[2024-01-24 15:10:19,840] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:19,842] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:19,842] [INFO] DQC Reference Directory: /var/lib/cwl/stg185d9d62-4074-4796-8795-ade0fbfc948b/dqc_reference
[2024-01-24 15:10:22,724] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:22,725] [INFO] Task started: Prodigal
[2024-01-24 15:10:22,725] [INFO] Running command: gunzip -c /var/lib/cwl/stge6cd656e-f0e5-4725-b67f-ff24ac343ea8/GCF_006351925.1_ASM635192v1_genomic.fna.gz | prodigal -d GCF_006351925.1_ASM635192v1_genomic.fna/cds.fna -a GCF_006351925.1_ASM635192v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:30,324] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:30,325] [INFO] Task started: HMMsearch
[2024-01-24 15:10:30,325] [INFO] Running command: hmmsearch --tblout GCF_006351925.1_ASM635192v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg185d9d62-4074-4796-8795-ade0fbfc948b/dqc_reference/reference_markers.hmm GCF_006351925.1_ASM635192v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:30,630] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:30,631] [INFO] Found 6/6 markers.
[2024-01-24 15:10:30,677] [INFO] Query marker FASTA was written to GCF_006351925.1_ASM635192v1_genomic.fna/markers.fasta
[2024-01-24 15:10:30,678] [INFO] Task started: Blastn
[2024-01-24 15:10:30,678] [INFO] Running command: blastn -query GCF_006351925.1_ASM635192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg185d9d62-4074-4796-8795-ade0fbfc948b/dqc_reference/reference_markers.fasta -out GCF_006351925.1_ASM635192v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:31,262] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:31,267] [INFO] Selected 19 target genomes.
[2024-01-24 15:10:31,268] [INFO] Target genome list was writen to GCF_006351925.1_ASM635192v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:31,298] [INFO] Task started: fastANI
[2024-01-24 15:10:31,298] [INFO] Running command: fastANI --query /var/lib/cwl/stge6cd656e-f0e5-4725-b67f-ff24ac343ea8/GCF_006351925.1_ASM635192v1_genomic.fna.gz --refList GCF_006351925.1_ASM635192v1_genomic.fna/target_genomes.txt --output GCF_006351925.1_ASM635192v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:43,915] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:43,916] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg185d9d62-4074-4796-8795-ade0fbfc948b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:43,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg185d9d62-4074-4796-8795-ade0fbfc948b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:43,933] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:10:43,933] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:43,933] [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 thermarum	strain=SYSU GA15002	GCA_006351925.1	1716543	1716543	type	True	100.0	1268	1268	95	conclusive
Clostridium thermarum	strain=SYSU GA15002	GCA_010367605.1	1716543	1716543	type	True	99.9503	1183	1268	95	conclusive
Clostridium isatidis	strain=DSM 15098	GCA_002285495.1	182773	182773	type	True	80.4446	73	1268	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	78.9512	87	1268	95	below_threshold
Clostridium swellfunianum	strain=CICC 10730	GCA_023656515.1	1367462	1367462	type	True	78.764	93	1268	95	below_threshold
Haloimpatiens massiliensis	strain=Mt13	GCA_900184255.1	1658110	1658110	type	True	77.985	80	1268	95	below_threshold
Clostridium oryzae	strain=DSM 28571	GCA_002029235.1	1450648	1450648	type	True	77.4925	93	1268	95	below_threshold
Clostridium polyendosporum	strain=JCM 30710	GCA_018332455.1	69208	69208	type	True	77.1337	58	1268	95	below_threshold
Clostridium uliginosum	strain=DSM 12992	GCA_900112485.1	119641	119641	type	True	76.6973	55	1268	95	below_threshold
Clostridium simiarum	strain=MSJ-4	GCA_018919175.1	2841506	2841506	type	True	76.6367	70	1268	95	below_threshold
Clostridium fallax	strain=DSM 2631	GCA_900129365.1	1533	1533	type	True	76.4744	73	1268	95	below_threshold
Clostridium tepidum	strain=IEH 97212	GCA_002008345.1	1962263	1962263	type	True	76.3302	66	1268	95	below_threshold
Clostridium celatum	strain=DSM 1785	GCA_000320405.1	36834	36834	type	True	76.0703	51	1268	95	below_threshold
Clostridium thailandense	strain=PL3	GCA_019207025.1	2794346	2794346	type	True	75.8073	57	1268	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:43,935] [INFO] DFAST Taxonomy check result was written to GCF_006351925.1_ASM635192v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:43,935] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:43,935] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:43,936] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg185d9d62-4074-4796-8795-ade0fbfc948b/dqc_reference/checkm_data
[2024-01-24 15:10:43,937] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:43,980] [INFO] Task started: CheckM
[2024-01-24 15:10:43,980] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006351925.1_ASM635192v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006351925.1_ASM635192v1_genomic.fna/checkm_input GCF_006351925.1_ASM635192v1_genomic.fna/checkm_result
[2024-01-24 15:11:13,609] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:13,610] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:13,632] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:13,632] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:13,633] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006351925.1_ASM635192v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:13,633] [INFO] Task started: Blastn
[2024-01-24 15:11:13,633] [INFO] Running command: blastn -query GCF_006351925.1_ASM635192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg185d9d62-4074-4796-8795-ade0fbfc948b/dqc_reference/reference_markers_gtdb.fasta -out GCF_006351925.1_ASM635192v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:14,482] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:14,486] [INFO] Selected 30 target genomes.
[2024-01-24 15:11:14,486] [INFO] Target genome list was writen to GCF_006351925.1_ASM635192v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:14,525] [INFO] Task started: fastANI
[2024-01-24 15:11:14,525] [INFO] Running command: fastANI --query /var/lib/cwl/stge6cd656e-f0e5-4725-b67f-ff24ac343ea8/GCF_006351925.1_ASM635192v1_genomic.fna.gz --refList GCF_006351925.1_ASM635192v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006351925.1_ASM635192v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:31,219] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:31,242] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:31,242] [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_006351925.1	s__UBA3947 sp006351925	100.0	1267	1268	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__UBA3947	95.0	98.14	96.28	0.94	0.88	3	conclusive
GCF_002285495.1	s__Clostridium isatidis	80.3548	73	1268	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.19	99.19	0.81	0.81	2	-
GCF_003614235.1	s__Clostridium_H haemolyticum	79.3007	71	1268	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_017100085.1	s__Clostridium_H botulinum_A	79.279	61	1268	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	79.165	83	1268	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_900167505.1	s__F0540 sp900167505	79.0539	97	1268	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__F0540	95.0	98.87	98.87	0.90	0.90	2	-
GCA_000753435.1	s__Clostridium_L amazonitimonense	78.9281	72	1268	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_L	95.0	99.33	97.98	0.97	0.93	4	-
GCF_900095445.1	s__UBA3947 sp900095445	78.6329	205	1268	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__UBA3947	95.0	99.63	99.63	0.84	0.84	2	-
GCA_012523855.1	s__UBA3947 sp003541575	78.2205	167	1268	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__UBA3947	95.0	99.30	99.30	0.72	0.72	2	-
GCF_001889325.1	s__Clostridium_F botulinum_A	78.0522	77	1268	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	95.92	95.51	0.89	0.85	52	-
GCA_002385545.1	s__UBA3947 sp002385545	77.7636	170	1268	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__UBA3947	95.0	99.68	99.68	0.86	0.86	2	-
GCF_002029235.1	s__Clostridium_AE oryzae	77.5258	92	1268	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AE	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018332455.1	s__Clostridium_AR polyendosporum	77.1355	58	1268	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_900142075.1	s__Clostridium_AA amylolyticum	77.05	76	1268	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AA	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004353185.1	s__Clostridium cuniculi	76.7621	55	1268	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.75	97.60	0.86	0.82	5	-
GCF_900112485.1	s__Clostridium uliginosum	76.6973	55	1268	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_009928445.1	s__Clostridium_AR sp009928445	76.6462	81	1268	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_900129365.1	s__Clostridium_AH fallax	76.4744	73	1268	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AH	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002008345.1	s__Clostridium_F tepidum	76.3386	67	1268	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.70	99.54	0.93	0.92	5	-
GCF_000320405.1	s__Clostridium celatum	76.0703	51	1268	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.74	99.48	0.95	0.91	3	-
GCF_019207025.1	s__Clostridium_AM sp019207025	75.9068	57	1268	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	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:31,244] [INFO] GTDB search result was written to GCF_006351925.1_ASM635192v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:31,245] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:31,249] [INFO] DFAST_QC result json was written to GCF_006351925.1_ASM635192v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:31,250] [INFO] DFAST_QC completed!
[2024-01-24 15:11:31,250] [INFO] Total running time: 0h1m11s