[2024-01-24 13:49:27,422] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:27,424] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:27,424] [INFO] DQC Reference Directory: /var/lib/cwl/stg386bfa28-a36d-42d1-80d5-927f2f58f8ae/dqc_reference
[2024-01-24 13:49:28,822] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:28,823] [INFO] Task started: Prodigal
[2024-01-24 13:49:28,823] [INFO] Running command: gunzip -c /var/lib/cwl/stgf504f444-196e-4de2-92ff-640f2b2f3500/GCF_000376945.1_ASM37694v1_genomic.fna.gz | prodigal -d GCF_000376945.1_ASM37694v1_genomic.fna/cds.fna -a GCF_000376945.1_ASM37694v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:41,253] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:41,254] [INFO] Task started: HMMsearch
[2024-01-24 13:49:41,254] [INFO] Running command: hmmsearch --tblout GCF_000376945.1_ASM37694v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg386bfa28-a36d-42d1-80d5-927f2f58f8ae/dqc_reference/reference_markers.hmm GCF_000376945.1_ASM37694v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:41,594] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:41,596] [INFO] Found 6/6 markers.
[2024-01-24 13:49:41,646] [INFO] Query marker FASTA was written to GCF_000376945.1_ASM37694v1_genomic.fna/markers.fasta
[2024-01-24 13:49:41,646] [INFO] Task started: Blastn
[2024-01-24 13:49:41,646] [INFO] Running command: blastn -query GCF_000376945.1_ASM37694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg386bfa28-a36d-42d1-80d5-927f2f58f8ae/dqc_reference/reference_markers.fasta -out GCF_000376945.1_ASM37694v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:42,436] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:42,439] [INFO] Selected 27 target genomes.
[2024-01-24 13:49:42,440] [INFO] Target genome list was writen to GCF_000376945.1_ASM37694v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:42,449] [INFO] Task started: fastANI
[2024-01-24 13:49:42,449] [INFO] Running command: fastANI --query /var/lib/cwl/stgf504f444-196e-4de2-92ff-640f2b2f3500/GCF_000376945.1_ASM37694v1_genomic.fna.gz --refList GCF_000376945.1_ASM37694v1_genomic.fna/target_genomes.txt --output GCF_000376945.1_ASM37694v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:00,757] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:00,758] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg386bfa28-a36d-42d1-80d5-927f2f58f8ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:00,759] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg386bfa28-a36d-42d1-80d5-927f2f58f8ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:00,777] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:00,777] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:00,777] [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
Leeia oryzae	strain=DSM 17879	GCA_000376945.1	356662	356662	type	True	100.0	1246	1251	95	conclusive
Leeia aquatica	strain=IMCC25680	GCA_012641365.1	2725557	2725557	type	True	77.2033	233	1251	95	below_threshold
Vogesella mureinivorans	strain=389	GCA_007644035.2	657276	657276	type	True	76.6972	151	1251	95	below_threshold
Silvimonas terrae	strain=DSM 18233	GCA_014202765.1	300266	300266	type	True	76.4836	108	1251	95	below_threshold
Silvimonas amylolytica	strain=CGMCC 1.8860	GCA_014645555.1	449663	449663	type	True	76.4817	101	1251	95	below_threshold
Methylovorus menthalis	strain=VKM B-2663	GCA_020523625.1	1002227	1002227	type	True	76.3672	52	1251	95	below_threshold
Chitinibacter tainanensis	strain=DSM 15459	GCA_000429785.1	230667	230667	type	True	76.2163	83	1251	95	below_threshold
Pseudoduganella plicata	strain=DSM 17505	GCA_004421005.1	321984	321984	type	True	75.8661	57	1251	95	below_threshold
Pseudoduganella rivuli	strain=FT92W	GCA_009674485.1	2666085	2666085	type	True	75.8541	75	1251	95	below_threshold
Massilia oculi	strain=CCUG 43427	GCA_003143515.1	945844	945844	type	True	75.8094	60	1251	95	below_threshold
Chitinimonas taiwanensis	strain=DSM 18899	GCA_900119825.1	240412	240412	type	True	75.7039	104	1251	95	below_threshold
Pseudoduganella plicata	strain=KCTC 12344	GCA_014651435.1	321984	321984	type	True	75.6083	55	1251	95	below_threshold
Pseudoduganella lurida	strain=CGMCC 1.10822	GCA_007830455.1	1036180	1036180	type	True	75.402	56	1251	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:00,780] [INFO] DFAST Taxonomy check result was written to GCF_000376945.1_ASM37694v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:00,780] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:00,780] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:00,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg386bfa28-a36d-42d1-80d5-927f2f58f8ae/dqc_reference/checkm_data
[2024-01-24 13:50:00,782] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:00,822] [INFO] Task started: CheckM
[2024-01-24 13:50:00,822] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000376945.1_ASM37694v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000376945.1_ASM37694v1_genomic.fna/checkm_input GCF_000376945.1_ASM37694v1_genomic.fna/checkm_result
[2024-01-24 13:50:40,234] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:40,236] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:40,253] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:40,254] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:40,254] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000376945.1_ASM37694v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:40,254] [INFO] Task started: Blastn
[2024-01-24 13:50:40,255] [INFO] Running command: blastn -query GCF_000376945.1_ASM37694v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg386bfa28-a36d-42d1-80d5-927f2f58f8ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_000376945.1_ASM37694v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:41,403] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:41,408] [INFO] Selected 27 target genomes.
[2024-01-24 13:50:41,408] [INFO] Target genome list was writen to GCF_000376945.1_ASM37694v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:41,461] [INFO] Task started: fastANI
[2024-01-24 13:50:41,462] [INFO] Running command: fastANI --query /var/lib/cwl/stgf504f444-196e-4de2-92ff-640f2b2f3500/GCF_000376945.1_ASM37694v1_genomic.fna.gz --refList GCF_000376945.1_ASM37694v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000376945.1_ASM37694v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:58,548] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:58,575] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:58,575] [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_000376945.1	s__Leeia oryzae	100.0	1246	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Leeiaceae;g__Leeia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012641365.1	s__Leeia aquatica	77.2025	234	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Leeiaceae;g__Leeia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019084025.1	s__DAT-1 sp019084025	76.7555	79	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__DAT-1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013911085.1	s__Aquitalea magnusonii_C	76.7341	141	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000335715.1	s__Vogesella sp000335715	76.7313	124	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902829295.1	s__Vogesella oryzae	76.5833	143	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Vogesella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202765.1	s__Silvimonas terrae	76.4745	107	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Silvimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429785.1	s__Chitinibacter tainanensis	76.2156	83	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinibacter	95.0	96.34	96.34	0.90	0.90	2	-
GCF_011601265.1	s__Iodobacter sp011601265	76.1173	67	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Iodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005503445.1	s__Chitinivorax sp005503445	76.0198	73	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SCOH01;g__Chitinivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009760905.1	s__Chitinibacter sp009760905	75.9119	60	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000383895.1	s__Duganella zoogloeoides	75.8911	51	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	96.93	95.29	0.93	0.88	4	-
GCF_004421005.1	s__Pseudoduganella plicata	75.835	55	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001423125.1	s__Duganella sp001423125	75.8017	57	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107095.1	s__Collimonas sp900107095	75.7861	56	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004298905.1	s__SCTK01 sp004298905	75.7497	50	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCTK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119825.1	s__Chitinimonas taiwanensis	75.7086	101	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__Chitinimonas	95.0	96.92	96.91	0.93	0.93	3	-
GCA_013284265.1	s__Rugamonas sp013284265	75.566	82	1251	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rugamonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:58,577] [INFO] GTDB search result was written to GCF_000376945.1_ASM37694v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:58,577] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:58,581] [INFO] DFAST_QC result json was written to GCF_000376945.1_ASM37694v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:58,581] [INFO] DFAST_QC completed!
[2024-01-24 13:50:58,582] [INFO] Total running time: 0h1m31s