[2024-01-24 10:48:09,162] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:48:09,165] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:48:09,166] [INFO] DQC Reference Directory: /var/lib/cwl/stgba6f1301-fb4c-4d29-bcb2-75a3262d84b2/dqc_reference
[2024-01-24 10:48:23,953] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:23,954] [INFO] Task started: Prodigal
[2024-01-24 10:48:23,954] [INFO] Running command: gunzip -c /var/lib/cwl/stg7415f310-9c4b-47f1-b7fa-35e547b4b14a/GCF_001263795.1_ASM126379v1_genomic.fna.gz | prodigal -d GCF_001263795.1_ASM126379v1_genomic.fna/cds.fna -a GCF_001263795.1_ASM126379v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:29,975] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:29,975] [INFO] Task started: HMMsearch
[2024-01-24 10:48:29,975] [INFO] Running command: hmmsearch --tblout GCF_001263795.1_ASM126379v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba6f1301-fb4c-4d29-bcb2-75a3262d84b2/dqc_reference/reference_markers.hmm GCF_001263795.1_ASM126379v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:30,293] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:30,295] [INFO] Found 6/6 markers.
[2024-01-24 10:48:30,327] [INFO] Query marker FASTA was written to GCF_001263795.1_ASM126379v1_genomic.fna/markers.fasta
[2024-01-24 10:48:30,328] [INFO] Task started: Blastn
[2024-01-24 10:48:30,328] [INFO] Running command: blastn -query GCF_001263795.1_ASM126379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba6f1301-fb4c-4d29-bcb2-75a3262d84b2/dqc_reference/reference_markers.fasta -out GCF_001263795.1_ASM126379v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:30,923] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:30,927] [INFO] Selected 24 target genomes.
[2024-01-24 10:48:30,928] [INFO] Target genome list was writen to GCF_001263795.1_ASM126379v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:31,639] [INFO] Task started: fastANI
[2024-01-24 10:48:31,639] [INFO] Running command: fastANI --query /var/lib/cwl/stg7415f310-9c4b-47f1-b7fa-35e547b4b14a/GCF_001263795.1_ASM126379v1_genomic.fna.gz --refList GCF_001263795.1_ASM126379v1_genomic.fna/target_genomes.txt --output GCF_001263795.1_ASM126379v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:46,921] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:46,921] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba6f1301-fb4c-4d29-bcb2-75a3262d84b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:46,922] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba6f1301-fb4c-4d29-bcb2-75a3262d84b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:46,938] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:48:46,938] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:46,938] [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 homopropionicum	strain=DSM 5847	GCA_001263795.1	36844	36844	type	True	100.0	1190	1193	95	conclusive
Clostridium homopropionicum	strain=DSM 5847	GCA_900113195.1	36844	36844	type	True	99.9959	1182	1193	95	conclusive
Clostridium thermopalmarium	strain=DSM 5974	GCA_002995795.1	29373	29373	suspected-type	True	78.2213	256	1193	95	below_threshold
Clostridium thermopalmarium	strain=DSM 5974	GCA_003097175.1	29373	29373	suspected-type	True	78.0926	254	1193	95	below_threshold
Clostridium massiliodielmoense	strain=MT26	GCA_900176615.1	1776385	1776385	type	True	77.7203	216	1193	95	below_threshold
Hathewaya histolytica	strain=NCTC503	GCA_901482605.1	1498	1498	type	True	76.7005	67	1193	95	below_threshold
Clostridium sporogenes	strain=NCIMB 10696	GCA_000973705.1	1509	1509	type	True	76.6401	154	1193	95	below_threshold
Clostridium acetireducens	strain=DSM 10703	GCA_001758365.1	76489	76489	type	True	76.6063	134	1193	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	76.5956	157	1193	95	below_threshold
Clostridium sporogenes	strain=NCTC13020	GCA_900461305.1	1509	1509	type	True	76.5883	157	1193	95	below_threshold
Clostridium sporogenes	strain=DSM 795	GCA_001020205.1	1509	1509	type	True	76.5874	157	1193	95	below_threshold
Clostridium pasteurianum	strain=DSM 525	GCA_000807255.1	1501	1501	type	True	76.5509	134	1193	95	below_threshold
Clostridium pasteurianum	strain=ATCC 6013	GCA_000807175.1	1501	1501	type	True	76.5451	131	1193	95	below_threshold
Clostridium pasteurianum	strain=ATCC 6013	GCA_001856645.1	1501	1501	type	True	76.5358	134	1193	95	below_threshold
Clostridium pasteurianum	strain=DSM 525	GCA_000330945.1	1501	1501	type	True	76.5284	134	1193	95	below_threshold
Clostridium faecium	strain=N37	GCA_014836835.1	2762223	2762223	type	True	76.5282	118	1193	95	below_threshold
Clostridium pasteurianum	strain=ATCC 6013	GCA_000724205.3	1501	1501	type	True	76.5186	135	1193	95	below_threshold
Clostridium carboxidivorans	strain=P7	GCA_001038625.1	217159	217159	type	True	76.3905	156	1193	95	below_threshold
Clostridium swellfunianum	strain=CICC 10730	GCA_023656515.1	1367462	1367462	type	True	76.3511	95	1193	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	76.2171	106	1193	95	below_threshold
Clostridium hydrogeniformans	strain=DSM 21757	GCA_000686705.1	349933	349933	type	True	75.9417	97	1193	95	below_threshold
Clostridium neonatale	strain=LCDC 99A005	GCA_002553615.1	137838	137838	type	True	75.9255	109	1193	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:46,940] [INFO] DFAST Taxonomy check result was written to GCF_001263795.1_ASM126379v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:46,941] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:46,941] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:46,941] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba6f1301-fb4c-4d29-bcb2-75a3262d84b2/dqc_reference/checkm_data
[2024-01-24 10:48:46,942] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:46,982] [INFO] Task started: CheckM
[2024-01-24 10:48:46,983] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001263795.1_ASM126379v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001263795.1_ASM126379v1_genomic.fna/checkm_input GCF_001263795.1_ASM126379v1_genomic.fna/checkm_result
[2024-01-24 10:49:13,733] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:13,737] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:13,831] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:13,832] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:13,832] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001263795.1_ASM126379v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:13,832] [INFO] Task started: Blastn
[2024-01-24 10:49:13,832] [INFO] Running command: blastn -query GCF_001263795.1_ASM126379v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba6f1301-fb4c-4d29-bcb2-75a3262d84b2/dqc_reference/reference_markers_gtdb.fasta -out GCF_001263795.1_ASM126379v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:14,933] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:14,937] [INFO] Selected 25 target genomes.
[2024-01-24 10:49:14,937] [INFO] Target genome list was writen to GCF_001263795.1_ASM126379v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:14,999] [INFO] Task started: fastANI
[2024-01-24 10:49:15,000] [INFO] Running command: fastANI --query /var/lib/cwl/stg7415f310-9c4b-47f1-b7fa-35e547b4b14a/GCF_001263795.1_ASM126379v1_genomic.fna.gz --refList GCF_001263795.1_ASM126379v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001263795.1_ASM126379v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:31,970] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:31,990] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:31,991] [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_001263795.1	s__Clostridium_H homopropionicum	100.0	1190	1193	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_002995795.1	s__Clostridium_H thermopalmarium	78.1727	260	1193	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0	99.57	99.32	0.95	0.92	4	-
GCA_009738435.1	s__Clostridium_H bovifaecis	78.0346	317	1193	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000204565.1	s__Clostridium_H botulinum_B	77.8379	212	1193	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0162	99.87	99.52	0.98	0.95	19	-
GCF_003614235.1	s__Clostridium_H haemolyticum	77.8279	226	1193	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_900176615.1	s__Clostridium_H massiliodielmoense	77.7351	215	1193	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0	98.64	96.44	0.92	0.87	5	-
GCF_017100085.1	s__Clostridium_H botulinum_A	77.6407	235	1193	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0162	99.30	99.03	0.94	0.90	14	-
GCF_000014125.1	s__Clostridium_H novyi	77.5997	224	1193	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_H	95.0	98.92	96.35	0.94	0.92	7	-
GCF_901482605.1	s__Hathewaya histolytica	76.7005	67	1193	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_001758365.1	s__Clostridium_C acetireducens	76.6063	134	1193	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001020205.1	s__Clostridium_F sporogenes	76.5618	159	1193	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.24	98.80	0.94	0.88	81	-
GCF_000807255.1	s__Clostridium_I pasteurianum	76.5509	134	1193	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_I	95.0	99.98	99.90	1.00	0.99	7	-
GCF_001276985.1	s__Clostridium_F botulinum	76.5405	158	1193	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	97.69	95.97	0.92	0.83	213	-
GCF_014836835.1	s__Clostridium_J sp900547625	76.5233	118	1193	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	-
GCF_900095445.1	s__UBA3947 sp900095445	76.4105	79	1193	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__UBA3947	95.0	99.63	99.63	0.84	0.84	2	-
GCF_018861705.1	s__Clostridium_AD psychrophilum	76.3289	113	1193	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018332455.1	s__Clostridium_AR polyendosporum	76.2496	104	1193	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AR	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861755.1	s__Clostridium_AD sp018861755	76.2078	112	1193	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900626095.1	s__Clostridium_AS rectalis	76.1552	124	1193	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AS	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:31,992] [INFO] GTDB search result was written to GCF_001263795.1_ASM126379v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:31,993] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:31,997] [INFO] DFAST_QC result json was written to GCF_001263795.1_ASM126379v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:31,997] [INFO] DFAST_QC completed!
[2024-01-24 10:49:31,997] [INFO] Total running time: 0h1m23s