[2024-01-24 11:12:25,602] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:25,604] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:25,604] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ce9c124-7bd9-4dc3-b29c-deebead1cd93/dqc_reference
[2024-01-24 11:12:27,085] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:27,094] [INFO] Task started: Prodigal
[2024-01-24 11:12:27,094] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f9468d9-3259-4a7e-a23f-675ea6d668ab/GCF_023656515.1_ASM2365651v1_genomic.fna.gz | prodigal -d GCF_023656515.1_ASM2365651v1_genomic.fna/cds.fna -a GCF_023656515.1_ASM2365651v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:35,874] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:35,875] [INFO] Task started: HMMsearch
[2024-01-24 11:12:35,875] [INFO] Running command: hmmsearch --tblout GCF_023656515.1_ASM2365651v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ce9c124-7bd9-4dc3-b29c-deebead1cd93/dqc_reference/reference_markers.hmm GCF_023656515.1_ASM2365651v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:36,250] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:36,252] [INFO] Found 6/6 markers.
[2024-01-24 11:12:36,301] [INFO] Query marker FASTA was written to GCF_023656515.1_ASM2365651v1_genomic.fna/markers.fasta
[2024-01-24 11:12:36,302] [INFO] Task started: Blastn
[2024-01-24 11:12:36,302] [INFO] Running command: blastn -query GCF_023656515.1_ASM2365651v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ce9c124-7bd9-4dc3-b29c-deebead1cd93/dqc_reference/reference_markers.fasta -out GCF_023656515.1_ASM2365651v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:36,964] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:36,967] [INFO] Selected 22 target genomes.
[2024-01-24 11:12:36,967] [INFO] Target genome list was writen to GCF_023656515.1_ASM2365651v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:36,989] [INFO] Task started: fastANI
[2024-01-24 11:12:36,989] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f9468d9-3259-4a7e-a23f-675ea6d668ab/GCF_023656515.1_ASM2365651v1_genomic.fna.gz --refList GCF_023656515.1_ASM2365651v1_genomic.fna/target_genomes.txt --output GCF_023656515.1_ASM2365651v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:52,024] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:52,025] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ce9c124-7bd9-4dc3-b29c-deebead1cd93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:52,025] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ce9c124-7bd9-4dc3-b29c-deebead1cd93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:52,041] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:12:52,041] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:12:52,041] [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 swellfunianum	strain=CICC 10730	GCA_023656515.1	1367462	1367462	type	True	100.0	1583	1584	95	conclusive
Clostridium paraputrificum	strain=NCTC11833	GCA_900447045.1	29363	29363	type	True	77.3622	94	1584	95	below_threshold
Clostridium putrefaciens	strain=NCTC9836	GCA_900461105.1	99675	99675	type	True	77.3552	82	1584	95	below_threshold
Clostridium prolinivorans	strain=PYR-10	GCA_004011155.1	2769420	2769420	type	True	77.2605	230	1584	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	76.7237	119	1584	95	below_threshold
Clostridium hydrogenum	strain=CUEA01	GCA_021432385.1	2855764	2855764	type	True	76.686	124	1584	95	below_threshold
Clostridium thailandense	strain=PL3	GCA_019207025.1	2794346	2794346	type	True	76.5771	138	1584	95	below_threshold
Clostridium polynesiense	strain=MS1	GCA_000820705.1	1325933	1325933	type	True	76.5446	91	1584	95	below_threshold
Clostridium lundense	strain=DSM 17049	GCA_000619945.1	319475	319475	type	True	76.4408	129	1584	95	below_threshold
Clostridium tetanomorphum	strain=DSM 4474	GCA_017873215.1	1553	1553	type	True	76.3266	112	1584	95	below_threshold
Clostridium uliginosum	strain=DSM 12992	GCA_900112485.1	119641	119641	type	True	76.2418	79	1584	95	below_threshold
Clostridium niameyense	strain=MT5	GCA_001243045.1	1622073	1622073	type	True	76.2199	81	1584	95	below_threshold
Clostridium tagluense	strain=A121	GCA_003865095.1	360422	360422	type	True	76.2153	110	1584	95	below_threshold
Clostridium liquoris	strain=DSM 100320	GCA_002995785.1	1289519	1289519	type	True	76.1558	99	1584	95	below_threshold
Clostridium fallax	strain=DSM 2631	GCA_900129365.1	1533	1533	type	True	75.9717	110	1584	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	75.8401	93	1584	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:12:52,043] [INFO] DFAST Taxonomy check result was written to GCF_023656515.1_ASM2365651v1_genomic.fna/tc_result.tsv
[2024-01-24 11:12:52,043] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:52,044] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:52,044] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ce9c124-7bd9-4dc3-b29c-deebead1cd93/dqc_reference/checkm_data
[2024-01-24 11:12:52,045] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:52,090] [INFO] Task started: CheckM
[2024-01-24 11:12:52,091] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023656515.1_ASM2365651v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023656515.1_ASM2365651v1_genomic.fna/checkm_input GCF_023656515.1_ASM2365651v1_genomic.fna/checkm_result
[2024-01-24 11:13:23,948] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:23,950] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:23,975] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:23,975] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:23,976] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023656515.1_ASM2365651v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:23,976] [INFO] Task started: Blastn
[2024-01-24 11:13:23,976] [INFO] Running command: blastn -query GCF_023656515.1_ASM2365651v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ce9c124-7bd9-4dc3-b29c-deebead1cd93/dqc_reference/reference_markers_gtdb.fasta -out GCF_023656515.1_ASM2365651v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:24,840] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:24,845] [INFO] Selected 28 target genomes.
[2024-01-24 11:13:24,846] [INFO] Target genome list was writen to GCF_023656515.1_ASM2365651v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:24,868] [INFO] Task started: fastANI
[2024-01-24 11:13:24,868] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f9468d9-3259-4a7e-a23f-675ea6d668ab/GCF_023656515.1_ASM2365651v1_genomic.fna.gz --refList GCF_023656515.1_ASM2365651v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023656515.1_ASM2365651v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:41,494] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:41,521] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:13:41,521] [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_016765585.1	s__F0540 sp016765585	78.9619	449	1584	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__F0540	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000466585.1	s__F0540 sp000466585	78.6483	384	1584	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__F0540	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184255.1	s__Haloimpatiens massiliensis	77.7053	108	1584	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Haloimpatiens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004103695.1	s__JN-9 sp004103695	77.6939	94	1584	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__JN-9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017100085.1	s__Clostridium_H botulinum_A	77.5039	79	1584	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_001038625.1	s__Clostridium_AM carboxidivorans	77.4267	151	1584	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	99.97	99.96	1.00	0.99	3	-
GCF_900461105.1	s__Clostridium_L putrefaciens	77.35	82	1584	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019207025.1	s__Clostridium_AM sp019207025	76.5521	137	1584	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011065905.1	s__Clostridium_AD estertheticum_B	76.5498	84	1584	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	97.19	97.19	0.83	0.83	2	-
GCF_000619945.1	s__Clostridium_AO lundense	76.4887	128	1584	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AO	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001243045.1	s__Clostridium_F niameyense	76.4248	82	1584	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.56	99.11	0.96	0.92	3	-
GCF_017873215.1	s__Clostridium_AO tetanomorphum	76.3314	113	1584	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AO	95.0	99.85	99.71	0.98	0.97	5	-
GCF_000686705.1	s__Clostridium_Z hydrogeniformans	76.2957	124	1584	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009928485.1	s__Clostridium sp009928485	76.279	118	1584	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_001405015.1	s__Clostridium disporicum	76.2565	80	1584	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.24	98.87	0.93	0.88	4	-
GCF_003865095.1	s__Clostridium_AD tagluense	76.2117	109	1584	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	96.49	95.92	0.80	0.78	4	-
GCF_002995785.1	s__Clostridium_AO liquoris	76.1741	98	1584	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AO	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014050525.1	s__Clostridium_B sp014050525	76.0949	70	1584	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543325.1	s__Clostridium sp900543325	75.7376	76	1584	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_015058525.1	s__Clostridium butyricum_A	75.6504	72	1584	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_017874415.1	s__Clostridium_B algifaecis	75.6436	72	1584	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:41,523] [INFO] GTDB search result was written to GCF_023656515.1_ASM2365651v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:41,524] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:41,532] [INFO] DFAST_QC result json was written to GCF_023656515.1_ASM2365651v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:41,532] [INFO] DFAST_QC completed!
[2024-01-24 11:13:41,532] [INFO] Total running time: 0h1m16s