[2024-01-24 12:44:43,716] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:43,720] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:43,720] [INFO] DQC Reference Directory: /var/lib/cwl/stgce143a90-1e88-4835-805e-f79606824590/dqc_reference
[2024-01-24 12:44:45,043] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:45,046] [INFO] Task started: Prodigal
[2024-01-24 12:44:45,046] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a3c4430-f8e4-499a-9c28-a67ebd184244/GCF_014635825.1_ASM1463582v1_genomic.fna.gz | prodigal -d GCF_014635825.1_ASM1463582v1_genomic.fna/cds.fna -a GCF_014635825.1_ASM1463582v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:06,054] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:06,054] [INFO] Task started: HMMsearch
[2024-01-24 12:45:06,054] [INFO] Running command: hmmsearch --tblout GCF_014635825.1_ASM1463582v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce143a90-1e88-4835-805e-f79606824590/dqc_reference/reference_markers.hmm GCF_014635825.1_ASM1463582v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:06,392] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:06,394] [INFO] Found 6/6 markers.
[2024-01-24 12:45:06,446] [INFO] Query marker FASTA was written to GCF_014635825.1_ASM1463582v1_genomic.fna/markers.fasta
[2024-01-24 12:45:06,447] [INFO] Task started: Blastn
[2024-01-24 12:45:06,447] [INFO] Running command: blastn -query GCF_014635825.1_ASM1463582v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce143a90-1e88-4835-805e-f79606824590/dqc_reference/reference_markers.fasta -out GCF_014635825.1_ASM1463582v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:07,149] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:07,155] [INFO] Selected 23 target genomes.
[2024-01-24 12:45:07,156] [INFO] Target genome list was writen to GCF_014635825.1_ASM1463582v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:07,168] [INFO] Task started: fastANI
[2024-01-24 12:45:07,169] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a3c4430-f8e4-499a-9c28-a67ebd184244/GCF_014635825.1_ASM1463582v1_genomic.fna.gz --refList GCF_014635825.1_ASM1463582v1_genomic.fna/target_genomes.txt --output GCF_014635825.1_ASM1463582v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:31,781] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:31,781] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce143a90-1e88-4835-805e-f79606824590/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:31,781] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce143a90-1e88-4835-805e-f79606824590/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:31,797] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:31,797] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:31,797] [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 galii	strain=CCM 8711	GCA_014635825.1	2005073	2005073	type	True	100.0	1606	1608	95	conclusive
Mucilaginibacter aquatilis	strain=HME9299	GCA_009755275.1	1517760	1517760	type	True	78.3632	441	1608	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	77.7617	257	1608	95	below_threshold
Mucilaginibacter robiniae	strain=F39-2	GCA_012849215.1	2728022	2728022	type	True	77.5886	331	1608	95	below_threshold
Mucilaginibacter xinganensis	strain=BJC16-A31	GCA_002257585.1	1234841	1234841	type	True	77.4347	170	1608	95	below_threshold
Mucilaginibacter pineti	strain=47C3B	GCA_900101875.1	1391627	1391627	type	True	77.4045	261	1608	95	below_threshold
Mucilaginibacter terrigena	strain=17JY9-4	GCA_004168255.1	2492395	2492395	type	True	77.3797	240	1608	95	below_threshold
Mucilaginibacter ginsenosidivorax	strain=KHI28	GCA_007971525.1	862126	862126	type	True	77.3491	259	1608	95	below_threshold
Mucilaginibacter lappiensis	strain=ATCC BAA-1855	GCA_900155965.1	354630	354630	type	True	77.2955	250	1608	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	77.2803	252	1608	95	below_threshold
Mucilaginibacter gossypiicola	strain=Gh-48	GCA_900110105.1	551995	551995	type	True	77.2374	241	1608	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	77.2345	263	1608	95	below_threshold
Mucilaginibacter endophyticus	strain=RS1	GCA_003351025.1	2675003	2675003	type	True	77.2023	254	1608	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	77.1793	260	1608	95	below_threshold
Mucilaginibacter inviolabilis	strain=HC2	GCA_011089895.1	2714892	2714892	type	True	77.1728	230	1608	95	below_threshold
Mucilaginibacter yixingensis	strain=DSM 26809	GCA_003050755.1	1295612	1295612	type	True	77.1021	237	1608	95	below_threshold
Mucilaginibacter mallensis	strain=MP1X4	GCA_900105165.1	652787	652787	type	True	77.0768	222	1608	95	below_threshold
Mucilaginibacter frigoritolerans	strain=ATCC BAA-1854	GCA_007830615.1	652788	652788	type	True	77.0738	200	1608	95	below_threshold
Mucilaginibacter pedocola	strain=TBZ30	GCA_002013915.1	1792845	1792845	type	True	77.0191	275	1608	95	below_threshold
Mucilaginibacter psychrotolerans	strain=NH7-4	GCA_004519315.1	1524096	1524096	type	True	76.9972	229	1608	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:31,799] [INFO] DFAST Taxonomy check result was written to GCF_014635825.1_ASM1463582v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:31,800] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:31,800] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:31,800] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce143a90-1e88-4835-805e-f79606824590/dqc_reference/checkm_data
[2024-01-24 12:45:31,801] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:31,852] [INFO] Task started: CheckM
[2024-01-24 12:45:31,852] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014635825.1_ASM1463582v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014635825.1_ASM1463582v1_genomic.fna/checkm_input GCF_014635825.1_ASM1463582v1_genomic.fna/checkm_result
[2024-01-24 12:46:29,123] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:29,125] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:29,143] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:29,144] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:29,144] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014635825.1_ASM1463582v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:29,145] [INFO] Task started: Blastn
[2024-01-24 12:46:29,145] [INFO] Running command: blastn -query GCF_014635825.1_ASM1463582v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgce143a90-1e88-4835-805e-f79606824590/dqc_reference/reference_markers_gtdb.fasta -out GCF_014635825.1_ASM1463582v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:29,947] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:29,953] [INFO] Selected 17 target genomes.
[2024-01-24 12:46:29,953] [INFO] Target genome list was writen to GCF_014635825.1_ASM1463582v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:29,971] [INFO] Task started: fastANI
[2024-01-24 12:46:29,971] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a3c4430-f8e4-499a-9c28-a67ebd184244/GCF_014635825.1_ASM1463582v1_genomic.fna.gz --refList GCF_014635825.1_ASM1463582v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014635825.1_ASM1463582v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:45,591] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:45,609] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:45,609] [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_014635825.1	s__Mucilaginibacter galii	100.0	1606	1608	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_009755275.1	s__Mucilaginibacter aquatilis	78.3723	440	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018390515.1	s__Mucilaginibacter sp018390515	77.9893	413	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009770985.1	s__Mucilaginibacter sp009770985	77.8991	390	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012849215.1	s__Mucilaginibacter sp012849215	77.5854	330	1608	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	77.5828	248	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002257585.1	s__Mucilaginibacter xinganensis	77.4006	172	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004168255.1	s__Mucilaginibacter terrigena	77.3694	241	1608	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	77.3648	267	1608	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	77.3509	259	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903644075.1	s__Mucilaginibacter sp903644075	77.2666	259	1608	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	77.1916	274	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093045.1	s__Mucilaginibacter sp010093045	77.1341	194	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	95.64	95.64	0.92	0.92	2	-
GCF_014773275.1	s__Mucilaginibacter rigui	77.1184	265	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003050755.1	s__Mucilaginibacter yixingensis	77.1031	237	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765905.1	s__Mucilaginibacter sp009765905	77.0689	208	1608	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449775.1	s__Mucilaginibacter sp018449775	77.0064	200	1608	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 12:46:45,611] [INFO] GTDB search result was written to GCF_014635825.1_ASM1463582v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:45,612] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:45,616] [INFO] DFAST_QC result json was written to GCF_014635825.1_ASM1463582v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:45,617] [INFO] DFAST_QC completed!
[2024-01-24 12:46:45,617] [INFO] Total running time: 0h2m2s