[2024-01-24 13:13:12,353] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:12,355] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:12,355] [INFO] DQC Reference Directory: /var/lib/cwl/stg758ecccb-020e-4481-bcc8-54f95d09212d/dqc_reference
[2024-01-24 13:13:13,820] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:13,824] [INFO] Task started: Prodigal
[2024-01-24 13:13:13,824] [INFO] Running command: gunzip -c /var/lib/cwl/stg347d2eb7-0559-4519-8a6a-c50e74c77c43/GCF_001593985.1_ASM159398v1_genomic.fna.gz | prodigal -d GCF_001593985.1_ASM159398v1_genomic.fna/cds.fna -a GCF_001593985.1_ASM159398v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:18,294] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:18,294] [INFO] Task started: HMMsearch
[2024-01-24 13:13:18,295] [INFO] Running command: hmmsearch --tblout GCF_001593985.1_ASM159398v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg758ecccb-020e-4481-bcc8-54f95d09212d/dqc_reference/reference_markers.hmm GCF_001593985.1_ASM159398v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:18,589] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:18,591] [INFO] Found 6/6 markers.
[2024-01-24 13:13:18,618] [INFO] Query marker FASTA was written to GCF_001593985.1_ASM159398v1_genomic.fna/markers.fasta
[2024-01-24 13:13:18,619] [INFO] Task started: Blastn
[2024-01-24 13:13:18,619] [INFO] Running command: blastn -query GCF_001593985.1_ASM159398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg758ecccb-020e-4481-bcc8-54f95d09212d/dqc_reference/reference_markers.fasta -out GCF_001593985.1_ASM159398v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:19,248] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:19,253] [INFO] Selected 23 target genomes.
[2024-01-24 13:13:19,253] [INFO] Target genome list was writen to GCF_001593985.1_ASM159398v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:19,812] [INFO] Task started: fastANI
[2024-01-24 13:13:19,812] [INFO] Running command: fastANI --query /var/lib/cwl/stg347d2eb7-0559-4519-8a6a-c50e74c77c43/GCF_001593985.1_ASM159398v1_genomic.fna.gz --refList GCF_001593985.1_ASM159398v1_genomic.fna/target_genomes.txt --output GCF_001593985.1_ASM159398v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:34,871] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:34,872] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg758ecccb-020e-4481-bcc8-54f95d09212d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:34,872] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg758ecccb-020e-4481-bcc8-54f95d09212d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:34,888] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:13:34,888] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:34,888] [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_003097175.1	29373	29373	suspected-type	True	99.4399	794	844	95	conclusive
Clostridium thermopalmarium	strain=DSM 5974	GCA_002995795.1	29373	29373	suspected-type	True	99.3943	796	844	95	conclusive
Clostridium massiliodielmoense	strain=MT26	GCA_900176615.1	1776385	1776385	type	True	78.5779	265	844	95	below_threshold
Clostridium collagenovorans	strain=DSM 3089	GCA_900130005.1	29357	29357	type	True	77.9783	91	844	95	below_threshold
Clostridium drakei	strain=SL1	GCA_003096175.1	332101	332101	type	True	77.2403	179	844	95	below_threshold
Clostridium drakei	strain=SL1	GCA_000633595.2	332101	332101	type	True	76.8455	165	844	95	below_threshold
Clostridium rectalis	strain=Marseille-P4200	GCA_900626095.1	2040295	2040295	type	True	76.8262	124	844	95	below_threshold
Clostridium faecium	strain=N37	GCA_014836835.1	2762223	2762223	type	True	76.7284	136	844	95	below_threshold
Hathewaya histolytica	strain=NCTC503	GCA_901482605.1	1498	1498	type	True	76.7113	90	844	95	below_threshold
Clostridium thailandense	strain=PL3	GCA_019207025.1	2794346	2794346	type	True	76.6044	143	844	95	below_threshold
Clostridium felsineum	strain=DSM 794	GCA_002006355.2	36839	36839	type	True	76.5792	126	844	95	below_threshold
Clostridium felsineum	strain=DSM 793	GCA_002006235.2	36839	36839	type	True	76.5343	121	844	95	below_threshold
Clostridium felsineum	strain=DSM 7320	GCA_002006215.2	36839	36839	type	True	76.5119	124	844	95	below_threshold
Clostridium fungisolvens	strain=TW1	GCA_014193895.1	1604897	1604897	type	True	76.5049	104	844	95	below_threshold
Clostridium cochlearium	strain=NCTC13027	GCA_900187165.1	1494	1494	type	True	76.4444	134	844	95	below_threshold
Sarcina ventriculi	strain=NCTC12966	GCA_900456775.1	1267	1267	type	True	76.4099	107	844	95	below_threshold
Clostridium mobile	strain=MSJ-11	GCA_018918285.1	2841512	2841512	type	True	76.3451	122	844	95	below_threshold
Clostridium arbusti	strain=SL206	GCA_000246895.2	1137848	1137848	type	True	76.1179	109	844	95	below_threshold
Clostridium oryzae	strain=DSM 28571	GCA_002029235.1	1450648	1450648	type	True	75.9992	68	844	95	below_threshold
Clostridium akagii	strain=DSM 12554	GCA_000686725.1	91623	91623	type	True	75.9545	97	844	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:34,890] [INFO] DFAST Taxonomy check result was written to GCF_001593985.1_ASM159398v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:34,890] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:34,891] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:34,891] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg758ecccb-020e-4481-bcc8-54f95d09212d/dqc_reference/checkm_data
[2024-01-24 13:13:34,892] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:34,923] [INFO] Task started: CheckM
[2024-01-24 13:13:34,923] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001593985.1_ASM159398v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001593985.1_ASM159398v1_genomic.fna/checkm_input GCF_001593985.1_ASM159398v1_genomic.fna/checkm_result
[2024-01-24 13:13:56,067] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:56,068] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:56,085] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:56,085] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:56,086] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001593985.1_ASM159398v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:56,086] [INFO] Task started: Blastn
[2024-01-24 13:13:56,087] [INFO] Running command: blastn -query GCF_001593985.1_ASM159398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg758ecccb-020e-4481-bcc8-54f95d09212d/dqc_reference/reference_markers_gtdb.fasta -out GCF_001593985.1_ASM159398v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:56,853] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:56,857] [INFO] Selected 14 target genomes.
[2024-01-24 13:13:56,857] [INFO] Target genome list was writen to GCF_001593985.1_ASM159398v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:56,866] [INFO] Task started: fastANI
[2024-01-24 13:13:56,866] [INFO] Running command: fastANI --query /var/lib/cwl/stg347d2eb7-0559-4519-8a6a-c50e74c77c43/GCF_001593985.1_ASM159398v1_genomic.fna.gz --refList GCF_001593985.1_ASM159398v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001593985.1_ASM159398v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:07,376] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:07,392] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:07,392] [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	99.3943	796	844	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	81.4931	582	844	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_000014125.1	s__Clostridium_H novyi	78.7994	281	844	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_003614235.1	s__Clostridium_H haemolyticum	78.729	274	844	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	78.7187	285	844	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_900176615.1	s__Clostridium_H massiliodielmoense	78.5779	265	844	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	78.5346	286	844	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_000968375.1	s__Clostridium_AM scatologenes	77.169	181	844	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	76.8603	164	844	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_004794105.1	s__Clostridium sartagoforme_B	76.4211	96	844	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.58	98.58	0.90	0.90	2	-
GCF_000816675.1	s__Clostridium_J argentinense	76.4032	131	844	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	76.1624	133	844	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	-
GCA_002341865.1	s__Clostridium_J sp002341865	76.0277	123	844	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_002006345.1	s__Clostridium puniceum	76.0144	123	844	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 13:14:07,394] [INFO] GTDB search result was written to GCF_001593985.1_ASM159398v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:07,394] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:07,398] [INFO] DFAST_QC result json was written to GCF_001593985.1_ASM159398v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:07,398] [INFO] DFAST_QC completed!
[2024-01-24 13:14:07,398] [INFO] Total running time: 0h0m55s