[2024-01-25 17:47:35,390] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:47:35,392] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:47:35,392] [INFO] DQC Reference Directory: /var/lib/cwl/stg02f9f65a-a13b-4990-8cdd-fa10ca02f8bc/dqc_reference
[2024-01-25 17:47:36,550] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:47:36,551] [INFO] Task started: Prodigal
[2024-01-25 17:47:36,551] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c97e120-4162-4f00-90d8-b6f2ffbf24eb/GCF_014836335.1_ASM1483633v1_genomic.fna.gz | prodigal -d GCF_014836335.1_ASM1483633v1_genomic.fna/cds.fna -a GCF_014836335.1_ASM1483633v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:47:42,330] [INFO] Task succeeded: Prodigal
[2024-01-25 17:47:42,330] [INFO] Task started: HMMsearch
[2024-01-25 17:47:42,330] [INFO] Running command: hmmsearch --tblout GCF_014836335.1_ASM1483633v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02f9f65a-a13b-4990-8cdd-fa10ca02f8bc/dqc_reference/reference_markers.hmm GCF_014836335.1_ASM1483633v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:47:42,579] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:47:42,580] [INFO] Found 6/6 markers.
[2024-01-25 17:47:42,615] [INFO] Query marker FASTA was written to GCF_014836335.1_ASM1483633v1_genomic.fna/markers.fasta
[2024-01-25 17:47:42,616] [INFO] Task started: Blastn
[2024-01-25 17:47:42,616] [INFO] Running command: blastn -query GCF_014836335.1_ASM1483633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02f9f65a-a13b-4990-8cdd-fa10ca02f8bc/dqc_reference/reference_markers.fasta -out GCF_014836335.1_ASM1483633v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:43,162] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:43,166] [INFO] Selected 24 target genomes.
[2024-01-25 17:47:43,166] [INFO] Target genome list was writen to GCF_014836335.1_ASM1483633v1_genomic.fna/target_genomes.txt
[2024-01-25 17:47:43,193] [INFO] Task started: fastANI
[2024-01-25 17:47:43,194] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c97e120-4162-4f00-90d8-b6f2ffbf24eb/GCF_014836335.1_ASM1483633v1_genomic.fna.gz --refList GCF_014836335.1_ASM1483633v1_genomic.fna/target_genomes.txt --output GCF_014836335.1_ASM1483633v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:47:59,597] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:59,598] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02f9f65a-a13b-4990-8cdd-fa10ca02f8bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:47:59,598] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02f9f65a-a13b-4990-8cdd-fa10ca02f8bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:47:59,611] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:47:59,611] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:47:59,612] [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 cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	100.0	1380	1384	95	conclusive
Clostridium vincentii	strain=DSM 10228	GCA_002995745.1	52704	52704	type	True	78.358	333	1384	95	below_threshold
Clostridium saccharobutylicum	strain=DSM 13864	GCA_000473995.1	169679	169679	type	True	78.31	349	1384	95	below_threshold
Clostridium saccharobutylicum	strain=DSM 13864	GCA_001657435.1	169679	169679	type	True	78.2604	321	1384	95	below_threshold
Clostridium paraputrificum	strain=NCTC11833	GCA_900447045.1	29363	29363	type	True	78.2366	316	1384	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	77.7421	277	1384	95	below_threshold
Clostridium moniliforme	strain=DSM 3984	GCA_017873235.1	39489	39489	type	True	77.6493	244	1384	95	below_threshold
Clostridium chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	77.6051	223	1384	95	below_threshold
Clostridium gelidum	strain=C5S11	GCA_019977655.1	704125	704125	type	True	77.583	346	1384	95	below_threshold
Clostridium puniceum	strain=DSM 2619	GCA_002006345.1	29367	29367	type	True	77.4973	365	1384	95	below_threshold
Clostridium cagae	strain=Marseille-P4344	GCA_900290265.1	2080751	2080751	type	True	77.4967	261	1384	95	below_threshold
Clostridium butyricum	strain=NBRC 13949	GCA_006742065.1	1492	1492	type	True	77.2079	264	1384	95	below_threshold
Clostridium isatidis	strain=DSM 15098	GCA_002285495.1	182773	182773	type	True	77.1861	178	1384	95	below_threshold
Clostridium butyricum	strain=DSM 10702	GCA_014131795.1	1492	1492	type	True	77.1426	262	1384	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	77.1068	254	1384	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	77.0956	199	1384	95	below_threshold
Clostridium butyricum	strain=NBRC 13949	GCA_007992895.1	1492	1492	type	True	77.084	260	1384	95	below_threshold
Clostridium butyricum	strain=DSM 10702	GCA_000409755.1	1492	1492	type	True	77.0208	262	1384	95	below_threshold
Clostridium intestinale	strain=DSM 6191	GCA_900130055.1	36845	36845	type	True	76.7081	195	1384	95	below_threshold
Clostridium massiliamazoniense	strain=ND2	GCA_001403635.1	1347366	1347366	type	True	76.6592	182	1384	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:47:59,613] [INFO] DFAST Taxonomy check result was written to GCF_014836335.1_ASM1483633v1_genomic.fna/tc_result.tsv
[2024-01-25 17:47:59,613] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:47:59,614] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:47:59,614] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02f9f65a-a13b-4990-8cdd-fa10ca02f8bc/dqc_reference/checkm_data
[2024-01-25 17:47:59,615] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:47:59,658] [INFO] Task started: CheckM
[2024-01-25 17:47:59,658] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014836335.1_ASM1483633v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014836335.1_ASM1483633v1_genomic.fna/checkm_input GCF_014836335.1_ASM1483633v1_genomic.fna/checkm_result
[2024-01-25 17:48:22,389] [INFO] Task succeeded: CheckM
[2024-01-25 17:48:22,392] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:48:22,421] [INFO] ===== Completeness check finished =====
[2024-01-25 17:48:22,421] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:48:22,422] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014836335.1_ASM1483633v1_genomic.fna/markers.fasta)
[2024-01-25 17:48:22,422] [INFO] Task started: Blastn
[2024-01-25 17:48:22,422] [INFO] Running command: blastn -query GCF_014836335.1_ASM1483633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg02f9f65a-a13b-4990-8cdd-fa10ca02f8bc/dqc_reference/reference_markers_gtdb.fasta -out GCF_014836335.1_ASM1483633v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:23,268] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:23,272] [INFO] Selected 22 target genomes.
[2024-01-25 17:48:23,272] [INFO] Target genome list was writen to GCF_014836335.1_ASM1483633v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:48:23,306] [INFO] Task started: fastANI
[2024-01-25 17:48:23,306] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c97e120-4162-4f00-90d8-b6f2ffbf24eb/GCF_014836335.1_ASM1483633v1_genomic.fna.gz --refList GCF_014836335.1_ASM1483633v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014836335.1_ASM1483633v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:48:37,274] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:37,286] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:48:37,287] [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_007115085.1	s__Clostridium sp007115085	99.4101	1243	1384	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.42	99.42	0.90	0.90	2	conclusive
GCA_015058405.1	s__Clostridium sp015058405	78.8236	390	1384	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_900116755.1	s__Clostridium sp900116755	78.4733	327	1384	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_002995745.1	s__Clostridium vincentii	78.3457	334	1384	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	78.3148	294	1384	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	78.2138	318	1384	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.58	95.42	0.89	0.83	29	-
GCA_015058375.1	s__Clostridium sp015058375	78.0769	282	1384	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	77.9829	285	1384	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_017873235.1	s__Clostridium moniliforme	77.623	246	1384	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_018918325.1	s__Clostridium sp018918325	77.5166	220	1384	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_902785295.1	s__Clostridium sp902785295	77.4698	250	1384	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	77.4541	253	1384	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.05	97.92	0.91	0.85	31	-
GCA_012519155.1	s__Clostridium sp012519155	77.3173	175	1384	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_012519845.1	s__Clostridium sp012519845	77.2867	240	1384	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_006742065.1	s__Clostridium butyricum	77.1982	265	1384	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.58	97.46	0.89	0.80	64	-
GCF_002760435.1	s__Clostridium sp002760435	77.1632	284	1384	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.99	99.99	0.98	0.98	2	-
GCF_900086595.1	s__Clostridium nigeriense	77.0962	234	1384	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.98	98.98	0.91	0.91	2	-
GCA_000435835.1	s__Clostridium sp000435835	76.6278	155	1384	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.44	99.22	0.92	0.88	4	-
GCF_900187165.1	s__Clostridium_G cochlearium	76.343	103	1384	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_G	95.0	99.06	98.56	0.90	0.85	10	-
GCA_902363375.1	s__Clostridium_J sp902363375	75.976	106	1384	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_009711765.1	s__MES13 sp009711765	74.7897	70	1384	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__MES13;g__MES13	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:48:37,288] [INFO] GTDB search result was written to GCF_014836335.1_ASM1483633v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:48:37,289] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:48:37,293] [INFO] DFAST_QC result json was written to GCF_014836335.1_ASM1483633v1_genomic.fna/dqc_result.json
[2024-01-25 17:48:37,293] [INFO] DFAST_QC completed!
[2024-01-25 17:48:37,293] [INFO] Total running time: 0h1m2s