[2024-01-25 19:04:05,800] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:04:05,802] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:04:05,803] [INFO] DQC Reference Directory: /var/lib/cwl/stg357a942e-5a64-4a05-85b4-49f9aebc9263/dqc_reference
[2024-01-25 19:04:06,964] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:04:06,965] [INFO] Task started: Prodigal
[2024-01-25 19:04:06,965] [INFO] Running command: gunzip -c /var/lib/cwl/stgad5a2b54-2336-4580-ba28-e25b25796860/GCF_024721155.1_ASM2472115v1_genomic.fna.gz | prodigal -d GCF_024721155.1_ASM2472115v1_genomic.fna/cds.fna -a GCF_024721155.1_ASM2472115v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:04:32,758] [INFO] Task succeeded: Prodigal
[2024-01-25 19:04:32,758] [INFO] Task started: HMMsearch
[2024-01-25 19:04:32,758] [INFO] Running command: hmmsearch --tblout GCF_024721155.1_ASM2472115v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg357a942e-5a64-4a05-85b4-49f9aebc9263/dqc_reference/reference_markers.hmm GCF_024721155.1_ASM2472115v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:04:33,089] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:04:33,091] [INFO] Found 6/6 markers.
[2024-01-25 19:04:33,147] [INFO] Query marker FASTA was written to GCF_024721155.1_ASM2472115v1_genomic.fna/markers.fasta
[2024-01-25 19:04:33,147] [INFO] Task started: Blastn
[2024-01-25 19:04:33,147] [INFO] Running command: blastn -query GCF_024721155.1_ASM2472115v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg357a942e-5a64-4a05-85b4-49f9aebc9263/dqc_reference/reference_markers.fasta -out GCF_024721155.1_ASM2472115v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:33,756] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:33,759] [INFO] Selected 17 target genomes.
[2024-01-25 19:04:33,760] [INFO] Target genome list was writen to GCF_024721155.1_ASM2472115v1_genomic.fna/target_genomes.txt
[2024-01-25 19:04:33,768] [INFO] Task started: fastANI
[2024-01-25 19:04:33,768] [INFO] Running command: fastANI --query /var/lib/cwl/stgad5a2b54-2336-4580-ba28-e25b25796860/GCF_024721155.1_ASM2472115v1_genomic.fna.gz --refList GCF_024721155.1_ASM2472115v1_genomic.fna/target_genomes.txt --output GCF_024721155.1_ASM2472115v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:04:51,837] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:51,838] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg357a942e-5a64-4a05-85b4-49f9aebc9263/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:04:51,838] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg357a942e-5a64-4a05-85b4-49f9aebc9263/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:04:51,850] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:04:51,850] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:04:51,850] [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	79.8269	811	2400	95	below_threshold
Mucilaginibacter mallensis	strain=MP1X4	GCA_900105165.1	652787	652787	type	True	78.3335	462	2400	95	below_threshold
Mucilaginibacter frigoritolerans	strain=ATCC BAA-1854	GCA_007830615.1	652788	652788	type	True	78.2893	514	2400	95	below_threshold
Mucilaginibacter gotjawali	strain=CECT 8628	GCA_014191635.1	1550579	1550579	type	True	78.0498	543	2400	95	below_threshold
Mucilaginibacter gotjawali	strain=SA3-7	GCA_002355435.1	1550579	1550579	type	True	78.0218	543	2400	95	below_threshold
Mucilaginibacter ginsenosidivorax	strain=KHI28	GCA_007971525.1	862126	862126	type	True	77.8096	501	2400	95	below_threshold
Mucilaginibacter lappiensis	strain=ATCC BAA-1855	GCA_900155965.1	354630	354630	type	True	77.7457	399	2400	95	below_threshold
Mucilaginibacter pineti	strain=47C3B	GCA_900101875.1	1391627	1391627	type	True	77.7095	434	2400	95	below_threshold
Mucilaginibacter lappiensis	strain=ANJLi2	GCA_014200545.1	354630	354630	type	True	77.6655	397	2400	95	below_threshold
Mucilaginibacter terrigena	strain=17JY9-4	GCA_004168255.1	2492395	2492395	type	True	77.6198	337	2400	95	below_threshold
Mucilaginibacter gossypiicola	strain=Gh-48	GCA_900110105.1	551995	551995	type	True	77.3801	431	2400	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	77.3608	335	2400	95	below_threshold
Mucilaginibacter pallidiroseus	strain=dk17	GCA_007846085.1	2599295	2599295	type	True	77.3575	234	2400	95	below_threshold
Mucilaginibacter celer	strain=HYN0043	GCA_003576455.2	2305508	2305508	type	True	77.2725	439	2400	95	below_threshold
Mucilaginibacter roseus	strain=LMG 28454	GCA_021215455.1	1528868	1528868	type	True	77.2174	247	2400	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	77.1977	229	2400	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	77.0892	277	2400	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:04:51,851] [INFO] DFAST Taxonomy check result was written to GCF_024721155.1_ASM2472115v1_genomic.fna/tc_result.tsv
[2024-01-25 19:04:51,852] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:04:51,852] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:04:51,852] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg357a942e-5a64-4a05-85b4-49f9aebc9263/dqc_reference/checkm_data
[2024-01-25 19:04:51,853] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:04:51,920] [INFO] Task started: CheckM
[2024-01-25 19:04:51,920] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024721155.1_ASM2472115v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024721155.1_ASM2472115v1_genomic.fna/checkm_input GCF_024721155.1_ASM2472115v1_genomic.fna/checkm_result
[2024-01-25 19:06:00,325] [INFO] Task succeeded: CheckM
[2024-01-25 19:06:00,326] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:06:00,347] [INFO] ===== Completeness check finished =====
[2024-01-25 19:06:00,348] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:06:00,348] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024721155.1_ASM2472115v1_genomic.fna/markers.fasta)
[2024-01-25 19:06:00,349] [INFO] Task started: Blastn
[2024-01-25 19:06:00,349] [INFO] Running command: blastn -query GCF_024721155.1_ASM2472115v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg357a942e-5a64-4a05-85b4-49f9aebc9263/dqc_reference/reference_markers_gtdb.fasta -out GCF_024721155.1_ASM2472115v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:01,128] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:01,131] [INFO] Selected 15 target genomes.
[2024-01-25 19:06:01,131] [INFO] Target genome list was writen to GCF_024721155.1_ASM2472115v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:06:01,139] [INFO] Task started: fastANI
[2024-01-25 19:06:01,140] [INFO] Running command: fastANI --query /var/lib/cwl/stgad5a2b54-2336-4580-ba28-e25b25796860/GCF_024721155.1_ASM2472115v1_genomic.fna.gz --refList GCF_024721155.1_ASM2472115v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024721155.1_ASM2472115v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:06:19,215] [INFO] Task succeeded: fastANI
[2024-01-25 19:06:19,224] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:06:19,224] [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_900142915.1	s__Mucilaginibacter sp900142915	80.7009	1177	2400	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	79.8199	813	2400	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	78.9744	460	2400	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	78.2817	515	2400	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	78.2537	465	2400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013288235.1	s__Mucilaginibacter sp013288235	78.0392	390	2400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.30	99.08	0.67	0.66	3	-
GCF_002355435.1	s__Mucilaginibacter gotjawali	78.0272	541	2400	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	78.0181	435	2400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.87	99.70	0.98	0.97	4	-
GCA_903915155.1	s__Mucilaginibacter sp903915155	77.9815	327	2400	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	77.9107	439	2400	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	77.8038	502	2400	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	77.7455	433	2400	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	77.7126	505	2400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	100.00	100.00	0.99	0.99	4	-
GCF_900101875.1	s__Mucilaginibacter pineti	77.7095	434	2400	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903913935.1	s__Mucilaginibacter sp903913935	77.6717	420	2400	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 19:06:19,235] [INFO] GTDB search result was written to GCF_024721155.1_ASM2472115v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:06:19,235] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:06:19,239] [INFO] DFAST_QC result json was written to GCF_024721155.1_ASM2472115v1_genomic.fna/dqc_result.json
[2024-01-25 19:06:19,239] [INFO] DFAST_QC completed!
[2024-01-25 19:06:19,239] [INFO] Total running time: 0h2m13s