[2023-06-13 02:32:38,181] [INFO] DFAST_QC pipeline started.
[2023-06-13 02:32:38,186] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 02:32:38,187] [INFO] DQC Reference Directory: /var/lib/cwl/stg803c0877-4a67-4066-94a7-5bf9646ebbf6/dqc_reference
[2023-06-13 02:32:39,750] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 02:32:39,751] [INFO] Task started: Prodigal
[2023-06-13 02:32:39,751] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a5e56a7-3a27-4549-a074-c5e9328b5d91/GCA_022773665.1_ASM2277366v1_genomic.fna.gz | prodigal -d GCA_022773665.1_ASM2277366v1_genomic.fna/cds.fna -a GCA_022773665.1_ASM2277366v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 02:32:44,029] [INFO] Task succeeded: Prodigal
[2023-06-13 02:32:44,029] [INFO] Task started: HMMsearch
[2023-06-13 02:32:44,030] [INFO] Running command: hmmsearch --tblout GCA_022773665.1_ASM2277366v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg803c0877-4a67-4066-94a7-5bf9646ebbf6/dqc_reference/reference_markers.hmm GCA_022773665.1_ASM2277366v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 02:32:44,364] [INFO] Task succeeded: HMMsearch
[2023-06-13 02:32:44,365] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3a5e56a7-3a27-4549-a074-c5e9328b5d91/GCA_022773665.1_ASM2277366v1_genomic.fna.gz]
[2023-06-13 02:32:44,405] [INFO] Query marker FASTA was written to GCA_022773665.1_ASM2277366v1_genomic.fna/markers.fasta
[2023-06-13 02:32:44,405] [INFO] Task started: Blastn
[2023-06-13 02:32:44,405] [INFO] Running command: blastn -query GCA_022773665.1_ASM2277366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg803c0877-4a67-4066-94a7-5bf9646ebbf6/dqc_reference/reference_markers.fasta -out GCA_022773665.1_ASM2277366v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:32:45,027] [INFO] Task succeeded: Blastn
[2023-06-13 02:32:45,036] [INFO] Selected 25 target genomes.
[2023-06-13 02:32:45,036] [INFO] Target genome list was writen to GCA_022773665.1_ASM2277366v1_genomic.fna/target_genomes.txt
[2023-06-13 02:32:45,040] [INFO] Task started: fastANI
[2023-06-13 02:32:45,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a5e56a7-3a27-4549-a074-c5e9328b5d91/GCA_022773665.1_ASM2277366v1_genomic.fna.gz --refList GCA_022773665.1_ASM2277366v1_genomic.fna/target_genomes.txt --output GCA_022773665.1_ASM2277366v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 02:33:01,493] [INFO] Task succeeded: fastANI
[2023-06-13 02:33:01,494] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg803c0877-4a67-4066-94a7-5bf9646ebbf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 02:33:01,494] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg803c0877-4a67-4066-94a7-5bf9646ebbf6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 02:33:01,514] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 02:33:01,514] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 02:33:01,515] [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 paraputrificum	strain=NCTC11833	GCA_900447045.1	29363	29363	type	True	78.6287	225	861	95	below_threshold
Clostridium vincentii	strain=DSM 10228	GCA_002995745.1	52704	52704	type	True	77.9443	183	861	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	77.941	228	861	95	below_threshold
Clostridium uliginosum	strain=DSM 12992	GCA_900112485.1	119641	119641	type	True	77.7846	211	861	95	below_threshold
Clostridium septicum	strain=DSM 7534	GCA_003606265.1	1504	1504	type	True	77.6002	193	861	95	below_threshold
Clostridium septicum	strain=FDAARGOS_1551	GCA_020736665.1	1504	1504	type	True	77.583	193	861	95	below_threshold
Clostridium cagae	strain=Marseille-P4344	GCA_900290265.1	2080751	2080751	type	True	77.5498	218	861	95	below_threshold
Clostridium chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	77.4202	203	861	95	below_threshold
Clostridium celatum	strain=DSM 1785	GCA_000320405.1	36834	36834	type	True	77.4196	207	861	95	below_threshold
Clostridium nigeriense	strain=Marseille-P2414	GCA_900086595.1	1805470	1805470	type	True	77.4181	210	861	95	below_threshold
Clostridium saudiense	strain=JCC	GCA_000577815.1	1414720	1414720	type	True	77.4122	201	861	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	77.3749	250	861	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	77.1161	223	861	95	below_threshold
Clostridium saccharobutylicum	strain=DSM 13864	GCA_000473995.1	169679	169679	type	True	77.1132	230	861	95	below_threshold
Clostridium chrysemydis	strain=PT	GCA_015234215.1	2665504	2665504	type	True	77.1125	174	861	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	77.079	183	861	95	below_threshold
Clostridium saccharobutylicum	strain=DSM 13864	GCA_001657435.1	169679	169679	type	True	77.075	222	861	95	below_threshold
Clostridium neonatale	strain=LCDC 99A005	GCA_002553615.1	137838	137838	type	True	77.0747	240	861	95	below_threshold
Clostridium neonatale	strain=LCDC no.99-A-005	GCA_001458595.1	137838	137838	type	True	77.0673	245	861	95	below_threshold
Clostridium gelidum	strain=C5S11	GCA_019977655.1	704125	704125	type	True	77.0213	222	861	95	below_threshold
Clostridium fallax	strain=DSM 2631	GCA_900129365.1	1533	1533	type	True	76.9814	182	861	95	below_threshold
Sarcina ventriculi	strain=NCTC12966	GCA_900456775.1	1267	1267	type	True	76.9745	170	861	95	below_threshold
Clostridium simiarum	strain=MSJ-4	GCA_018919175.1	2841506	2841506	type	True	76.1392	112	861	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	75.9906	150	861	95	below_threshold
Clostridium autoethanogenum	strain=DSM 10061	GCA_000484505.2	84023	84023	suspected-type	True	75.8683	82	861	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 02:33:01,520] [INFO] DFAST Taxonomy check result was written to GCA_022773665.1_ASM2277366v1_genomic.fna/tc_result.tsv
[2023-06-13 02:33:01,520] [INFO] ===== Taxonomy check completed =====
[2023-06-13 02:33:01,521] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 02:33:01,521] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg803c0877-4a67-4066-94a7-5bf9646ebbf6/dqc_reference/checkm_data
[2023-06-13 02:33:01,524] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 02:33:01,572] [INFO] Task started: CheckM
[2023-06-13 02:33:01,572] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022773665.1_ASM2277366v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022773665.1_ASM2277366v1_genomic.fna/checkm_input GCA_022773665.1_ASM2277366v1_genomic.fna/checkm_result
[2023-06-13 02:33:22,971] [INFO] Task succeeded: CheckM
[2023-06-13 02:33:22,972] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 02:33:22,991] [INFO] ===== Completeness check finished =====
[2023-06-13 02:33:22,991] [INFO] ===== Start GTDB Search =====
[2023-06-13 02:33:22,991] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022773665.1_ASM2277366v1_genomic.fna/markers.fasta)
[2023-06-13 02:33:22,992] [INFO] Task started: Blastn
[2023-06-13 02:33:22,992] [INFO] Running command: blastn -query GCA_022773665.1_ASM2277366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg803c0877-4a67-4066-94a7-5bf9646ebbf6/dqc_reference/reference_markers_gtdb.fasta -out GCA_022773665.1_ASM2277366v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:33:23,781] [INFO] Task succeeded: Blastn
[2023-06-13 02:33:23,786] [INFO] Selected 16 target genomes.
[2023-06-13 02:33:23,787] [INFO] Target genome list was writen to GCA_022773665.1_ASM2277366v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 02:33:23,836] [INFO] Task started: fastANI
[2023-06-13 02:33:23,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a5e56a7-3a27-4549-a074-c5e9328b5d91/GCA_022773665.1_ASM2277366v1_genomic.fna.gz --refList GCA_022773665.1_ASM2277366v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022773665.1_ASM2277366v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 02:33:33,289] [INFO] Task succeeded: fastANI
[2023-06-13 02:33:33,309] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 02:33:33,310] [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
GCA_902785295.1	s__Clostridium sp902785295	95.1172	620	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900317445.1	s__Clostridium sp900317445	90.9647	481	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900539375.1	s__Clostridium sp900539375	89.5052	592	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.09	99.02	0.89	0.86	4	-
GCF_900447045.1	s__Clostridium paraputrificum	78.6645	223	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.58	95.42	0.89	0.83	29	-
GCA_018372875.1	s__Clostridium sp018372875	78.6201	220	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.91	98.91	0.87	0.87	2	-
GCA_012519155.1	s__Clostridium sp012519155	78.3405	223	861	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_900116755.1	s__Clostridium sp900116755	78.3346	211	861	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_002995745.1	s__Clostridium vincentii	77.9443	183	861	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_015058405.1	s__Clostridium sp015058405	77.8972	242	861	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_012519845.1	s__Clostridium sp012519845	77.7998	231	861	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_001735765.2	s__Clostridium taeniosporum	77.6651	232	861	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_000789395.1	s__Clostridium baratii	77.6581	222	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	96.53	95.37	0.92	0.89	15	-
GCA_910588715.1	s__Clostridium sp910588715	77.6381	208	861	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_000498355.1	s__Clostridium sp000498355	77.5741	225	861	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_002327185.1	s__Clostridium chauvoei	77.4052	204	861	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_000473995.1	s__Clostridium saccharobutylicum	77.1079	232	861	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.89	95.82	0.99	0.83	65	-
--------------------------------------------------------------------------------
[2023-06-13 02:33:33,312] [INFO] GTDB search result was written to GCA_022773665.1_ASM2277366v1_genomic.fna/result_gtdb.tsv
[2023-06-13 02:33:33,313] [INFO] ===== GTDB Search completed =====
[2023-06-13 02:33:33,317] [INFO] DFAST_QC result json was written to GCA_022773665.1_ASM2277366v1_genomic.fna/dqc_result.json
[2023-06-13 02:33:33,318] [INFO] DFAST_QC completed!
[2023-06-13 02:33:33,318] [INFO] Total running time: 0h0m55s