[2024-01-24 11:05:03,929] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,937] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,937] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4186113-6fc5-450f-a669-5334df3af85c/dqc_reference
[2024-01-24 11:05:05,812] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,813] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,813] [INFO] Running command: gunzip -c /var/lib/cwl/stg39f46220-a92f-4926-94f1-0698c5845a7d/GCF_001403615.1_Desnusiella_massiliensis_genomic.fna.gz | prodigal -d GCF_001403615.1_Desnusiella_massiliensis_genomic.fna/cds.fna -a GCF_001403615.1_Desnusiella_massiliensis_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:14,132] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:14,132] [INFO] Task started: HMMsearch
[2024-01-24 11:05:14,132] [INFO] Running command: hmmsearch --tblout GCF_001403615.1_Desnusiella_massiliensis_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4186113-6fc5-450f-a669-5334df3af85c/dqc_reference/reference_markers.hmm GCF_001403615.1_Desnusiella_massiliensis_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:14,539] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:14,540] [INFO] Found 6/6 markers.
[2024-01-24 11:05:14,582] [INFO] Query marker FASTA was written to GCF_001403615.1_Desnusiella_massiliensis_genomic.fna/markers.fasta
[2024-01-24 11:05:14,583] [INFO] Task started: Blastn
[2024-01-24 11:05:14,583] [INFO] Running command: blastn -query GCF_001403615.1_Desnusiella_massiliensis_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4186113-6fc5-450f-a669-5334df3af85c/dqc_reference/reference_markers.fasta -out GCF_001403615.1_Desnusiella_massiliensis_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:15,131] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:15,134] [INFO] Selected 28 target genomes.
[2024-01-24 11:05:15,134] [INFO] Target genome list was writen to GCF_001403615.1_Desnusiella_massiliensis_genomic.fna/target_genomes.txt
[2024-01-24 11:05:15,158] [INFO] Task started: fastANI
[2024-01-24 11:05:15,158] [INFO] Running command: fastANI --query /var/lib/cwl/stg39f46220-a92f-4926-94f1-0698c5845a7d/GCF_001403615.1_Desnusiella_massiliensis_genomic.fna.gz --refList GCF_001403615.1_Desnusiella_massiliensis_genomic.fna/target_genomes.txt --output GCF_001403615.1_Desnusiella_massiliensis_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:32,572] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:32,572] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4186113-6fc5-450f-a669-5334df3af85c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:32,573] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4186113-6fc5-450f-a669-5334df3af85c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:32,586] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:05:32,586] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:32,586] [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
Desnuesiella massiliensis	strain=mt10	GCA_001403615.1	1650662	1650662	type	True	100.0	1828	1828	95	conclusive
Clostridium oryzae	strain=DSM 28571	GCA_002029235.1	1450648	1450648	type	True	78.7051	122	1828	95	below_threshold
Clostridium lundense	strain=DSM 17049	GCA_000619945.1	319475	319475	type	True	78.5566	220	1828	95	below_threshold
Hathewaya histolytica	strain=NCTC503	GCA_901482605.1	1498	1498	type	True	77.0592	116	1828	95	below_threshold
Clostridium magnum	strain=DSM 2767	GCA_001623875.1	33954	33954	type	True	77.0522	195	1828	95	below_threshold
Clostridium chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	77.0161	128	1828	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	76.9259	178	1828	95	below_threshold
Clostridium polyendosporum	strain=JCM 30710	GCA_018332455.1	69208	69208	type	True	76.8839	157	1828	95	below_threshold
Clostridium fallax	strain=DSM 2631	GCA_900129365.1	1533	1533	type	True	76.6661	167	1828	95	below_threshold
Clostridium magnum	strain=DSM 2767	GCA_900129955.1	33954	33954	type	True	76.6577	182	1828	95	below_threshold
Clostridium nigeriense	strain=Marseille-P2414	GCA_900086595.1	1805470	1805470	type	True	76.6553	147	1828	95	below_threshold
Clostridium frigidicarnis	strain=DSM 12271	GCA_900111985.1	84698	84698	type	True	76.5812	215	1828	95	below_threshold
Clostridium uliginosum	strain=DSM 12992	GCA_900112485.1	119641	119641	type	True	76.5181	149	1828	95	below_threshold
Clostridium faecium	strain=N37	GCA_014836835.1	2762223	2762223	type	True	76.3161	174	1828	95	below_threshold
Clostridium neonatale	strain=LCDC 99A005	GCA_002553615.1	137838	137838	type	True	76.2883	145	1828	95	below_threshold
Clostridium neonatale	strain=LCDC no.99-A-005	GCA_001458595.1	137838	137838	type	True	76.1766	137	1828	95	below_threshold
Clostridium tepidum	strain=IEH 97212	GCA_002008345.1	1962263	1962263	type	True	76.0412	178	1828	95	below_threshold
Clostridium thermobutyricum	strain=DSM 4928	GCA_002050515.1	29372	29372	type	True	76.0103	155	1828	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:32,590] [INFO] DFAST Taxonomy check result was written to GCF_001403615.1_Desnusiella_massiliensis_genomic.fna/tc_result.tsv
[2024-01-24 11:05:32,590] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:32,591] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:32,591] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4186113-6fc5-450f-a669-5334df3af85c/dqc_reference/checkm_data
[2024-01-24 11:05:32,592] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:32,647] [INFO] Task started: CheckM
[2024-01-24 11:05:32,648] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001403615.1_Desnusiella_massiliensis_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001403615.1_Desnusiella_massiliensis_genomic.fna/checkm_input GCF_001403615.1_Desnusiella_massiliensis_genomic.fna/checkm_result
[2024-01-24 11:06:00,829] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:00,830] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:00,858] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:00,858] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:00,858] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001403615.1_Desnusiella_massiliensis_genomic.fna/markers.fasta)
[2024-01-24 11:06:00,858] [INFO] Task started: Blastn
[2024-01-24 11:06:00,858] [INFO] Running command: blastn -query GCF_001403615.1_Desnusiella_massiliensis_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4186113-6fc5-450f-a669-5334df3af85c/dqc_reference/reference_markers_gtdb.fasta -out GCF_001403615.1_Desnusiella_massiliensis_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:01,601] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:01,604] [INFO] Selected 29 target genomes.
[2024-01-24 11:06:01,604] [INFO] Target genome list was writen to GCF_001403615.1_Desnusiella_massiliensis_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:01,634] [INFO] Task started: fastANI
[2024-01-24 11:06:01,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg39f46220-a92f-4926-94f1-0698c5845a7d/GCF_001403615.1_Desnusiella_massiliensis_genomic.fna.gz --refList GCF_001403615.1_Desnusiella_massiliensis_genomic.fna/target_genomes_gtdb.txt --output GCF_001403615.1_Desnusiella_massiliensis_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:19,931] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:19,945] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:19,946] [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_001403615.1	s__Desnuesiella massiliensis	100.0	1828	1828	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Desnuesiella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002029235.1	s__Clostridium_AE oryzae	78.7051	122	1828	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_900205925.1	s__Clostridium_AK peptidivorans	77.945	170	1828	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AK	95.0	N/A	N/A	N/A	N/A	1	-
GCF_901482605.1	s__Hathewaya histolytica	77.0815	115	1828	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_001623875.1	s__Clostridium_AM magnum	77.0657	194	1828	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AM	95.0	99.97	99.97	0.98	0.98	2	-
GCF_002327185.1	s__Clostridium chauvoei	77.0606	129	1828	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.96	99.88	0.99	0.99	5	-
GCF_900461105.1	s__Clostridium_L putrefaciens	76.9116	177	1828	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_018332455.1	s__Clostridium_AR polyendosporum	76.8839	157	1828	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_000424205.1	s__Clostridium_X cadaveris	76.8214	156	1828	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	-
GCA_002423705.1	s__Clostridium_X sp002423705	76.7394	161	1828	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_X	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900086595.1	s__Clostridium nigeriense	76.6784	145	1828	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.98	98.98	0.91	0.91	2	-
GCF_900129365.1	s__Clostridium_AH fallax	76.6538	168	1828	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_900111985.1	s__Clostridium_Z frigidicarnis	76.609	212	1828	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_900112485.1	s__Clostridium uliginosum	76.5288	148	1828	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_902809985.1	s__Clostridium_B sp902809985	76.4606	84	1828	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_B	95.0	99.08	99.06	0.93	0.92	3	-
GCF_001458595.1	s__Clostridium neonatale	76.1218	137	1828	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.07	98.42	0.91	0.80	11	-
GCF_002008345.1	s__Clostridium_F tepidum	76.0506	177	1828	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_900116755.1	s__Clostridium sp900116755	76.0272	118	1828	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	75.9818	158	1828	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_000577815.1	s__Clostridium saudiense	75.9742	124	1828	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.39	99.24	0.89	0.87	14	-
GCF_015670405.1	s__Clostridium sp015670405	75.9715	120	1828	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_002403785.1	s__Clostridium_AD sp002403785	75.7434	99	1828	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AD	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001594005.1	s__Clostridium_AC tepidiprofundi	75.6838	96	1828	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AC	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900604495.1	s__GCA-900066495 sp900066495	75.5411	75	1828	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__GCA-900066495	95.0	99.74	99.60	0.96	0.94	5	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:19,947] [INFO] GTDB search result was written to GCF_001403615.1_Desnusiella_massiliensis_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:19,947] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:19,951] [INFO] DFAST_QC result json was written to GCF_001403615.1_Desnusiella_massiliensis_genomic.fna/dqc_result.json
[2024-01-24 11:06:19,951] [INFO] DFAST_QC completed!
[2024-01-24 11:06:19,951] [INFO] Total running time: 0h1m16s