017874425.1_ASM1787442v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017874425.1_ASM1787442v1_genomic.fna/checkm_input GCF_017874425.1_ASM1787442v1_genomic.fna/checkm_result
[2024-01-24 13:58:43,015] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:43,016] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:43,036] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:43,036] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:43,037] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017874425.1_ASM1787442v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:43,037] [INFO] Task started: Blastn
[2024-01-24 13:58:43,037] [INFO] Running command: blastn -query GCF_017874425.1_ASM1787442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2db051f8-2b9e-48fb-bd26-8a14a85f7f3d/dqc_reference/reference_markers_gtdb.fasta -out GCF_017874425.1_ASM1787442v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:43,913] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:43,916] [INFO] Selected 20 target genomes.
[2024-01-24 13:58:43,916] [INFO] Target genome list was writen to GCF_017874425.1_ASM1787442v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:43,947] [INFO] Task started: fastANI
[2024-01-24 13:58:43,948] [INFO] Running command: fastANI --query /var/lib/cwl/stg47b123af-00b2-4f33-b012-8429ec78df82/GCF_017874425.1_ASM1787442v1_genomic.fna.gz --refList GCF_017874425.1_ASM1787442v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017874425.1_ASM1787442v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:59,037] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:59,059] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:59,060] [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_017874425.1	s__Clostridium_J punense	100.0	1522	1525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	99.96	99.96	0.97	0.97	2	conclusive
GCF_000300195.1	s__Clostridium_J tunisiense	84.7357	996	1525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	96.47	95.03	0.88	0.88	3	-
GCA_002453475.1	s__Clostridium_J sp002453475	78.0311	214	1525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000732635.1	s__Clostridium_J sulfidigenes	77.9606	225	1525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	97.10	95.50	0.86	0.78	28	-
GCA_002381695.1	s__Clostridium_J sp002381695	77.815	250	1525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002316385.1	s__Clostridium_J sp002316385	77.7866	223	1525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363375.1	s__Clostridium_J sp902363375	77.7801	194	1525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000285575.1	s__Clostridium_J senegalense	77.6538	196	1525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	97.19	95.52	0.93	0.91	5	-
GCA_002341865.1	s__Clostridium_J sp002341865	77.5785	249	1525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000816675.1	s__Clostridium_J argentinense	77.5238	262	1525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	99.28	97.50	0.97	0.91	8	-
GCA_002455975.1	s__Clostridium_J sp002455975	77.3625	235	1525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000612845.1	s__Clostridium_J ihumii	77.2998	224	1525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014836835.1	s__Clostridium_J sp900547625	77.2638	241	1525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	99.59	99.59	0.89	0.87	3	-
GCA_900548455.1	s__Clostridium_J sp900548455	76.9716	185	1525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003614235.1	s__Clostridium_H haemolyticum	76.6023	116	1525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0	98.44	97.38	0.90	0.84	13	-
GCF_000320405.1	s__Clostridium celatum	76.3577	104	1525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.74	99.48	0.95	0.91	3	-
GCF_017873245.1	s__Clostridium tertium	76.3094	122	1525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.32	97.37	0.91	0.89	19	-
GCF_001243045.1	s__Clostridium_F niameyense	76.2475	121	1525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.56	99.11	0.96	0.92	3	-
GCF_012843905.1	s__Clostridium sp012843905	76.0183	90	1525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:59,061] [INFO] GTDB search result was written to GCF_017874425.1_ASM1787442v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:59,062] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:59,067] [INFO] DFAST_QC result json was written to GCF_017874425.1_ASM1787442v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:59,067] [INFO] DFAST_QC completed!
[2024-01-24 13:58:59,067] [INFO] Total running time: 0h1m16s