[2024-01-25 18:58:36,230] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:58:36,231] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:58:36,232] [INFO] DQC Reference Directory: /var/lib/cwl/stg50cdc0fe-5b1e-4274-a6c6-1212e1d9ea3f/dqc_reference
[2024-01-25 18:58:37,359] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:58:37,362] [INFO] Task started: Prodigal
[2024-01-25 18:58:37,362] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb54385f-8e6b-4ae0-9c8b-6cf17d5f5a2b/GCF_030409315.1_ASM3040931v1_genomic.fna.gz | prodigal -d GCF_030409315.1_ASM3040931v1_genomic.fna/cds.fna -a GCF_030409315.1_ASM3040931v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:59:01,303] [INFO] Task succeeded: Prodigal
[2024-01-25 18:59:01,303] [INFO] Task started: HMMsearch
[2024-01-25 18:59:01,303] [INFO] Running command: hmmsearch --tblout GCF_030409315.1_ASM3040931v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50cdc0fe-5b1e-4274-a6c6-1212e1d9ea3f/dqc_reference/reference_markers.hmm GCF_030409315.1_ASM3040931v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:59:01,606] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:59:01,607] [INFO] Found 6/6 markers.
[2024-01-25 18:59:01,659] [INFO] Query marker FASTA was written to GCF_030409315.1_ASM3040931v1_genomic.fna/markers.fasta
[2024-01-25 18:59:01,659] [INFO] Task started: Blastn
[2024-01-25 18:59:01,659] [INFO] Running command: blastn -query GCF_030409315.1_ASM3040931v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50cdc0fe-5b1e-4274-a6c6-1212e1d9ea3f/dqc_reference/reference_markers.fasta -out GCF_030409315.1_ASM3040931v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:02,222] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:02,225] [INFO] Selected 19 target genomes.
[2024-01-25 18:59:02,226] [INFO] Target genome list was writen to GCF_030409315.1_ASM3040931v1_genomic.fna/target_genomes.txt
[2024-01-25 18:59:02,252] [INFO] Task started: fastANI
[2024-01-25 18:59:02,253] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb54385f-8e6b-4ae0-9c8b-6cf17d5f5a2b/GCF_030409315.1_ASM3040931v1_genomic.fna.gz --refList GCF_030409315.1_ASM3040931v1_genomic.fna/target_genomes.txt --output GCF_030409315.1_ASM3040931v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:59:26,031] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:26,031] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50cdc0fe-5b1e-4274-a6c6-1212e1d9ea3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:59:26,032] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50cdc0fe-5b1e-4274-a6c6-1212e1d9ea3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:59:26,043] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:59:26,043] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:59:26,043] [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
Mucilaginibacter ginsenosidivorax	strain=KHI28	GCA_007971525.1	862126	862126	type	True	80.7047	1259	2272	95	below_threshold
Mucilaginibacter pineti	strain=47C3B	GCA_900101875.1	1391627	1391627	type	True	79.8534	890	2272	95	below_threshold
Mucilaginibacter lappiensis	strain=ATCC BAA-1855	GCA_900155965.1	354630	354630	type	True	78.7815	781	2272	95	below_threshold
Mucilaginibacter lappiensis	strain=ANJLi2	GCA_014200545.1	354630	354630	type	True	78.7739	786	2272	95	below_threshold
Mucilaginibacter kameinonensis	strain=SCK	GCA_003675385.1	452286	452286	type	True	78.766	800	2272	95	below_threshold
Mucilaginibacter gossypiicola	strain=Gh-48	GCA_900110105.1	551995	551995	type	True	78.7641	831	2272	95	below_threshold
Mucilaginibacter inviolabilis	strain=HC2	GCA_011089895.1	2714892	2714892	type	True	78.761	775	2272	95	below_threshold
Mucilaginibacter celer	strain=HYN0043	GCA_003576455.2	2305508	2305508	type	True	78.7457	838	2272	95	below_threshold
Mucilaginibacter rubeus	strain=CGMCC 1.15913	GCA_014643835.1	2027860	2027860	suspected-type	True	78.7449	767	2272	95	below_threshold
Mucilaginibacter oryzae	strain=DSM 19975	GCA_003148845.1	468058	468058	type	True	78.5627	706	2272	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	77.9224	392	2272	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	77.8755	454	2272	95	below_threshold
Mucilaginibacter auburnensis	strain=DSM 28175	GCA_002797815.1	1457233	1457233	type	True	77.7858	257	2272	95	below_threshold
Mucilaginibacter corticis	strain=MAH-19	GCA_007558865.1	2597670	2597670	type	True	77.7191	381	2272	95	below_threshold
Mucilaginibacter pallidiroseus	strain=dk17	GCA_007846085.1	2599295	2599295	type	True	77.6736	331	2272	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	77.5984	319	2272	95	below_threshold
Mucilaginibacter polytrichastri	strain=RG4-7	GCA_001911425.1	1302689	1302689	type	True	77.244	364	2272	95	below_threshold
Mucilaginibacter roseus	strain=LMG 28454	GCA_021215455.1	1528868	1528868	type	True	77.2097	289	2272	95	below_threshold
Mucilaginibacter polytrichastri	strain=DSM 26907	GCA_900116355.1	1302689	1302689	type	True	77.1921	363	2272	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:59:26,045] [INFO] DFAST Taxonomy check result was written to GCF_030409315.1_ASM3040931v1_genomic.fna/tc_result.tsv
[2024-01-25 18:59:26,045] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:59:26,045] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:59:26,046] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50cdc0fe-5b1e-4274-a6c6-1212e1d9ea3f/dqc_reference/checkm_data
[2024-01-25 18:59:26,046] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:59:26,113] [INFO] Task started: CheckM
[2024-01-25 18:59:26,113] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409315.1_ASM3040931v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409315.1_ASM3040931v1_genomic.fna/checkm_input GCF_030409315.1_ASM3040931v1_genomic.fna/checkm_result
[2024-01-25 19:00:30,090] [INFO] Task succeeded: CheckM
[2024-01-25 19:00:30,092] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:00:30,112] [INFO] ===== Completeness check finished =====
[2024-01-25 19:00:30,112] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:00:30,113] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409315.1_ASM3040931v1_genomic.fna/markers.fasta)
[2024-01-25 19:00:30,113] [INFO] Task started: Blastn
[2024-01-25 19:00:30,113] [INFO] Running command: blastn -query GCF_030409315.1_ASM3040931v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50cdc0fe-5b1e-4274-a6c6-1212e1d9ea3f/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409315.1_ASM3040931v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:00:30,885] [INFO] Task succeeded: Blastn
[2024-01-25 19:00:30,889] [INFO] Selected 16 target genomes.
[2024-01-25 19:00:30,889] [INFO] Target genome list was writen to GCF_030409315.1_ASM3040931v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:00:30,909] [INFO] Task started: fastANI
[2024-01-25 19:00:30,909] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb54385f-8e6b-4ae0-9c8b-6cf17d5f5a2b/GCF_030409315.1_ASM3040931v1_genomic.fna.gz --refList GCF_030409315.1_ASM3040931v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409315.1_ASM3040931v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:00:53,273] [INFO] Task succeeded: fastANI
[2024-01-25 19:00:53,283] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:00:53,283] [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_014205845.1	s__Mucilaginibacter sp014205845	81.1224	1236	2272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007971525.1	s__Mucilaginibacter ginsenosidivorax	80.7124	1258	2272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110415.1	s__Mucilaginibacter sp900110415	80.6476	1165	2272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101875.1	s__Mucilaginibacter pineti	79.8534	890	2272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200575.1	s__Mucilaginibacter sp014200575	79.1175	774	2272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013149275.1	s__Mucilaginibacter sp013149275	79.0129	754	2272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103125.1	s__Mucilaginibacter sp900103125	78.9734	801	2272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110105.1	s__Mucilaginibacter gossypiicola	78.7756	829	2272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900155965.1	s__Mucilaginibacter lappiensis	78.7655	784	2272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.12	98.24	0.94	0.88	3	-
GCF_003675385.1	s__Mucilaginibacter kameinonensis	78.7602	801	2272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	95.21	95.21	0.87	0.87	2	-
GCF_014643835.1	s__Mucilaginibacter rubeus	78.7341	768	2272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	97.62	97.51	0.93	0.92	3	-
GCF_003576455.2	s__Mucilaginibacter celer	78.7231	843	2272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664165.1	s__Mucilaginibacter sp003664165	78.7204	857	2272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148845.1	s__Mucilaginibacter oryzae	78.5601	706	2272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001636615.1	s__Mucilaginibacter sp001636615	77.9127	480	2272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200495.1	s__Mucilaginibacter sp014200495	77.7397	439	2272	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:00:53,285] [INFO] GTDB search result was written to GCF_030409315.1_ASM3040931v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:00:53,286] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:00:53,289] [INFO] DFAST_QC result json was written to GCF_030409315.1_ASM3040931v1_genomic.fna/dqc_result.json
[2024-01-25 19:00:53,289] [INFO] DFAST_QC completed!
[2024-01-25 19:00:53,289] [INFO] Total running time: 0h2m17s