[2024-01-24 13:36:45,027] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,029] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,029] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1dffe1a-a341-4d09-ba40-4cb8f7bfb3db/dqc_reference
[2024-01-24 13:36:46,324] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:46,326] [INFO] Task started: Prodigal
[2024-01-24 13:36:46,326] [INFO] Running command: gunzip -c /var/lib/cwl/stgff5d962b-ab36-41ee-861b-51951cfbf79b/GCF_000686705.1_ASM68670v1_genomic.fna.gz | prodigal -d GCF_000686705.1_ASM68670v1_genomic.fna/cds.fna -a GCF_000686705.1_ASM68670v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:52,142] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:52,143] [INFO] Task started: HMMsearch
[2024-01-24 13:36:52,143] [INFO] Running command: hmmsearch --tblout GCF_000686705.1_ASM68670v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1dffe1a-a341-4d09-ba40-4cb8f7bfb3db/dqc_reference/reference_markers.hmm GCF_000686705.1_ASM68670v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:52,441] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:52,443] [INFO] Found 6/6 markers.
[2024-01-24 13:36:52,481] [INFO] Query marker FASTA was written to GCF_000686705.1_ASM68670v1_genomic.fna/markers.fasta
[2024-01-24 13:36:52,482] [INFO] Task started: Blastn
[2024-01-24 13:36:52,482] [INFO] Running command: blastn -query GCF_000686705.1_ASM68670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1dffe1a-a341-4d09-ba40-4cb8f7bfb3db/dqc_reference/reference_markers.fasta -out GCF_000686705.1_ASM68670v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:53,061] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:53,065] [INFO] Selected 22 target genomes.
[2024-01-24 13:36:53,066] [INFO] Target genome list was writen to GCF_000686705.1_ASM68670v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:53,105] [INFO] Task started: fastANI
[2024-01-24 13:36:53,105] [INFO] Running command: fastANI --query /var/lib/cwl/stgff5d962b-ab36-41ee-861b-51951cfbf79b/GCF_000686705.1_ASM68670v1_genomic.fna.gz --refList GCF_000686705.1_ASM68670v1_genomic.fna/target_genomes.txt --output GCF_000686705.1_ASM68670v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:07,708] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:07,708] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1dffe1a-a341-4d09-ba40-4cb8f7bfb3db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:07,708] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1dffe1a-a341-4d09-ba40-4cb8f7bfb3db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:07,724] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:07,725] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:07,725] [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 hydrogeniformans	strain=DSM 21757	GCA_000686705.1	349933	349933	type	True	100.0	1352	1353	95	conclusive
Clostridium frigidicarnis	strain=DSM 12271	GCA_900111985.1	84698	84698	type	True	78.3702	406	1353	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	77.0991	221	1353	95	below_threshold
Clostridium fallax	strain=DSM 2631	GCA_900129365.1	1533	1533	type	True	77.0614	207	1353	95	below_threshold
Clostridium mobile	strain=MSJ-11	GCA_018918285.1	2841512	2841512	type	True	77.0003	151	1353	95	below_threshold
Clostridium cavendishii	strain=DSM 21758	GCA_900141845.1	349931	349931	type	True	76.717	221	1353	95	below_threshold
Clostridium polyendosporum	strain=JCM 30710	GCA_018332455.1	69208	69208	type	True	76.6874	133	1353	95	below_threshold
Clostridium uliginosum	strain=DSM 12992	GCA_900112485.1	119641	119641	type	True	76.6625	159	1353	95	below_threshold
Clostridium faecium	strain=N37	GCA_014836835.1	2762223	2762223	type	True	76.4814	197	1353	95	below_threshold
Clostridium niameyense	strain=MT5	GCA_001243045.1	1622073	1622073	type	True	76.3596	153	1353	95	below_threshold
Clostridium putrefaciens	strain=NCTC9836	GCA_900461105.1	99675	99675	type	True	76.3051	161	1353	95	below_threshold
Clostridium perfringens	strain=ATCC 13124	GCA_000013285.1	1502	1502	type	True	76.2797	175	1353	95	below_threshold
Clostridium manihotivorum	strain=CT4	GCA_004015185.1	2320868	2320868	type	True	76.2665	163	1353	95	below_threshold
Clostridium scatologenes	strain=ATCC 25775	GCA_000968375.1	1548	1548	type	True	76.258	198	1353	95	below_threshold
Clostridium senegalense	strain=type strain: JC122	GCA_000285575.1	1465809	1465809	type	True	76.1677	194	1353	95	below_threshold
Clostridium drakei	strain=SL1	GCA_003096175.1	332101	332101	type	True	76.1115	197	1353	95	below_threshold
Clostridium drakei	strain=SL1	GCA_000633595.2	332101	332101	type	True	76.0342	191	1353	95	below_threshold
Clostridium luticellarii	strain=DSM 29923	GCA_002995845.1	1691940	1691940	type	True	75.7692	60	1353	95	below_threshold
Clostridium tyrobutyricum	strain=DSM 2637	GCA_000429805.1	1519	1519	type	True	75.7352	77	1353	95	below_threshold
Caminicella sporogenes	strain=DSM 14501	GCA_900142285.1	166485	166485	type	True	75.0081	64	1353	95	below_threshold
Caminicella sporogenes	strain=AM 1114	GCA_003609595.1	166485	166485	type	True	74.9602	64	1353	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:07,726] [INFO] DFAST Taxonomy check result was written to GCF_000686705.1_ASM68670v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:07,727] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:07,727] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:07,727] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1dffe1a-a341-4d09-ba40-4cb8f7bfb3db/dqc_reference/checkm_data
[2024-01-24 13:37:07,728] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:07,769] [INFO] Task started: CheckM
[2024-01-24 13:37:07,769] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000686705.1_ASM68670v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000686705.1_ASM68670v1_genomic.fna/checkm_input GCF_000686705.1_ASM68670v1_genomic.fna/checkm_result
[2024-01-24 13:37:33,342] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:33,343] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:33,367] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:33,368] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:33,368] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000686705.1_ASM68670v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:33,368] [INFO] Task started: Blastn
[2024-01-24 13:37:33,369] [INFO] Running command: blastn -query GCF_000686705.1_ASM68670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1dffe1a-a341-4d09-ba40-4cb8f7bfb3db/dqc_reference/reference_markers_gtdb.fasta -out GCF_000686705.1_ASM68670v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:34,147] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:34,152] [INFO] Selected 23 target genomes.
[2024-01-24 13:37:34,153] [INFO] Target genome list was writen to GCF_000686705.1_ASM68670v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:34,174] [INFO] Task started: fastANI
[2024-01-24 13:37:34,174] [INFO] Running command: fastANI --query /var/lib/cwl/stgff5d962b-ab36-41ee-861b-51951cfbf79b/GCF_000686705.1_ASM68670v1_genomic.fna.gz --refList GCF_000686705.1_ASM68670v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000686705.1_ASM68670v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:50,145] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:50,163] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:50,163] [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_000686705.1	s__Clostridium_Z hydrogeniformans	100.0	1352	1353	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	conclusive
GCF_900111985.1	s__Clostridium_Z frigidicarnis	78.389	405	1353	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_000424205.1	s__Clostridium_X cadaveris	77.4148	173	1353	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_X	95.0	99.52	99.40	0.92	0.82	7	-
GCF_900129365.1	s__Clostridium_AH fallax	77.056	205	1353	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	-
GCA_002453475.1	s__Clostridium_J sp002453475	76.9273	167	1353	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_900141845.1	s__Clostridium_AG cavendishii	76.6999	222	1353	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AG	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018332455.1	s__Clostridium_AR polyendosporum	76.6874	133	1353	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_900112485.1	s__Clostridium uliginosum	76.6308	159	1353	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_014836835.1	s__Clostridium_J sp900547625	76.5099	194	1353	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_J	95.0	99.59	99.59	0.89	0.87	3	-
GCF_002050515.1	s__Clostridium thermobutyricum	76.3698	180	1353	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_001243045.1	s__Clostridium_F niameyense	76.3596	153	1353	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_900461105.1	s__Clostridium_L putrefaciens	76.316	160	1353	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_900185645.1	s__Clostridium_AK sp900185645	76.2719	135	1353	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AK	95.0	96.24	95.22	0.84	0.82	3	-
GCF_000968375.1	s__Clostridium_AM scatologenes	76.2642	196	1353	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_000013285.1	s__Clostridium_P perfringens	76.2607	173	1353	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	98.05	95.74	0.91	0.81	315	-
GCF_015555905.1	s__Clostridium sp015555905	76.1941	173	1353	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.95	98.95	0.73	0.73	2	-
GCF_000577815.1	s__Clostridium saudiense	76.0674	163	1353	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.39	99.24	0.89	0.87	14	-
GCA_900769625.1	s__Clostridium sp900769625	76.0567	99	1353	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_003288255.1	s__Hathewaya sp003288255	76.0397	139	1353	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Hathewaya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000204565.1	s__Clostridium_H botulinum_B	76.0347	137	1353	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_000633595.2	s__Clostridium_AM drakei	76.0325	190	1353	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_017100085.1	s__Clostridium_H botulinum_A	75.9755	128	1353	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	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:50,165] [INFO] GTDB search result was written to GCF_000686705.1_ASM68670v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:50,166] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:50,170] [INFO] DFAST_QC result json was written to GCF_000686705.1_ASM68670v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:50,170] [INFO] DFAST_QC completed!
[2024-01-24 13:37:50,170] [INFO] Total running time: 0h1m5s