[2024-01-24 13:58:55,881] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:55,885] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:55,885] [INFO] DQC Reference Directory: /var/lib/cwl/stge6cd72c5-910a-479b-8b98-f8ad58d70290/dqc_reference
[2024-01-24 13:58:57,299] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:57,306] [INFO] Task started: Prodigal
[2024-01-24 13:58:57,306] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e32bab0-9593-461c-833e-e8cc936ae1c5/GCF_002849655.1_ASM284965v1_genomic.fna.gz | prodigal -d GCF_002849655.1_ASM284965v1_genomic.fna/cds.fna -a GCF_002849655.1_ASM284965v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:59:13,053] [INFO] Task succeeded: Prodigal
[2024-01-24 13:59:13,054] [INFO] Task started: HMMsearch
[2024-01-24 13:59:13,054] [INFO] Running command: hmmsearch --tblout GCF_002849655.1_ASM284965v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6cd72c5-910a-479b-8b98-f8ad58d70290/dqc_reference/reference_markers.hmm GCF_002849655.1_ASM284965v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:59:13,402] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:59:13,404] [INFO] Found 6/6 markers.
[2024-01-24 13:59:13,446] [INFO] Query marker FASTA was written to GCF_002849655.1_ASM284965v1_genomic.fna/markers.fasta
[2024-01-24 13:59:13,446] [INFO] Task started: Blastn
[2024-01-24 13:59:13,446] [INFO] Running command: blastn -query GCF_002849655.1_ASM284965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6cd72c5-910a-479b-8b98-f8ad58d70290/dqc_reference/reference_markers.fasta -out GCF_002849655.1_ASM284965v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:14,232] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:14,236] [INFO] Selected 25 target genomes.
[2024-01-24 13:59:14,237] [INFO] Target genome list was writen to GCF_002849655.1_ASM284965v1_genomic.fna/target_genomes.txt
[2024-01-24 13:59:14,265] [INFO] Task started: fastANI
[2024-01-24 13:59:14,265] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e32bab0-9593-461c-833e-e8cc936ae1c5/GCF_002849655.1_ASM284965v1_genomic.fna.gz --refList GCF_002849655.1_ASM284965v1_genomic.fna/target_genomes.txt --output GCF_002849655.1_ASM284965v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:34,143] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:34,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6cd72c5-910a-479b-8b98-f8ad58d70290/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:34,144] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6cd72c5-910a-479b-8b98-f8ad58d70290/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:34,165] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:59:34,165] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:59:34,165] [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
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	79.0147	320	1481	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_013416545.1	645616	645616	type	True	78.9442	320	1481	95	below_threshold
Eoetvoesia caeni	strain=DSM 25520	GCA_003315175.1	645616	645616	type	True	78.9345	319	1481	95	below_threshold
Parapusillimonas granuli	strain=DSM 18079	GCA_014202705.1	380911	380911	type	True	78.6746	410	1481	95	below_threshold
Parapusillimonas granuli	strain=LMG 24012	GCA_013416525.1	380911	380911	type	True	78.5931	406	1481	95	below_threshold
Pusillimonas caeni	strain=KCTC 42353	GCA_003545815.1	1348472	1348472	type	True	78.5565	329	1481	95	below_threshold
Pusillimonas harenae	strain=DSM 25667	GCA_013416515.1	657015	657015	type	True	78.4856	327	1481	95	below_threshold
Pusillimonas harenae	strain=JCM 16917	GCA_004153685.1	657015	657015	type	True	78.4346	330	1481	95	below_threshold
Pusillimonas faecipullorum	strain=CC-YST705	GCA_020539505.1	2755040	2755040	type	True	77.9924	137	1481	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	77.9128	316	1481	95	below_threshold
Paralcaligenes ureilyticus	strain=DSM 24591	GCA_004346225.1	627131	627131	type	True	77.859	259	1481	95	below_threshold
Pusillimonas soli	strain=DSM 25264	GCA_013416335.1	659016	659016	type	True	77.8441	281	1481	95	below_threshold
Pusillimonas soli	strain=KCTC 22455	GCA_004153445.1	659016	659016	type	True	77.843	281	1481	95	below_threshold
Candidimonas nitroreducens	strain=SC-089	GCA_002209565.1	683354	683354	type	True	77.7114	341	1481	95	below_threshold
Achromobacter pulmonis	strain=LMG 26696	GCA_902859765.1	1389932	1389932	type	True	77.6213	262	1481	95	below_threshold
Achromobacter anxifer	strain=LMG 26857	GCA_903652925.1	1287737	1287737	type	True	77.6029	298	1481	95	below_threshold
Achromobacter marplatensis	strain=B2	GCA_002209535.1	470868	470868	type	True	77.1886	259	1481	95	below_threshold
Achromobacter kerstersii	strain=LMG 3441	GCA_902859595.1	1353890	1353890	type	True	77.1536	241	1481	95	below_threshold
Achromobacter denitrificans	strain=NCTC8582	GCA_900444675.1	32002	32002	type	True	77.0628	282	1481	95	below_threshold
Achromobacter denitrificans	strain=FDAARGOS_786	GCA_013267395.1	32002	32002	type	True	77.0015	287	1481	95	below_threshold
Achromobacter denitrificans	strain=LMG 1231	GCA_902859715.1	32002	32002	type	True	76.9454	281	1481	95	below_threshold
Achromobacter denitrificans	strain=NBRC 15125	GCA_001571365.1	32002	32002	type	True	76.9429	278	1481	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	76.3204	71	1481	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.2159	105	1481	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	76.0982	78	1481	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:34,167] [INFO] DFAST Taxonomy check result was written to GCF_002849655.1_ASM284965v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:34,167] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:34,167] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:34,168] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6cd72c5-910a-479b-8b98-f8ad58d70290/dqc_reference/checkm_data
[2024-01-24 13:59:34,168] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:34,211] [INFO] Task started: CheckM
[2024-01-24 13:59:34,211] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002849655.1_ASM284965v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002849655.1_ASM284965v1_genomic.fna/checkm_input GCF_002849655.1_ASM284965v1_genomic.fna/checkm_result
[2024-01-24 14:00:20,512] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:20,514] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:20,536] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:20,537] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:20,537] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002849655.1_ASM284965v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:20,538] [INFO] Task started: Blastn
[2024-01-24 14:00:20,538] [INFO] Running command: blastn -query GCF_002849655.1_ASM284965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6cd72c5-910a-479b-8b98-f8ad58d70290/dqc_reference/reference_markers_gtdb.fasta -out GCF_002849655.1_ASM284965v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:21,993] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:21,997] [INFO] Selected 12 target genomes.
[2024-01-24 14:00:21,998] [INFO] Target genome list was writen to GCF_002849655.1_ASM284965v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:22,007] [INFO] Task started: fastANI
[2024-01-24 14:00:22,007] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e32bab0-9593-461c-833e-e8cc936ae1c5/GCF_002849655.1_ASM284965v1_genomic.fna.gz --refList GCF_002849655.1_ASM284965v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002849655.1_ASM284965v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:34,114] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:34,125] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:34,125] [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_002849655.1	s__Candidimonas_A sp002849655	100.0	1478	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002849615.1	s__Candidimonas_A sp002849615	84.4973	959	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129885.1	s__Candidimonas_A bauzanensis	80.3575	660	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339425.1	s__Candidimonas_A sp004339425	79.4814	527	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013416445.1	s__Candidimonas_A sp013416445	79.2364	434	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000209655.1	s__Pusillimonas_C sp000209655	78.9257	388	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003971065.1	s__Candidimonas_A sp003971065	78.8916	438	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013416525.1	s__Parapusillimonas granuli	78.583	407	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_019166065.1	s__Candidimonas humi	77.9234	315	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017745595.1	s__Bordetella_A petrii_C	77.8658	304	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004153445.1	s__Pusillimonas_B soli	77.843	281	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001571365.1	s__Achromobacter denitrificans	76.9331	279	1481	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.42	98.61	0.95	0.90	14	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:34,129] [INFO] GTDB search result was written to GCF_002849655.1_ASM284965v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:34,130] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:34,134] [INFO] DFAST_QC result json was written to GCF_002849655.1_ASM284965v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:34,135] [INFO] DFAST_QC completed!
[2024-01-24 14:00:34,135] [INFO] Total running time: 0h1m38s