[2024-01-24 11:51:36,075] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:36,077] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:36,077] [INFO] DQC Reference Directory: /var/lib/cwl/stg46e383b7-01e3-41eb-941e-41cf7f057f61/dqc_reference
[2024-01-24 11:51:37,387] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:37,388] [INFO] Task started: Prodigal
[2024-01-24 11:51:37,388] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c1baa1c-6b54-45d6-aa50-1f87b0583619/GCF_024055575.1_ASM2405557v1_genomic.fna.gz | prodigal -d GCF_024055575.1_ASM2405557v1_genomic.fna/cds.fna -a GCF_024055575.1_ASM2405557v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:52:07,766] [INFO] Task succeeded: Prodigal
[2024-01-24 11:52:07,767] [INFO] Task started: HMMsearch
[2024-01-24 11:52:07,767] [INFO] Running command: hmmsearch --tblout GCF_024055575.1_ASM2405557v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46e383b7-01e3-41eb-941e-41cf7f057f61/dqc_reference/reference_markers.hmm GCF_024055575.1_ASM2405557v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:52:08,122] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:52:08,124] [INFO] Found 6/6 markers.
[2024-01-24 11:52:08,182] [INFO] Query marker FASTA was written to GCF_024055575.1_ASM2405557v1_genomic.fna/markers.fasta
[2024-01-24 11:52:08,183] [INFO] Task started: Blastn
[2024-01-24 11:52:08,183] [INFO] Running command: blastn -query GCF_024055575.1_ASM2405557v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46e383b7-01e3-41eb-941e-41cf7f057f61/dqc_reference/reference_markers.fasta -out GCF_024055575.1_ASM2405557v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:08,782] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:08,787] [INFO] Selected 18 target genomes.
[2024-01-24 11:52:08,787] [INFO] Target genome list was writen to GCF_024055575.1_ASM2405557v1_genomic.fna/target_genomes.txt
[2024-01-24 11:52:08,795] [INFO] Task started: fastANI
[2024-01-24 11:52:08,795] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c1baa1c-6b54-45d6-aa50-1f87b0583619/GCF_024055575.1_ASM2405557v1_genomic.fna.gz --refList GCF_024055575.1_ASM2405557v1_genomic.fna/target_genomes.txt --output GCF_024055575.1_ASM2405557v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:52:24,215] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:24,215] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46e383b7-01e3-41eb-941e-41cf7f057f61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:52:24,215] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46e383b7-01e3-41eb-941e-41cf7f057f61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:52:24,229] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:52:24,229] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:52:24,229] [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	79.3114	763	2309	95	below_threshold
Mucilaginibacter frigoritolerans	strain=ATCC BAA-1854	GCA_007830615.1	652788	652788	type	True	78.1374	445	2309	95	below_threshold
Mucilaginibacter gotjawali	strain=CECT 8628	GCA_014191635.1	1550579	1550579	type	True	77.8649	539	2309	95	below_threshold
Mucilaginibacter gotjawali	strain=SA3-7	GCA_002355435.1	1550579	1550579	type	True	77.8525	552	2309	95	below_threshold
Mucilaginibacter mallensis	strain=MP1X4	GCA_900105165.1	652787	652787	type	True	77.7006	380	2309	95	below_threshold
Mucilaginibacter lappiensis	strain=ANJLi2	GCA_014200545.1	354630	354630	type	True	77.5593	356	2309	95	below_threshold
Mucilaginibacter lappiensis	strain=ATCC BAA-1855	GCA_900155965.1	354630	354630	type	True	77.5529	349	2309	95	below_threshold
Mucilaginibacter corticis	strain=MAH-19	GCA_007558865.1	2597670	2597670	type	True	77.5079	309	2309	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	77.4915	358	2309	95	below_threshold
Mucilaginibacter pallidiroseus	strain=dk17	GCA_007846085.1	2599295	2599295	type	True	77.4851	243	2309	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=CCM 8625	GCA_014635525.1	1812349	1812349	type	True	77.436	344	2309	95	below_threshold
Mucilaginibacter segetis	strain=SD-g	GCA_016522075.1	2793071	2793071	type	True	77.4255	225	2309	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=DSM 100995	GCA_014196695.1	1812349	1812349	type	True	77.3875	343	2309	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	77.3781	350	2309	95	below_threshold
Mucilaginibacter roseus	strain=LMG 28454	GCA_021215455.1	1528868	1528868	type	True	77.3666	234	2309	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	77.2927	283	2309	95	below_threshold
Mucilaginibacter polytrichastri	strain=RG4-7	GCA_001911425.1	1302689	1302689	type	True	77.2638	263	2309	95	below_threshold
Mucilaginibacter polytrichastri	strain=DSM 26907	GCA_900116355.1	1302689	1302689	type	True	77.1145	251	2309	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:52:24,231] [INFO] DFAST Taxonomy check result was written to GCF_024055575.1_ASM2405557v1_genomic.fna/tc_result.tsv
[2024-01-24 11:52:24,231] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:52:24,231] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:52:24,232] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46e383b7-01e3-41eb-941e-41cf7f057f61/dqc_reference/checkm_data
[2024-01-24 11:52:24,232] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:52:24,296] [INFO] Task started: CheckM
[2024-01-24 11:52:24,296] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024055575.1_ASM2405557v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024055575.1_ASM2405557v1_genomic.fna/checkm_input GCF_024055575.1_ASM2405557v1_genomic.fna/checkm_result
[2024-01-24 11:53:44,720] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:44,722] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:44,747] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:44,747] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:44,748] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024055575.1_ASM2405557v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:44,748] [INFO] Task started: Blastn
[2024-01-24 11:53:44,748] [INFO] Running command: blastn -query GCF_024055575.1_ASM2405557v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46e383b7-01e3-41eb-941e-41cf7f057f61/dqc_reference/reference_markers_gtdb.fasta -out GCF_024055575.1_ASM2405557v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:45,600] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:45,607] [INFO] Selected 13 target genomes.
[2024-01-24 11:53:45,608] [INFO] Target genome list was writen to GCF_024055575.1_ASM2405557v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:45,618] [INFO] Task started: fastANI
[2024-01-24 11:53:45,618] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c1baa1c-6b54-45d6-aa50-1f87b0583619/GCF_024055575.1_ASM2405557v1_genomic.fna.gz --refList GCF_024055575.1_ASM2405557v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024055575.1_ASM2405557v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:57,570] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:57,582] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:53:57,582] [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	79.5935	976	2309	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	79.3184	762	2309	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	78.4468	440	2309	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	78.2598	410	2309	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.30	99.08	0.67	0.66	3	-
GCF_007830615.1	s__Mucilaginibacter frigoritolerans	78.1459	444	2309	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002413785.1	s__Mucilaginibacter sp002413785	78.005	477	2309	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.87	99.70	0.98	0.97	4	-
GCA_903864275.1	s__Mucilaginibacter sp903864275	77.8976	543	2309	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	100.00	100.00	0.99	0.99	4	-
GCA_903915155.1	s__Mucilaginibacter sp903915155	77.8922	330	2309	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	77.8519	552	2309	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_013288685.1	s__Mucilaginibacter sp013288685	77.8244	415	2309	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	77.6969	185	2309	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	77.6349	426	2309	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013286565.1	s__Mucilaginibacter sp013286565	77.1152	233	2309	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 11:53:57,584] [INFO] GTDB search result was written to GCF_024055575.1_ASM2405557v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:57,584] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:57,588] [INFO] DFAST_QC result json was written to GCF_024055575.1_ASM2405557v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:57,588] [INFO] DFAST_QC completed!
[2024-01-24 11:53:57,588] [INFO] Total running time: 0h2m22s