[2024-01-25 17:38:05,441] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:38:05,442] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:38:05,442] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d84df34-db44-408d-b4e5-afac8acdd6a6/dqc_reference
[2024-01-25 17:38:06,564] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:38:06,569] [INFO] Task started: Prodigal
[2024-01-25 17:38:06,570] [INFO] Running command: gunzip -c /var/lib/cwl/stgd7c6db9e-9300-44b2-925d-86e52cc48906/GCF_013283875.1_ASM1328387v1_genomic.fna.gz | prodigal -d GCF_013283875.1_ASM1328387v1_genomic.fna/cds.fna -a GCF_013283875.1_ASM1328387v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:38:30,498] [INFO] Task succeeded: Prodigal
[2024-01-25 17:38:30,498] [INFO] Task started: HMMsearch
[2024-01-25 17:38:30,498] [INFO] Running command: hmmsearch --tblout GCF_013283875.1_ASM1328387v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d84df34-db44-408d-b4e5-afac8acdd6a6/dqc_reference/reference_markers.hmm GCF_013283875.1_ASM1328387v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:38:30,789] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:38:30,790] [INFO] Found 6/6 markers.
[2024-01-25 17:38:30,837] [INFO] Query marker FASTA was written to GCF_013283875.1_ASM1328387v1_genomic.fna/markers.fasta
[2024-01-25 17:38:30,838] [INFO] Task started: Blastn
[2024-01-25 17:38:30,838] [INFO] Running command: blastn -query GCF_013283875.1_ASM1328387v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d84df34-db44-408d-b4e5-afac8acdd6a6/dqc_reference/reference_markers.fasta -out GCF_013283875.1_ASM1328387v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:31,431] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:31,437] [INFO] Selected 17 target genomes.
[2024-01-25 17:38:31,438] [INFO] Target genome list was writen to GCF_013283875.1_ASM1328387v1_genomic.fna/target_genomes.txt
[2024-01-25 17:38:31,443] [INFO] Task started: fastANI
[2024-01-25 17:38:31,443] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7c6db9e-9300-44b2-925d-86e52cc48906/GCF_013283875.1_ASM1328387v1_genomic.fna.gz --refList GCF_013283875.1_ASM1328387v1_genomic.fna/target_genomes.txt --output GCF_013283875.1_ASM1328387v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:38:49,321] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:49,322] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d84df34-db44-408d-b4e5-afac8acdd6a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:38:49,322] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d84df34-db44-408d-b4e5-afac8acdd6a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:38:49,333] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:38:49,333] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:38:49,333] [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 mali	strain=G2-14	GCA_013283875.1	2740462	2740462	type	True	100.0	2011	2014	95	conclusive
Mucilaginibacter boryungensis	strain=KCTC 23157	GCA_015221995.1	768480	768480	type	True	79.2887	748	2014	95	below_threshold
Mucilaginibacter myungsuensis	strain=KCTC 22746	GCA_015222005.1	649104	649104	type	True	78.1974	527	2014	95	below_threshold
Mucilaginibacter yixingensis	strain=DSM 26809	GCA_003050755.1	1295612	1295612	type	True	77.8265	466	2014	95	below_threshold
Mucilaginibacter roseus	strain=LMG 28454	GCA_021215455.1	1528868	1528868	type	True	77.6939	233	2014	95	below_threshold
Mucilaginibacter terrigena	strain=17JY9-4	GCA_004168255.1	2492395	2492395	type	True	77.6281	381	2014	95	below_threshold
Mucilaginibacter oryzae	strain=DSM 19975	GCA_003148845.1	468058	468058	type	True	77.5435	378	2014	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=CCM 8625	GCA_014635525.1	1812349	1812349	type	True	77.5275	354	2014	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=DSM 100995	GCA_014196695.1	1812349	1812349	type	True	77.4387	360	2014	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	77.4231	240	2014	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	77.4183	353	2014	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	77.417	374	2014	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	77.3565	359	2014	95	below_threshold
Mucilaginibacter galii	strain=CCM 8711	GCA_014635825.1	2005073	2005073	type	True	77.3093	265	2014	95	below_threshold
Mucilaginibacter rubeus	strain=CGMCC 1.15913	GCA_014643835.1	2027860	2027860	suspected-type	True	77.2267	359	2014	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	77.215	263	2014	95	below_threshold
Mucilaginibacter gossypii	strain=Gh-67	GCA_900100945.1	551996	551996	type	True	77.191	346	2014	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:38:49,334] [INFO] DFAST Taxonomy check result was written to GCF_013283875.1_ASM1328387v1_genomic.fna/tc_result.tsv
[2024-01-25 17:38:49,335] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:38:49,335] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:38:49,335] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d84df34-db44-408d-b4e5-afac8acdd6a6/dqc_reference/checkm_data
[2024-01-25 17:38:49,336] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:38:49,395] [INFO] Task started: CheckM
[2024-01-25 17:38:49,395] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013283875.1_ASM1328387v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013283875.1_ASM1328387v1_genomic.fna/checkm_input GCF_013283875.1_ASM1328387v1_genomic.fna/checkm_result
[2024-01-25 17:39:52,844] [INFO] Task succeeded: CheckM
[2024-01-25 17:39:52,845] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:39:52,901] [INFO] ===== Completeness check finished =====
[2024-01-25 17:39:52,902] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:39:52,904] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013283875.1_ASM1328387v1_genomic.fna/markers.fasta)
[2024-01-25 17:39:52,904] [INFO] Task started: Blastn
[2024-01-25 17:39:52,904] [INFO] Running command: blastn -query GCF_013283875.1_ASM1328387v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d84df34-db44-408d-b4e5-afac8acdd6a6/dqc_reference/reference_markers_gtdb.fasta -out GCF_013283875.1_ASM1328387v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:53,765] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:53,768] [INFO] Selected 15 target genomes.
[2024-01-25 17:39:53,768] [INFO] Target genome list was writen to GCF_013283875.1_ASM1328387v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:39:53,782] [INFO] Task started: fastANI
[2024-01-25 17:39:53,782] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7c6db9e-9300-44b2-925d-86e52cc48906/GCF_013283875.1_ASM1328387v1_genomic.fna.gz --refList GCF_013283875.1_ASM1328387v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013283875.1_ASM1328387v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:40:10,439] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:10,449] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:40:10,450] [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_013283875.1	s__Mucilaginibacter mali	100.0	2012	2014	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_015221995.1	s__Mucilaginibacter boryungensis	79.2945	746	2014	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015222005.1	s__Mucilaginibacter myungsuensis	78.1979	527	2014	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	77.8304	467	2014	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	77.8224	337	2014	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	95.64	95.64	0.92	0.92	2	-
GCF_015223065.1	s__Mucilaginibacter sp015223065	77.5882	315	2014	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148845.1	s__Mucilaginibacter oryzae	77.5444	378	2014	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	77.456	380	2014	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004378255.1	s__Mucilaginibacter phyllosphaerae	77.4031	354	2014	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_001705515.1	s__Mucilaginibacter sp001705515	77.3665	383	2014	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	77.2733	249	2014	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	77.268	268	2014	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643835.1	s__Mucilaginibacter rubeus	77.2209	359	2014	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	97.62	97.51	0.93	0.92	3	-
GCF_001911425.1	s__Mucilaginibacter polytrichastri	77.215	291	2014	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_013289045.1	s__Mucilaginibacter sp013289045	76.7393	188	2014	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 17:40:10,451] [INFO] GTDB search result was written to GCF_013283875.1_ASM1328387v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:40:10,452] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:40:10,455] [INFO] DFAST_QC result json was written to GCF_013283875.1_ASM1328387v1_genomic.fna/dqc_result.json
[2024-01-25 17:40:10,455] [INFO] DFAST_QC completed!
[2024-01-25 17:40:10,455] [INFO] Total running time: 0h2m5s