[2024-01-24 12:15:18,542] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:18,551] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:18,551] [INFO] DQC Reference Directory: /var/lib/cwl/stgb11c3949-1c50-485b-a1e9-c357e4fd5427/dqc_reference
[2024-01-24 12:15:19,805] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:19,806] [INFO] Task started: Prodigal
[2024-01-24 12:15:19,806] [INFO] Running command: gunzip -c /var/lib/cwl/stgb35dc2f7-866c-406f-884c-c48ebabacd48/GCF_002257585.1_ASM225758v1_genomic.fna.gz | prodigal -d GCF_002257585.1_ASM225758v1_genomic.fna/cds.fna -a GCF_002257585.1_ASM225758v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:41,532] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:41,533] [INFO] Task started: HMMsearch
[2024-01-24 12:15:41,533] [INFO] Running command: hmmsearch --tblout GCF_002257585.1_ASM225758v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb11c3949-1c50-485b-a1e9-c357e4fd5427/dqc_reference/reference_markers.hmm GCF_002257585.1_ASM225758v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:41,813] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:41,815] [INFO] Found 6/6 markers.
[2024-01-24 12:15:41,859] [INFO] Query marker FASTA was written to GCF_002257585.1_ASM225758v1_genomic.fna/markers.fasta
[2024-01-24 12:15:41,860] [INFO] Task started: Blastn
[2024-01-24 12:15:41,860] [INFO] Running command: blastn -query GCF_002257585.1_ASM225758v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb11c3949-1c50-485b-a1e9-c357e4fd5427/dqc_reference/reference_markers.fasta -out GCF_002257585.1_ASM225758v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:42,477] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:42,480] [INFO] Selected 19 target genomes.
[2024-01-24 12:15:42,481] [INFO] Target genome list was writen to GCF_002257585.1_ASM225758v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:42,485] [INFO] Task started: fastANI
[2024-01-24 12:15:42,485] [INFO] Running command: fastANI --query /var/lib/cwl/stgb35dc2f7-866c-406f-884c-c48ebabacd48/GCF_002257585.1_ASM225758v1_genomic.fna.gz --refList GCF_002257585.1_ASM225758v1_genomic.fna/target_genomes.txt --output GCF_002257585.1_ASM225758v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:00,536] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:00,536] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb11c3949-1c50-485b-a1e9-c357e4fd5427/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:00,536] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb11c3949-1c50-485b-a1e9-c357e4fd5427/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:00,551] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:16:00,551] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:16:00,551] [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 xinganensis	strain=BJC16-A31	GCA_002257585.1	1234841	1234841	type	True	100.0	1767	1767	95	conclusive
Mucilaginibacter frigoritolerans	strain=ATCC BAA-1854	GCA_007830615.1	652788	652788	type	True	78.5663	471	1767	95	below_threshold
Mucilaginibacter gotjawali	strain=SA3-7	GCA_002355435.1	1550579	1550579	type	True	78.3065	505	1767	95	below_threshold
Mucilaginibacter gotjawali	strain=CECT 8628	GCA_014191635.1	1550579	1550579	type	True	78.1613	494	1767	95	below_threshold
Mucilaginibacter mallensis	strain=MP1X4	GCA_900105165.1	652787	652787	type	True	78.1114	355	1767	95	below_threshold
Mucilaginibacter pineti	strain=47C3B	GCA_900101875.1	1391627	1391627	type	True	77.7923	409	1767	95	below_threshold
Mucilaginibacter gossypiicola	strain=Gh-48	GCA_900110105.1	551995	551995	type	True	77.6794	365	1767	95	below_threshold
Mucilaginibacter gossypii	strain=Gh-67	GCA_900100945.1	551996	551996	type	True	77.6785	358	1767	95	below_threshold
Mucilaginibacter roseus	strain=LMG 28454	GCA_021215455.1	1528868	1528868	type	True	77.5111	208	1767	95	below_threshold
Mucilaginibacter rubeus	strain=CGMCC 1.15913	GCA_014643835.1	2027860	2027860	suspected-type	True	77.4752	387	1767	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	77.4648	319	1767	95	below_threshold
Mucilaginibacter lappiensis	strain=ATCC BAA-1855	GCA_900155965.1	354630	354630	type	True	77.4582	376	1767	95	below_threshold
Mucilaginibacter inviolabilis	strain=HC2	GCA_011089895.1	2714892	2714892	type	True	77.4537	393	1767	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	77.4214	302	1767	95	below_threshold
Mucilaginibacter galii	strain=CCM 8711	GCA_014635825.1	2005073	2005073	type	True	77.4076	167	1767	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	77.4038	256	1767	95	below_threshold
Mucilaginibacter celer	strain=HYN0043	GCA_003576455.2	2305508	2305508	type	True	77.3863	389	1767	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	77.2818	202	1767	95	below_threshold
Mucilaginibacter terrenus	strain=ZH6	GCA_003432065.1	2482727	2482727	type	True	77.2498	210	1767	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:00,553] [INFO] DFAST Taxonomy check result was written to GCF_002257585.1_ASM225758v1_genomic.fna/tc_result.tsv
[2024-01-24 12:16:00,553] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:00,554] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:00,554] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb11c3949-1c50-485b-a1e9-c357e4fd5427/dqc_reference/checkm_data
[2024-01-24 12:16:00,555] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:00,602] [INFO] Task started: CheckM
[2024-01-24 12:16:00,602] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002257585.1_ASM225758v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002257585.1_ASM225758v1_genomic.fna/checkm_input GCF_002257585.1_ASM225758v1_genomic.fna/checkm_result
[2024-01-24 12:16:59,198] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:59,200] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:59,415] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:59,416] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:59,416] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002257585.1_ASM225758v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:59,416] [INFO] Task started: Blastn
[2024-01-24 12:16:59,416] [INFO] Running command: blastn -query GCF_002257585.1_ASM225758v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb11c3949-1c50-485b-a1e9-c357e4fd5427/dqc_reference/reference_markers_gtdb.fasta -out GCF_002257585.1_ASM225758v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:17:00,213] [INFO] Task succeeded: Blastn
[2024-01-24 12:17:00,216] [INFO] Selected 17 target genomes.
[2024-01-24 12:17:00,216] [INFO] Target genome list was writen to GCF_002257585.1_ASM225758v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:17:00,238] [INFO] Task started: fastANI
[2024-01-24 12:17:00,238] [INFO] Running command: fastANI --query /var/lib/cwl/stgb35dc2f7-866c-406f-884c-c48ebabacd48/GCF_002257585.1_ASM225758v1_genomic.fna.gz --refList GCF_002257585.1_ASM225758v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002257585.1_ASM225758v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:14,717] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:14,730] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:17:14,731] [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_002257585.1	s__Mucilaginibacter xinganensis	100.0	1767	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900142915.1	s__Mucilaginibacter sp900142915	81.2925	1090	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013286325.1	s__Mucilaginibacter sp013286325	78.994	433	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830615.1	s__Mucilaginibacter frigoritolerans	78.553	471	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355435.1	s__Mucilaginibacter gotjawali	78.2708	504	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_002413785.1	s__Mucilaginibacter sp002413785	78.2318	443	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.87	99.70	0.98	0.97	4	-
GCA_013288235.1	s__Mucilaginibacter sp013288235	78.1823	361	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.30	99.08	0.67	0.66	3	-
GCF_900105165.1	s__Mucilaginibacter mallensis	78.1411	355	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903915155.1	s__Mucilaginibacter sp903915155	77.91	286	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013288685.1	s__Mucilaginibacter sp013288685	77.8989	303	1767	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	77.8256	360	1767	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	77.776	411	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013288465.1	s__Mucilaginibacter sp013288465	77.7111	161	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408825.1	s__Mucilaginibacter sp013408825	77.6313	278	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205845.1	s__Mucilaginibacter sp014205845	77.5953	399	1767	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	77.4434	333	1767	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:14,732] [INFO] GTDB search result was written to GCF_002257585.1_ASM225758v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:14,733] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:14,737] [INFO] DFAST_QC result json was written to GCF_002257585.1_ASM225758v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:14,737] [INFO] DFAST_QC completed!
[2024-01-24 12:17:14,737] [INFO] Total running time: 0h1m56s