[2024-01-24 11:26:11,906] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:11,908] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:11,908] [INFO] DQC Reference Directory: /var/lib/cwl/stge0e2d79d-c185-41b7-98be-9f43f78bec21/dqc_reference
[2024-01-24 11:26:13,348] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:13,349] [INFO] Task started: Prodigal
[2024-01-24 11:26:13,350] [INFO] Running command: gunzip -c /var/lib/cwl/stg411477a0-7bc2-4e9f-850a-a7a080acc0d1/GCF_002995795.1_ASM299579v1_genomic.fna.gz | prodigal -d GCF_002995795.1_ASM299579v1_genomic.fna/cds.fna -a GCF_002995795.1_ASM299579v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:17,992] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:17,992] [INFO] Task started: HMMsearch
[2024-01-24 11:26:17,993] [INFO] Running command: hmmsearch --tblout GCF_002995795.1_ASM299579v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0e2d79d-c185-41b7-98be-9f43f78bec21/dqc_reference/reference_markers.hmm GCF_002995795.1_ASM299579v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:18,328] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:18,329] [INFO] Found 6/6 markers.
[2024-01-24 11:26:18,378] [INFO] Query marker FASTA was written to GCF_002995795.1_ASM299579v1_genomic.fna/markers.fasta
[2024-01-24 11:26:18,378] [INFO] Task started: Blastn
[2024-01-24 11:26:18,378] [INFO] Running command: blastn -query GCF_002995795.1_ASM299579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0e2d79d-c185-41b7-98be-9f43f78bec21/dqc_reference/reference_markers.fasta -out GCF_002995795.1_ASM299579v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:18,993] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:18,996] [INFO] Selected 24 target genomes.
[2024-01-24 11:26:18,997] [INFO] Target genome list was writen to GCF_002995795.1_ASM299579v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:19,056] [INFO] Task started: fastANI
[2024-01-24 11:26:19,056] [INFO] Running command: fastANI --query /var/lib/cwl/stg411477a0-7bc2-4e9f-850a-a7a080acc0d1/GCF_002995795.1_ASM299579v1_genomic.fna.gz --refList GCF_002995795.1_ASM299579v1_genomic.fna/target_genomes.txt --output GCF_002995795.1_ASM299579v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:33,970] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:33,971] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0e2d79d-c185-41b7-98be-9f43f78bec21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:33,971] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0e2d79d-c185-41b7-98be-9f43f78bec21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:33,987] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:26:33,988] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:33,988] [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 thermopalmarium	strain=DSM 5974	GCA_002995795.1	29373	29373	suspected-type	True	100.0	905	908	95	conclusive
Clostridium thermopalmarium	strain=DSM 5974	GCA_003097175.1	29373	29373	suspected-type	True	99.9912	900	908	95	conclusive
Clostridium massiliodielmoense	strain=MT26	GCA_900176615.1	1776385	1776385	type	True	78.5513	263	908	95	below_threshold
Clostridium homopropionicum	strain=DSM 5847	GCA_900113195.1	36844	36844	type	True	78.0824	267	908	95	below_threshold
Clostridium homopropionicum	strain=DSM 5847	GCA_001263795.1	36844	36844	type	True	78.0359	271	908	95	below_threshold
Clostridium oryzae	strain=DSM 28571	GCA_002029235.1	1450648	1450648	type	True	77.7029	81	908	95	below_threshold
Clostridium drakei	strain=SL1	GCA_003096175.1	332101	332101	type	True	76.8845	181	908	95	below_threshold
Clostridium drakei	strain=SL1	GCA_000633595.2	332101	332101	type	True	76.8016	174	908	95	below_threshold
Clostridium faecium	strain=N37	GCA_014836835.1	2762223	2762223	type	True	76.7871	125	908	95	below_threshold
Clostridium thailandense	strain=PL3	GCA_019207025.1	2794346	2794346	type	True	76.692	129	908	95	below_threshold
Clostridium rectalis	strain=Marseille-P4200	GCA_900626095.1	2040295	2040295	type	True	76.6792	126	908	95	below_threshold
Clostridium fungisolvens	strain=TW1	GCA_014193895.1	1604897	1604897	type	True	76.4768	104	908	95	below_threshold
Clostridium collagenovorans	strain=DSM 3089	GCA_900130005.1	29357	29357	type	True	76.4661	81	908	95	below_threshold
Clostridium cochlearium	strain=NCTC13027	GCA_900187165.1	1494	1494	type	True	76.464	129	908	95	below_threshold
Clostridium felsineum	strain=DSM 794	GCA_002006355.2	36839	36839	type	True	76.4424	107	908	95	below_threshold
Clostridium mobile	strain=MSJ-11	GCA_018918285.1	2841512	2841512	type	True	76.4373	124	908	95	below_threshold
Clostridium felsineum	strain=DSM 793	GCA_002006235.2	36839	36839	type	True	76.3971	117	908	95	below_threshold
Clostridium felsineum	strain=DSM 7320	GCA_002006215.2	36839	36839	type	True	76.3669	114	908	95	below_threshold
Sarcina ventriculi	strain=NCTC12966	GCA_900456775.1	1267	1267	type	True	76.2265	103	908	95	below_threshold
Clostridium arbusti	strain=SL206	GCA_000246895.2	1137848	1137848	type	True	76.1671	92	908	95	below_threshold
Clostridium akagii	strain=DSM 12554	GCA_000686725.1	91623	91623	type	True	76.0114	105	908	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:33,990] [INFO] DFAST Taxonomy check result was written to GCF_002995795.1_ASM299579v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:33,990] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:33,990] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:33,991] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0e2d79d-c185-41b7-98be-9f43f78bec21/dqc_reference/checkm_data
[2024-01-24 11:26:33,992] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:34,026] [INFO] Task started: CheckM
[2024-01-24 11:26:34,026] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002995795.1_ASM299579v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002995795.1_ASM299579v1_genomic.fna/checkm_input GCF_002995795.1_ASM299579v1_genomic.fna/checkm_result
[2024-01-24 11:26:55,903] [INFO] Task succeeded: CheckM
[2024-01-24 11:26:55,904] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:26:55,924] [INFO] ===== Completeness check finished =====
[2024-01-24 11:26:55,925] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:26:55,925] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002995795.1_ASM299579v1_genomic.fna/markers.fasta)
[2024-01-24 11:26:55,926] [INFO] Task started: Blastn
[2024-01-24 11:26:55,926] [INFO] Running command: blastn -query GCF_002995795.1_ASM299579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0e2d79d-c185-41b7-98be-9f43f78bec21/dqc_reference/reference_markers_gtdb.fasta -out GCF_002995795.1_ASM299579v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:56,731] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:56,735] [INFO] Selected 15 target genomes.
[2024-01-24 11:26:56,735] [INFO] Target genome list was writen to GCF_002995795.1_ASM299579v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:26:56,745] [INFO] Task started: fastANI
[2024-01-24 11:26:56,745] [INFO] Running command: fastANI --query /var/lib/cwl/stg411477a0-7bc2-4e9f-850a-a7a080acc0d1/GCF_002995795.1_ASM299579v1_genomic.fna.gz --refList GCF_002995795.1_ASM299579v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002995795.1_ASM299579v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:06,589] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:06,608] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:06,609] [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_002995795.1	s__Clostridium_H thermopalmarium	100.0	905	908	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	conclusive
GCA_009738435.1	s__Clostridium_H bovifaecis	81.4225	583	908	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_900176615.1	s__Clostridium_H massiliodielmoense	78.5728	261	908	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	78.4852	274	908	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_003614235.1	s__Clostridium_H haemolyticum	78.3561	277	908	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_000204565.1	s__Clostridium_H botulinum_B	78.3064	294	908	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_000014125.1	s__Clostridium_H novyi	78.2498	279	908	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_001263795.1	s__Clostridium_H homopropionicum	78.0142	272	908	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	-
GCF_000968375.1	s__Clostridium_AM scatologenes	77.0983	173	908	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	96.092	N/A	N/A	N/A	N/A	1	-
GCF_000633595.2	s__Clostridium_AM drakei	76.7878	175	908	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	96.092	100.00	100.00	1.00	1.00	2	-
GCF_000816675.1	s__Clostridium_J argentinense	76.6496	129	908	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	-
GCF_000612845.1	s__Clostridium_J ihumii	76.3517	119	908	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_002006345.1	s__Clostridium puniceum	76.1383	119	908	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_004794105.1	s__Clostridium sartagoforme_B	75.9732	102	908	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.58	98.58	0.90	0.90	2	-
GCA_002341865.1	s__Clostridium_J sp002341865	75.9586	126	908	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	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:06,610] [INFO] GTDB search result was written to GCF_002995795.1_ASM299579v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:06,611] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:06,615] [INFO] DFAST_QC result json was written to GCF_002995795.1_ASM299579v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:06,615] [INFO] DFAST_QC completed!
[2024-01-24 11:27:06,615] [INFO] Total running time: 0h0m55s