[2024-01-24 15:02:24,182] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:24,184] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:24,184] [INFO] DQC Reference Directory: /var/lib/cwl/stg41ce2875-7f56-4f0d-997b-f6c7d187b130/dqc_reference
[2024-01-24 15:02:26,424] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:26,425] [INFO] Task started: Prodigal
[2024-01-24 15:02:26,426] [INFO] Running command: gunzip -c /var/lib/cwl/stgec99b3a5-0709-43a9-acef-e8d7aeac5707/GCF_010367605.1_ASM1036760v1_genomic.fna.gz | prodigal -d GCF_010367605.1_ASM1036760v1_genomic.fna/cds.fna -a GCF_010367605.1_ASM1036760v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:33,661] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:33,661] [INFO] Task started: HMMsearch
[2024-01-24 15:02:33,661] [INFO] Running command: hmmsearch --tblout GCF_010367605.1_ASM1036760v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41ce2875-7f56-4f0d-997b-f6c7d187b130/dqc_reference/reference_markers.hmm GCF_010367605.1_ASM1036760v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:33,972] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:33,973] [INFO] Found 6/6 markers.
[2024-01-24 15:02:34,009] [INFO] Query marker FASTA was written to GCF_010367605.1_ASM1036760v1_genomic.fna/markers.fasta
[2024-01-24 15:02:34,010] [INFO] Task started: Blastn
[2024-01-24 15:02:34,010] [INFO] Running command: blastn -query GCF_010367605.1_ASM1036760v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41ce2875-7f56-4f0d-997b-f6c7d187b130/dqc_reference/reference_markers.fasta -out GCF_010367605.1_ASM1036760v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:34,637] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:34,641] [INFO] Selected 19 target genomes.
[2024-01-24 15:02:34,641] [INFO] Target genome list was writen to GCF_010367605.1_ASM1036760v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:34,664] [INFO] Task started: fastANI
[2024-01-24 15:02:34,665] [INFO] Running command: fastANI --query /var/lib/cwl/stgec99b3a5-0709-43a9-acef-e8d7aeac5707/GCF_010367605.1_ASM1036760v1_genomic.fna.gz --refList GCF_010367605.1_ASM1036760v1_genomic.fna/target_genomes.txt --output GCF_010367605.1_ASM1036760v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:50,020] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:50,021] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41ce2875-7f56-4f0d-997b-f6c7d187b130/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:50,022] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41ce2875-7f56-4f0d-997b-f6c7d187b130/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:50,034] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:02:50,034] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:50,034] [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_010367605.1	1716543	1716543	type	True	100.0	1183	1189	95	conclusive
Clostridium thermarum	strain=SYSU GA15002	GCA_006351925.1	1716543	1716543	type	True	99.9954	1187	1189	95	conclusive
Clostridium isatidis	strain=DSM 15098	GCA_002285495.1	182773	182773	type	True	77.8081	55	1189	95	below_threshold
Clostridium oryzae	strain=DSM 28571	GCA_002029235.1	1450648	1450648	type	True	77.2476	93	1189	95	below_threshold
Clostridium polyendosporum	strain=JCM 30710	GCA_018332455.1	69208	69208	type	True	76.7194	61	1189	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	76.6463	61	1189	95	below_threshold
Clostridium fallax	strain=DSM 2631	GCA_900129365.1	1533	1533	type	True	76.569	58	1189	95	below_threshold
Clostridium swellfunianum	strain=CICC 10730	GCA_023656515.1	1367462	1367462	type	True	76.5668	89	1189	95	below_threshold
Clostridium simiarum	strain=MSJ-4	GCA_018919175.1	2841506	2841506	type	True	76.5431	70	1189	95	below_threshold
Clostridium celatum	strain=DSM 1785	GCA_000320405.1	36834	36834	type	True	76.239	51	1189	95	below_threshold
Clostridium uliginosum	strain=DSM 12992	GCA_900112485.1	119641	119641	type	True	76.2092	63	1189	95	below_threshold
Clostridium tepidum	strain=IEH 97212	GCA_002008345.1	1962263	1962263	type	True	76.1836	66	1189	95	below_threshold
Haloimpatiens massiliensis	strain=Mt13	GCA_900184255.1	1658110	1658110	type	True	76.1733	69	1189	95	below_threshold
Clostridium thailandense	strain=PL3	GCA_019207025.1	2794346	2794346	type	True	75.7841	63	1189	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:50,037] [INFO] DFAST Taxonomy check result was written to GCF_010367605.1_ASM1036760v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:50,038] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:50,038] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:50,039] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41ce2875-7f56-4f0d-997b-f6c7d187b130/dqc_reference/checkm_data
[2024-01-24 15:02:50,040] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:50,088] [INFO] Task started: CheckM
[2024-01-24 15:02:50,089] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010367605.1_ASM1036760v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010367605.1_ASM1036760v1_genomic.fna/checkm_input GCF_010367605.1_ASM1036760v1_genomic.fna/checkm_result
[2024-01-24 15:03:19,173] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:19,174] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:19,210] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:19,210] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:19,210] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010367605.1_ASM1036760v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:19,211] [INFO] Task started: Blastn
[2024-01-24 15:03:19,211] [INFO] Running command: blastn -query GCF_010367605.1_ASM1036760v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41ce2875-7f56-4f0d-997b-f6c7d187b130/dqc_reference/reference_markers_gtdb.fasta -out GCF_010367605.1_ASM1036760v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:20,066] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:20,070] [INFO] Selected 30 target genomes.
[2024-01-24 15:03:20,070] [INFO] Target genome list was writen to GCF_010367605.1_ASM1036760v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:20,097] [INFO] Task started: fastANI
[2024-01-24 15:03:20,097] [INFO] Running command: fastANI --query /var/lib/cwl/stgec99b3a5-0709-43a9-acef-e8d7aeac5707/GCF_010367605.1_ASM1036760v1_genomic.fna.gz --refList GCF_010367605.1_ASM1036760v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010367605.1_ASM1036760v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:39,102] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:39,118] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:39,119] [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	99.9954	1187	1189	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_900167505.1	s__F0540 sp900167505	78.5687	102	1189	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__F0540	95.0	98.87	98.87	0.90	0.90	2	-
GCF_900095445.1	s__UBA3947 sp900095445	78.5193	194	1189	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	77.8875	174	1189	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_002285495.1	s__Clostridium isatidis	77.8081	55	1189	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.19	99.19	0.81	0.81	2	-
GCA_002385545.1	s__UBA3947 sp002385545	77.6015	178	1189	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	77.2767	92	1189	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	-
GCA_000753435.1	s__Clostridium_L amazonitimonense	76.9616	70	1189	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_900142075.1	s__Clostridium_AA amylolyticum	76.8665	69	1189	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_018332455.1	s__Clostridium_AR polyendosporum	76.7194	61	1189	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	76.5326	57	1189	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_004353185.1	s__Clostridium cuniculi	76.4916	58	1189	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_001038625.1	s__Clostridium_AM carboxidivorans	76.4682	77	1189	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_009928445.1	s__Clostridium_AR sp009928445	76.4109	81	1189	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_001889325.1	s__Clostridium_F botulinum_A	76.3059	72	1189	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	-
GCF_000320405.1	s__Clostridium celatum	76.239	51	1189	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_900112485.1	s__Clostridium uliginosum	76.2092	63	1189	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_002008345.1	s__Clostridium_F tepidum	76.1856	66	1189	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_017100085.1	s__Clostridium_H botulinum_A	76.0636	56	1189	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_019207025.1	s__Clostridium_AM sp019207025	75.8054	62	1189	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 15:03:39,122] [INFO] GTDB search result was written to GCF_010367605.1_ASM1036760v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:39,122] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:39,127] [INFO] DFAST_QC result json was written to GCF_010367605.1_ASM1036760v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:39,127] [INFO] DFAST_QC completed!
[2024-01-24 15:03:39,127] [INFO] Total running time: 0h1m15s