[2024-01-24 11:58:20,620] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:20,621] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:20,622] [INFO] DQC Reference Directory: /var/lib/cwl/stg74a847df-ff50-4c75-a5aa-c31eb6409c83/dqc_reference
[2024-01-24 11:58:21,847] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:21,848] [INFO] Task started: Prodigal
[2024-01-24 11:58:21,848] [INFO] Running command: gunzip -c /var/lib/cwl/stg04732d45-a6c7-466d-a7d3-c6f80ce70e29/GCF_004153685.1_ASM415368v1_genomic.fna.gz | prodigal -d GCF_004153685.1_ASM415368v1_genomic.fna/cds.fna -a GCF_004153685.1_ASM415368v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:58:32,764] [INFO] Task succeeded: Prodigal
[2024-01-24 11:58:32,765] [INFO] Task started: HMMsearch
[2024-01-24 11:58:32,765] [INFO] Running command: hmmsearch --tblout GCF_004153685.1_ASM415368v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74a847df-ff50-4c75-a5aa-c31eb6409c83/dqc_reference/reference_markers.hmm GCF_004153685.1_ASM415368v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:58:33,023] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:58:33,025] [INFO] Found 6/6 markers.
[2024-01-24 11:58:33,058] [INFO] Query marker FASTA was written to GCF_004153685.1_ASM415368v1_genomic.fna/markers.fasta
[2024-01-24 11:58:33,058] [INFO] Task started: Blastn
[2024-01-24 11:58:33,058] [INFO] Running command: blastn -query GCF_004153685.1_ASM415368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74a847df-ff50-4c75-a5aa-c31eb6409c83/dqc_reference/reference_markers.fasta -out GCF_004153685.1_ASM415368v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:58:33,827] [INFO] Task succeeded: Blastn
[2024-01-24 11:58:33,832] [INFO] Selected 16 target genomes.
[2024-01-24 11:58:33,833] [INFO] Target genome list was writen to GCF_004153685.1_ASM415368v1_genomic.fna/target_genomes.txt
[2024-01-24 11:58:33,842] [INFO] Task started: fastANI
[2024-01-24 11:58:33,842] [INFO] Running command: fastANI --query /var/lib/cwl/stg04732d45-a6c7-466d-a7d3-c6f80ce70e29/GCF_004153685.1_ASM415368v1_genomic.fna.gz --refList GCF_004153685.1_ASM415368v1_genomic.fna/target_genomes.txt --output GCF_004153685.1_ASM415368v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:58:45,110] [INFO] Task succeeded: fastANI
[2024-01-24 11:58:45,111] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74a847df-ff50-4c75-a5aa-c31eb6409c83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:58:45,112] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74a847df-ff50-4c75-a5aa-c31eb6409c83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:58:45,128] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:58:45,129] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:58:45,129] [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
Pusillimonas harenae	strain=JCM 16917	GCA_004153685.1	657015	657015	type	True	100.0	1117	1118	95	conclusive
Pusillimonas harenae	strain=DSM 25667	GCA_013416515.1	657015	657015	type	True	99.996	1117	1118	95	conclusive
Parapusillimonas granuli	strain=DSM 18079	GCA_014202705.1	380911	380911	type	True	78.6125	348	1118	95	below_threshold
Parapusillimonas granuli	strain=LMG 24012	GCA_013416525.1	380911	380911	type	True	78.5468	342	1118	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	78.4338	260	1118	95	below_threshold
Pusillimonas caeni	strain=KCTC 42353	GCA_003545815.1	1348472	1348472	type	True	78.2279	244	1118	95	below_threshold
Pusillimonas noertemannii	strain=DSM 10065	GCA_003545825.1	305977	305977	type	True	78.0431	271	1118	95	below_threshold
Candidimonas nitroreducens	strain=SC-089	GCA_002209565.1	683354	683354	type	True	77.5424	287	1118	95	below_threshold
Achromobacter spanius	strain=DSM 23806	GCA_002812705.1	217203	217203	suspected-type	True	77.3038	194	1118	95	below_threshold
Paenalcaligenes niemegkensis	strain=NGK35	GCA_022230885.1	2895469	2895469	type	True	77.2436	90	1118	95	below_threshold
Achromobacter spanius	strain=LMG 5911	GCA_902859605.1	217203	217203	suspected-type	True	77.2175	186	1118	95	below_threshold
Bordetella trematum	strain=NCTC12995	GCA_900445945.1	123899	123899	type	True	77.1957	181	1118	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	77.1359	188	1118	95	below_threshold
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	76.2934	57	1118	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:58:45,130] [INFO] DFAST Taxonomy check result was written to GCF_004153685.1_ASM415368v1_genomic.fna/tc_result.tsv
[2024-01-24 11:58:45,131] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:58:45,131] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:58:45,131] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74a847df-ff50-4c75-a5aa-c31eb6409c83/dqc_reference/checkm_data
[2024-01-24 11:58:45,132] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:58:45,165] [INFO] Task started: CheckM
[2024-01-24 11:58:45,165] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004153685.1_ASM415368v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004153685.1_ASM415368v1_genomic.fna/checkm_input GCF_004153685.1_ASM415368v1_genomic.fna/checkm_result
[2024-01-24 11:59:20,449] [INFO] Task succeeded: CheckM
[2024-01-24 11:59:20,472] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:59:20,506] [INFO] ===== Completeness check finished =====
[2024-01-24 11:59:20,506] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:59:20,507] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004153685.1_ASM415368v1_genomic.fna/markers.fasta)
[2024-01-24 11:59:20,507] [INFO] Task started: Blastn
[2024-01-24 11:59:20,507] [INFO] Running command: blastn -query GCF_004153685.1_ASM415368v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74a847df-ff50-4c75-a5aa-c31eb6409c83/dqc_reference/reference_markers_gtdb.fasta -out GCF_004153685.1_ASM415368v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:21,896] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:21,900] [INFO] Selected 13 target genomes.
[2024-01-24 11:59:21,900] [INFO] Target genome list was writen to GCF_004153685.1_ASM415368v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:59:21,915] [INFO] Task started: fastANI
[2024-01-24 11:59:21,916] [INFO] Running command: fastANI --query /var/lib/cwl/stg04732d45-a6c7-466d-a7d3-c6f80ce70e29/GCF_004153685.1_ASM415368v1_genomic.fna.gz --refList GCF_004153685.1_ASM415368v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004153685.1_ASM415368v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:59:32,810] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:32,833] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:59:32,833] [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_004153685.1	s__Pusillimonas_C harenae	100.0	1117	1118	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_C	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000209655.1	s__Pusillimonas_C sp000209655	84.0627	884	1118	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013416405.1	s__Pusillimonas_C sp013416405	81.2216	670	1118	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_004022565.1	s__Pusillimonas_D thiosulfatoxidans	78.6404	359	1118	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pusillimonas_D	95.0	97.98	97.65	0.84	0.81	3	-
GCF_013416525.1	s__Parapusillimonas granuli	78.547	342	1118	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	100.00	100.00	0.99	0.99	2	-
GCA_013416435.1	s__Parapusillimonas sp013416435	78.5464	344	1118	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parapusillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129885.1	s__Candidimonas_A bauzanensis	78.4869	405	1118	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	78.4813	319	1118	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	78.2805	361	1118	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_000067205.1	s__Bordetella_A petrii	77.4336	229	1118	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_002812705.1	s__Achromobacter spanius	77.2884	196	1118	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	99.99	99.98	0.99	0.98	4	-
GCF_017356245.1	s__Bordetella_A petrii_D	77.1761	248	1118	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_002119725.1	s__Bordetella_C sp002119725	76.9594	139	1118	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_C	95.0	98.76	98.76	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:59:32,835] [INFO] GTDB search result was written to GCF_004153685.1_ASM415368v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:59:32,835] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:59:32,838] [INFO] DFAST_QC result json was written to GCF_004153685.1_ASM415368v1_genomic.fna/dqc_result.json
[2024-01-24 11:59:32,838] [INFO] DFAST_QC completed!
[2024-01-24 11:59:32,838] [INFO] Total running time: 0h1m12s