[2024-01-24 11:59:11,822] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:11,824] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:11,824] [INFO] DQC Reference Directory: /var/lib/cwl/stg4adfff29-e7d3-403e-804a-ff26cbea79dd/dqc_reference
[2024-01-24 11:59:13,165] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:13,166] [INFO] Task started: Prodigal
[2024-01-24 11:59:13,167] [INFO] Running command: gunzip -c /var/lib/cwl/stg26dca8f1-04c9-4a6f-9145-77cd7f33cbc4/GCF_003324525.1_ASM332452v1_genomic.fna.gz | prodigal -d GCF_003324525.1_ASM332452v1_genomic.fna/cds.fna -a GCF_003324525.1_ASM332452v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:30,169] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:30,169] [INFO] Task started: HMMsearch
[2024-01-24 11:59:30,169] [INFO] Running command: hmmsearch --tblout GCF_003324525.1_ASM332452v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4adfff29-e7d3-403e-804a-ff26cbea79dd/dqc_reference/reference_markers.hmm GCF_003324525.1_ASM332452v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:30,470] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:30,471] [INFO] Found 6/6 markers.
[2024-01-24 11:59:30,513] [INFO] Query marker FASTA was written to GCF_003324525.1_ASM332452v1_genomic.fna/markers.fasta
[2024-01-24 11:59:30,514] [INFO] Task started: Blastn
[2024-01-24 11:59:30,514] [INFO] Running command: blastn -query GCF_003324525.1_ASM332452v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4adfff29-e7d3-403e-804a-ff26cbea79dd/dqc_reference/reference_markers.fasta -out GCF_003324525.1_ASM332452v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:31,145] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:31,148] [INFO] Selected 21 target genomes.
[2024-01-24 11:59:31,149] [INFO] Target genome list was writen to GCF_003324525.1_ASM332452v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:31,158] [INFO] Task started: fastANI
[2024-01-24 11:59:31,158] [INFO] Running command: fastANI --query /var/lib/cwl/stg26dca8f1-04c9-4a6f-9145-77cd7f33cbc4/GCF_003324525.1_ASM332452v1_genomic.fna.gz --refList GCF_003324525.1_ASM332452v1_genomic.fna/target_genomes.txt --output GCF_003324525.1_ASM332452v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:48,637] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:48,638] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4adfff29-e7d3-403e-804a-ff26cbea79dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:48,638] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4adfff29-e7d3-403e-804a-ff26cbea79dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:48,653] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:48,653] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:48,653] [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 hurinus	strain=ZR32	GCA_003324525.1	2201324	2201324	type	True	100.0	1282	1283	95	conclusive
Mucilaginibacter roseus	strain=LMG 28454	GCA_021215455.1	1528868	1528868	type	True	78.0359	287	1283	95	below_threshold
Mucilaginibacter limnophilus	strain=YBJ-36	GCA_004005815.1	1932778	1932778	type	True	77.9975	318	1283	95	below_threshold
Mucilaginibacter xinganensis	strain=BJC16-A31	GCA_002257585.1	1234841	1234841	type	True	77.6525	169	1283	95	below_threshold
Mucilaginibacter terrigena	strain=17JY9-4	GCA_004168255.1	2492395	2492395	type	True	77.4985	202	1283	95	below_threshold
Mucilaginibacter gossypii	strain=Gh-67	GCA_900100945.1	551996	551996	type	True	77.4751	196	1283	95	below_threshold
Mucilaginibacter corticis	strain=MAH-19	GCA_007558865.1	2597670	2597670	type	True	77.4022	194	1283	95	below_threshold
Mucilaginibacter celer	strain=HYN0043	GCA_003576455.2	2305508	2305508	type	True	77.3797	201	1283	95	below_threshold
Mucilaginibacter gotjawali	strain=CECT 8628	GCA_014191635.1	1550579	1550579	type	True	77.3762	165	1283	95	below_threshold
Mucilaginibacter rubeus	strain=CGMCC 1.15913	GCA_014643835.1	2027860	2027860	suspected-type	True	77.367	210	1283	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	77.2875	146	1283	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=CCM 8625	GCA_014635525.1	1812349	1812349	type	True	77.2109	197	1283	95	below_threshold
Mucilaginibacter endophyticus	strain=RS1	GCA_003351025.1	2675003	2675003	type	True	77.1916	204	1283	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	77.1825	198	1283	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=DSM 100995	GCA_014196695.1	1812349	1812349	type	True	77.1824	198	1283	95	below_threshold
Mucilaginibacter gossypiicola	strain=Gh-48	GCA_900110105.1	551995	551995	type	True	77.1221	204	1283	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	77.1042	178	1283	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	77.0942	203	1283	95	below_threshold
Mucilaginibacter terrenus	strain=ZH6	GCA_003432065.1	2482727	2482727	type	True	76.9589	184	1283	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:48,656] [INFO] DFAST Taxonomy check result was written to GCF_003324525.1_ASM332452v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:48,657] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:48,657] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:48,657] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4adfff29-e7d3-403e-804a-ff26cbea79dd/dqc_reference/checkm_data
[2024-01-24 11:59:48,659] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:48,703] [INFO] Task started: CheckM
[2024-01-24 11:59:48,703] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003324525.1_ASM332452v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003324525.1_ASM332452v1_genomic.fna/checkm_input GCF_003324525.1_ASM332452v1_genomic.fna/checkm_result
[2024-01-24 12:00:36,572] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:36,573] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:36,598] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:36,598] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:36,599] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003324525.1_ASM332452v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:36,599] [INFO] Task started: Blastn
[2024-01-24 12:00:36,599] [INFO] Running command: blastn -query GCF_003324525.1_ASM332452v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4adfff29-e7d3-403e-804a-ff26cbea79dd/dqc_reference/reference_markers_gtdb.fasta -out GCF_003324525.1_ASM332452v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:37,425] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:37,428] [INFO] Selected 20 target genomes.
[2024-01-24 12:00:37,429] [INFO] Target genome list was writen to GCF_003324525.1_ASM332452v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:37,443] [INFO] Task started: fastANI
[2024-01-24 12:00:37,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg26dca8f1-04c9-4a6f-9145-77cd7f33cbc4/GCF_003324525.1_ASM332452v1_genomic.fna.gz --refList GCF_003324525.1_ASM332452v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003324525.1_ASM332452v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:55,266] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:55,288] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:55,288] [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_003324525.1	s__Mucilaginibacter hurinus	100.0	1282	1283	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_004005815.1	s__Mucilaginibacter limnophilus	77.997	318	1283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223065.1	s__Mucilaginibacter sp015223065	77.6885	291	1283	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	77.6022	176	1283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100945.1	s__Mucilaginibacter gossypii	77.4911	195	1283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	96.19	95.83	0.85	0.84	10	-
GCF_007971525.1	s__Mucilaginibacter ginsenosidivorax	77.4469	205	1283	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	77.4358	213	1283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576455.2	s__Mucilaginibacter celer	77.4225	201	1283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007558865.1	s__Mucilaginibacter corticis	77.4022	194	1283	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	77.3913	195	1283	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	77.3885	200	1283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	95.64	95.64	0.92	0.92	2	-
GCF_014643835.1	s__Mucilaginibacter rubeus	77.367	210	1283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	97.62	97.51	0.93	0.92	3	-
GCF_003635105.1	s__Mucilaginibacter sp003635105	77.3547	206	1283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009928685.1	s__Mucilaginibacter sp009928685	77.2679	147	1283	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	77.2107	203	1283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.12	98.24	0.94	0.88	3	-
GCF_004378255.1	s__Mucilaginibacter phyllosphaerae	77.1825	198	1283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	100.00	100.00	1.00	1.00	3	-
GCA_002403905.1	s__Mucilaginibacter sp002403905	77.076	149	1283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.52	99.50	0.82	0.82	3	-
GCA_013288465.1	s__Mucilaginibacter sp013288465	76.9749	89	1283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003432065.1	s__Mucilaginibacter sp003432065	76.9451	185	1283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903864275.1	s__Mucilaginibacter sp903864275	76.7789	158	1283	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	100.00	100.00	0.99	0.99	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:55,290] [INFO] GTDB search result was written to GCF_003324525.1_ASM332452v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:55,291] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:55,296] [INFO] DFAST_QC result json was written to GCF_003324525.1_ASM332452v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:55,296] [INFO] DFAST_QC completed!
[2024-01-24 12:00:55,296] [INFO] Total running time: 0h1m43s