[2024-01-24 14:39:01,520] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:01,525] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:01,525] [INFO] DQC Reference Directory: /var/lib/cwl/stg47f5434e-1b9e-460f-94c0-53ab37decdce/dqc_reference
[2024-01-24 14:39:04,242] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:04,243] [INFO] Task started: Prodigal
[2024-01-24 14:39:04,243] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b830eb2-5cc8-4ca2-b936-8644ddc93dc0/GCF_002995745.1_ASM299574v1_genomic.fna.gz | prodigal -d GCF_002995745.1_ASM299574v1_genomic.fna/cds.fna -a GCF_002995745.1_ASM299574v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:09,464] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:09,464] [INFO] Task started: HMMsearch
[2024-01-24 14:39:09,464] [INFO] Running command: hmmsearch --tblout GCF_002995745.1_ASM299574v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47f5434e-1b9e-460f-94c0-53ab37decdce/dqc_reference/reference_markers.hmm GCF_002995745.1_ASM299574v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:09,709] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:09,711] [INFO] Found 6/6 markers.
[2024-01-24 14:39:09,748] [INFO] Query marker FASTA was written to GCF_002995745.1_ASM299574v1_genomic.fna/markers.fasta
[2024-01-24 14:39:09,748] [INFO] Task started: Blastn
[2024-01-24 14:39:09,749] [INFO] Running command: blastn -query GCF_002995745.1_ASM299574v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47f5434e-1b9e-460f-94c0-53ab37decdce/dqc_reference/reference_markers.fasta -out GCF_002995745.1_ASM299574v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:10,863] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:10,866] [INFO] Selected 24 target genomes.
[2024-01-24 14:39:10,867] [INFO] Target genome list was writen to GCF_002995745.1_ASM299574v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:10,920] [INFO] Task started: fastANI
[2024-01-24 14:39:10,921] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b830eb2-5cc8-4ca2-b936-8644ddc93dc0/GCF_002995745.1_ASM299574v1_genomic.fna.gz --refList GCF_002995745.1_ASM299574v1_genomic.fna/target_genomes.txt --output GCF_002995745.1_ASM299574v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:27,969] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:27,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47f5434e-1b9e-460f-94c0-53ab37decdce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:27,970] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47f5434e-1b9e-460f-94c0-53ab37decdce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:27,985] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:27,985] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:27,985] [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 vincentii	strain=DSM 10228	GCA_002995745.1	52704	52704	type	True	100.0	1120	1123	95	conclusive
Clostridium gelidum	strain=C5S11	GCA_019977655.1	704125	704125	type	True	78.6565	320	1123	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	78.2526	343	1123	95	below_threshold
Clostridium uliginosum	strain=DSM 12992	GCA_900112485.1	119641	119641	type	True	78.2176	248	1123	95	below_threshold
Clostridium puniceum	strain=DSM 2619	GCA_002006345.1	29367	29367	type	True	77.9061	265	1123	95	below_threshold
Clostridium cagae	strain=Marseille-P4344	GCA_900290265.1	2080751	2080751	type	True	77.749	219	1123	95	below_threshold
Clostridium paraputrificum	strain=NCTC11833	GCA_900447045.1	29363	29363	type	True	77.6043	266	1123	95	below_threshold
Clostridium chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	77.2171	186	1123	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=N1-4(HMT)	GCA_000340885.1	36745	36745	type	True	77.1709	231	1123	95	below_threshold
Clostridium septicum	strain=FDAARGOS_1551	GCA_020736665.1	1504	1504	type	True	77.1304	195	1123	95	below_threshold
Clostridium sardiniense	strain=DSM 2632	GCA_016907995.1	29369	29369	type	True	76.9858	195	1123	95	below_threshold
Sarcina ventriculi	strain=NCTC12966	GCA_900456775.1	1267	1267	type	True	76.6784	128	1123	95	below_threshold
Clostridium mediterraneense	strain=Marseille-P2434	GCA_900091705.1	1805472	1805472	type	True	76.5571	127	1123	95	below_threshold
Clostridium zeae	strain=CSC2	GCA_017312485.1	2759022	2759022	type	True	76.4921	137	1123	95	below_threshold
Haloimpatiens massiliensis	strain=Mt13	GCA_900184255.1	1658110	1658110	type	True	76.0757	93	1123	95	below_threshold
Clostridium felsineum	strain=DSM 793	GCA_002006235.2	36839	36839	type	True	75.7629	101	1123	95	below_threshold
Clostridium felsineum	strain=DSM 7320	GCA_002006215.2	36839	36839	type	True	75.7368	109	1123	95	below_threshold
Clostridium felsineum	strain=DSM 794	GCA_002006355.2	36839	36839	type	True	75.708	109	1123	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:27,987] [INFO] DFAST Taxonomy check result was written to GCF_002995745.1_ASM299574v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:27,987] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:27,988] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:27,988] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47f5434e-1b9e-460f-94c0-53ab37decdce/dqc_reference/checkm_data
[2024-01-24 14:39:27,989] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:28,026] [INFO] Task started: CheckM
[2024-01-24 14:39:28,026] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002995745.1_ASM299574v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002995745.1_ASM299574v1_genomic.fna/checkm_input GCF_002995745.1_ASM299574v1_genomic.fna/checkm_result
[2024-01-24 14:39:50,582] [INFO] Task succeeded: CheckM
[2024-01-24 14:39:50,584] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:39:50,601] [INFO] ===== Completeness check finished =====
[2024-01-24 14:39:50,601] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:39:50,601] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002995745.1_ASM299574v1_genomic.fna/markers.fasta)
[2024-01-24 14:39:50,602] [INFO] Task started: Blastn
[2024-01-24 14:39:50,602] [INFO] Running command: blastn -query GCF_002995745.1_ASM299574v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47f5434e-1b9e-460f-94c0-53ab37decdce/dqc_reference/reference_markers_gtdb.fasta -out GCF_002995745.1_ASM299574v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:51,417] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:51,421] [INFO] Selected 24 target genomes.
[2024-01-24 14:39:51,421] [INFO] Target genome list was writen to GCF_002995745.1_ASM299574v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:39:51,436] [INFO] Task started: fastANI
[2024-01-24 14:39:51,437] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b830eb2-5cc8-4ca2-b936-8644ddc93dc0/GCF_002995745.1_ASM299574v1_genomic.fna.gz --refList GCF_002995745.1_ASM299574v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002995745.1_ASM299574v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:06,526] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:06,543] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:06,543] [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_002995745.1	s__Clostridium vincentii	100.0	1120	1123	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007115085.1	s__Clostridium sp007115085	78.2126	338	1123	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.42	99.42	0.90	0.90	2	-
GCA_015058405.1	s__Clostridium sp015058405	78.0233	250	1123	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	77.903	268	1123	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_018372875.1	s__Clostridium sp018372875	77.671	240	1123	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.91	98.91	0.87	0.87	2	-
GCF_900447045.1	s__Clostridium paraputrificum	77.624	265	1123	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.58	95.42	0.89	0.83	29	-
GCF_900116755.1	s__Clostridium sp900116755	77.6079	238	1123	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_015058375.1	s__Clostridium sp015058375	77.3483	193	1123	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_900539375.1	s__Clostridium sp900539375	77.3291	228	1123	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.09	99.02	0.89	0.86	4	-
GCF_003606265.1	s__Clostridium septicum	77.1648	193	1123	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.65	99.48	0.94	0.92	5	-
GCA_900317445.1	s__Clostridium sp900317445	77.1555	171	1123	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	100.00	100.00	0.99	0.99	2	-
GCA_012519845.1	s__Clostridium sp012519845	77.0745	209	1123	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_015550425.1	s__Clostridium sp015550425	76.9901	177	1123	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.01	99.01	0.93	0.93	2	-
GCF_000401215.1	s__Clostridium sartagoforme_A	76.9323	180	1123	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.25	98.25	0.85	0.85	2	-
GCA_900766315.1	s__Clostridium sp900766315	76.8998	182	1123	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_000789395.1	s__Clostridium baratii	76.8638	199	1123	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	96.53	95.37	0.92	0.89	15	-
GCA_017888565.1	s__Clostridium sp017888565	76.8518	185	1123	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_012519155.1	s__Clostridium sp012519155	76.7702	160	1123	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_000498355.1	s__Clostridium sp000498355	76.7593	193	1123	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_900540255.1	s__Clostridium sp900540255	76.703	158	1123	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.08	99.08	0.90	0.89	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:06,545] [INFO] GTDB search result was written to GCF_002995745.1_ASM299574v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:06,546] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:06,550] [INFO] DFAST_QC result json was written to GCF_002995745.1_ASM299574v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:06,551] [INFO] DFAST_QC completed!
[2024-01-24 14:40:06,551] [INFO] Total running time: 0h1m5s