[2024-01-24 12:45:20,098] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:20,100] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:20,100] [INFO] DQC Reference Directory: /var/lib/cwl/stg6b5fd485-f20f-4b01-ac17-f9044fb374bc/dqc_reference
[2024-01-24 12:45:21,419] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:21,420] [INFO] Task started: Prodigal
[2024-01-24 12:45:21,421] [INFO] Running command: gunzip -c /var/lib/cwl/stg64692533-4c97-4973-a598-611c4bac7de5/GCF_016907995.1_ASM1690799v1_genomic.fna.gz | prodigal -d GCF_016907995.1_ASM1690799v1_genomic.fna/cds.fna -a GCF_016907995.1_ASM1690799v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:27,051] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:27,052] [INFO] Task started: HMMsearch
[2024-01-24 12:45:27,052] [INFO] Running command: hmmsearch --tblout GCF_016907995.1_ASM1690799v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6b5fd485-f20f-4b01-ac17-f9044fb374bc/dqc_reference/reference_markers.hmm GCF_016907995.1_ASM1690799v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:27,398] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:27,400] [INFO] Found 6/6 markers.
[2024-01-24 12:45:27,438] [INFO] Query marker FASTA was written to GCF_016907995.1_ASM1690799v1_genomic.fna/markers.fasta
[2024-01-24 12:45:27,438] [INFO] Task started: Blastn
[2024-01-24 12:45:27,438] [INFO] Running command: blastn -query GCF_016907995.1_ASM1690799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b5fd485-f20f-4b01-ac17-f9044fb374bc/dqc_reference/reference_markers.fasta -out GCF_016907995.1_ASM1690799v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:28,037] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:28,041] [INFO] Selected 20 target genomes.
[2024-01-24 12:45:28,042] [INFO] Target genome list was writen to GCF_016907995.1_ASM1690799v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:28,056] [INFO] Task started: fastANI
[2024-01-24 12:45:28,056] [INFO] Running command: fastANI --query /var/lib/cwl/stg64692533-4c97-4973-a598-611c4bac7de5/GCF_016907995.1_ASM1690799v1_genomic.fna.gz --refList GCF_016907995.1_ASM1690799v1_genomic.fna/target_genomes.txt --output GCF_016907995.1_ASM1690799v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:42,366] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:42,367] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6b5fd485-f20f-4b01-ac17-f9044fb374bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:42,368] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6b5fd485-f20f-4b01-ac17-f9044fb374bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:42,388] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:42,388] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:42,388] [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 sardiniense	strain=DSM 2632	GCA_016907995.1	29369	29369	type	True	100.0	1285	1286	95	conclusive
Clostridium moniliforme	strain=DSM 3984	GCA_017873235.1	39489	39489	type	True	82.549	622	1286	95	below_threshold
Clostridium thermobutyricum	strain=DSM 4928	GCA_002050515.1	29372	29372	type	True	78.7382	423	1286	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	78.6858	411	1286	95	below_threshold
Clostridium paraputrificum	strain=NCTC11833	GCA_900447045.1	29363	29363	type	True	77.8948	280	1286	95	below_threshold
Clostridium septicum	strain=FDAARGOS_1551	GCA_020736665.1	1504	1504	type	True	77.8524	318	1286	95	below_threshold
Clostridium cagae	strain=Marseille-P4344	GCA_900290265.1	2080751	2080751	type	True	77.8228	282	1286	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	77.6385	218	1286	95	below_threshold
Clostridium saccharobutylicum	strain=DSM 13864	GCA_001657435.1	169679	169679	type	True	77.4602	236	1286	95	below_threshold
Clostridium uliginosum	strain=DSM 12992	GCA_900112485.1	119641	119641	type	True	77.4357	287	1286	95	below_threshold
Clostridium saccharobutylicum	strain=DSM 13864	GCA_000473995.1	169679	169679	type	True	77.3815	265	1286	95	below_threshold
Clostridium chromiireducens	strain=DSM 23318	GCA_002029255.1	225345	225345	type	True	77.324	201	1286	95	below_threshold
Clostridium celatum	strain=DSM 1785	GCA_000320405.1	36834	36834	type	True	77.3207	265	1286	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	77.2994	256	1286	95	below_threshold
Clostridium butyricum	strain=DSM 10702	GCA_000409755.1	1492	1492	type	True	77.251	270	1286	95	below_threshold
Clostridium massiliamazoniense	strain=ND2	GCA_001403635.1	1347366	1347366	type	True	77.0073	259	1286	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=ATCC 27021	GCA_000334435.1	36745	36745	type	True	76.955	246	1286	95	below_threshold
Clostridium gelidum	strain=C5S11	GCA_019977655.1	704125	704125	type	True	76.9202	278	1286	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=N1-4(HMT)	GCA_000340885.1	36745	36745	type	True	76.9077	253	1286	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:42,391] [INFO] DFAST Taxonomy check result was written to GCF_016907995.1_ASM1690799v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:42,391] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:42,391] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:42,391] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6b5fd485-f20f-4b01-ac17-f9044fb374bc/dqc_reference/checkm_data
[2024-01-24 12:45:42,392] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:42,431] [INFO] Task started: CheckM
[2024-01-24 12:45:42,432] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016907995.1_ASM1690799v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016907995.1_ASM1690799v1_genomic.fna/checkm_input GCF_016907995.1_ASM1690799v1_genomic.fna/checkm_result
[2024-01-24 12:46:05,806] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:05,809] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:05,861] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:05,862] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:05,862] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016907995.1_ASM1690799v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:05,863] [INFO] Task started: Blastn
[2024-01-24 12:46:05,863] [INFO] Running command: blastn -query GCF_016907995.1_ASM1690799v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6b5fd485-f20f-4b01-ac17-f9044fb374bc/dqc_reference/reference_markers_gtdb.fasta -out GCF_016907995.1_ASM1690799v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:06,693] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:06,696] [INFO] Selected 10 target genomes.
[2024-01-24 12:46:06,697] [INFO] Target genome list was writen to GCF_016907995.1_ASM1690799v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:06,705] [INFO] Task started: fastANI
[2024-01-24 12:46:06,705] [INFO] Running command: fastANI --query /var/lib/cwl/stg64692533-4c97-4973-a598-611c4bac7de5/GCF_016907995.1_ASM1690799v1_genomic.fna.gz --refList GCF_016907995.1_ASM1690799v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016907995.1_ASM1690799v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:14,002] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:14,020] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:14,020] [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_016907995.1	s__Clostridium sardiniense	100.0	1285	1286	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_017873235.1	s__Clostridium moniliforme	82.5621	621	1286	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	82.1218	668	1286	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	96.53	95.37	0.92	0.89	15	-
GCF_000498355.1	s__Clostridium sp000498355	81.6507	626	1286	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_002050515.1	s__Clostridium thermobutyricum	78.7176	427	1286	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.10	97.10	0.91	0.89	3	-
GCF_015234215.1	s__Clostridium sp015234215	78.6666	413	1286	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_900290265.1	s__Clostridium cagae	77.8124	282	1286	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.09	97.56	0.90	0.85	15	-
GCA_015058405.1	s__Clostridium sp015058405	77.683	217	1286	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_015667795.1	s__Clostridium sp015667795	77.5707	313	1286	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	77.0098	198	1286	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 12:46:14,023] [INFO] GTDB search result was written to GCF_016907995.1_ASM1690799v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:14,024] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:14,030] [INFO] DFAST_QC result json was written to GCF_016907995.1_ASM1690799v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:14,030] [INFO] DFAST_QC completed!
[2024-01-24 12:46:14,031] [INFO] Total running time: 0h0m54s