[2023-06-19 08:50:04,033] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:50:04,035] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:50:04,035] [INFO] DQC Reference Directory: /var/lib/cwl/stg4219fdc3-6744-47d8-89b3-2fb9ae3fc2b7/dqc_reference
[2023-06-19 08:50:05,216] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:50:05,216] [INFO] Task started: Prodigal
[2023-06-19 08:50:05,217] [INFO] Running command: gunzip -c /var/lib/cwl/stg4efea5cd-0292-4fbb-b0a3-8ba18f453a6f/GCA_018005775.1_ASM1800577v1_genomic.fna.gz | prodigal -d GCA_018005775.1_ASM1800577v1_genomic.fna/cds.fna -a GCA_018005775.1_ASM1800577v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:50:08,935] [INFO] Task succeeded: Prodigal
[2023-06-19 08:50:08,935] [INFO] Task started: HMMsearch
[2023-06-19 08:50:08,936] [INFO] Running command: hmmsearch --tblout GCA_018005775.1_ASM1800577v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4219fdc3-6744-47d8-89b3-2fb9ae3fc2b7/dqc_reference/reference_markers.hmm GCA_018005775.1_ASM1800577v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:50:09,082] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:50:09,083] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4efea5cd-0292-4fbb-b0a3-8ba18f453a6f/GCA_018005775.1_ASM1800577v1_genomic.fna.gz]
[2023-06-19 08:50:09,100] [INFO] Query marker FASTA was written to GCA_018005775.1_ASM1800577v1_genomic.fna/markers.fasta
[2023-06-19 08:50:09,100] [INFO] Task started: Blastn
[2023-06-19 08:50:09,100] [INFO] Running command: blastn -query GCA_018005775.1_ASM1800577v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4219fdc3-6744-47d8-89b3-2fb9ae3fc2b7/dqc_reference/reference_markers.fasta -out GCA_018005775.1_ASM1800577v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:50:09,664] [INFO] Task succeeded: Blastn
[2023-06-19 08:50:09,679] [INFO] Selected 15 target genomes.
[2023-06-19 08:50:09,680] [INFO] Target genome list was writen to GCA_018005775.1_ASM1800577v1_genomic.fna/target_genomes.txt
[2023-06-19 08:50:09,680] [INFO] Task started: fastANI
[2023-06-19 08:50:09,680] [INFO] Running command: fastANI --query /var/lib/cwl/stg4efea5cd-0292-4fbb-b0a3-8ba18f453a6f/GCA_018005775.1_ASM1800577v1_genomic.fna.gz --refList GCA_018005775.1_ASM1800577v1_genomic.fna/target_genomes.txt --output GCA_018005775.1_ASM1800577v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:50:19,663] [INFO] Task succeeded: fastANI
[2023-06-19 08:50:19,664] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4219fdc3-6744-47d8-89b3-2fb9ae3fc2b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:50:19,664] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4219fdc3-6744-47d8-89b3-2fb9ae3fc2b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:50:19,685] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:50:19,686] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 08:50:19,686] [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
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	81.6132	207	322	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_001298675.1	343013	343013	type	True	81.594	200	322	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	81.5466	202	322	95	below_threshold
Melaminivora jejuensis	strain=KCTC 32230	GCA_017811175.1	1267217	1267217	type	True	81.5455	227	322	95	below_threshold
Acidovorax anthurii	strain=CFPB 3232	GCA_003269065.1	78229	78229	type	True	81.0906	194	322	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	80.8939	200	322	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	80.6134	189	322	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	80.265	189	322	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	80.0541	168	322	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	79.7379	158	322	95	below_threshold
Simplicispira metamorpha	strain=DSM 1837	GCA_004341365.1	80881	80881	type	True	79.6475	162	322	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	78.8923	148	322	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	78.7918	172	322	95	below_threshold
Diaphorobacter aerolatus	strain=KACC 16536	GCA_014489535.1	1288495	1288495	type	True	78.7054	143	322	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	78.5864	171	322	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 08:50:19,695] [INFO] DFAST Taxonomy check result was written to GCA_018005775.1_ASM1800577v1_genomic.fna/tc_result.tsv
[2023-06-19 08:50:19,696] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:50:19,696] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:50:19,696] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4219fdc3-6744-47d8-89b3-2fb9ae3fc2b7/dqc_reference/checkm_data
[2023-06-19 08:50:19,698] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:50:19,715] [INFO] Task started: CheckM
[2023-06-19 08:50:19,715] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018005775.1_ASM1800577v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018005775.1_ASM1800577v1_genomic.fna/checkm_input GCA_018005775.1_ASM1800577v1_genomic.fna/checkm_result
[2023-06-19 08:50:36,164] [INFO] Task succeeded: CheckM
[2023-06-19 08:50:36,165] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 8.80%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:50:36,181] [INFO] ===== Completeness check finished =====
[2023-06-19 08:50:36,181] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:50:36,182] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018005775.1_ASM1800577v1_genomic.fna/markers.fasta)
[2023-06-19 08:50:36,182] [INFO] Task started: Blastn
[2023-06-19 08:50:36,182] [INFO] Running command: blastn -query GCA_018005775.1_ASM1800577v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4219fdc3-6744-47d8-89b3-2fb9ae3fc2b7/dqc_reference/reference_markers_gtdb.fasta -out GCA_018005775.1_ASM1800577v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:50:36,917] [INFO] Task succeeded: Blastn
[2023-06-19 08:50:36,921] [INFO] Selected 7 target genomes.
[2023-06-19 08:50:36,921] [INFO] Target genome list was writen to GCA_018005775.1_ASM1800577v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:50:36,924] [INFO] Task started: fastANI
[2023-06-19 08:50:36,924] [INFO] Running command: fastANI --query /var/lib/cwl/stg4efea5cd-0292-4fbb-b0a3-8ba18f453a6f/GCA_018005775.1_ASM1800577v1_genomic.fna.gz --refList GCA_018005775.1_ASM1800577v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018005775.1_ASM1800577v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:50:41,650] [INFO] Task succeeded: fastANI
[2023-06-19 08:50:41,657] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:50:41,657] [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
GCA_018054745.1	s__Alicycliphilus sp018054745	97.9179	262	322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	99.31	99.29	0.86	0.83	3	conclusive
GCA_018240995.1	s__Alicycliphilus sp018240995	87.6471	231	322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240985.1	s__Alicycliphilus sp018240985	86.186	238	322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	99.65	99.65	0.85	0.85	2	-
GCA_018241405.1	s__Alicycliphilus sp018241405	86.183	252	322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	98.75	98.75	0.95	0.95	2	-
GCF_000204645.1	s__Alicycliphilus denitrificans	85.9254	253	322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	97.26	95.80	0.83	0.76	8	-
GCA_018242005.1	s__Alicycliphilus sp018242005	85.1749	236	322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alicycliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001725235.1	s__Acidovorax_C sp001725235	82.474	223	322	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_C	95.0	98.36	96.90	0.87	0.83	3	-
--------------------------------------------------------------------------------
[2023-06-19 08:50:41,665] [INFO] GTDB search result was written to GCA_018005775.1_ASM1800577v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:50:41,666] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:50:41,670] [INFO] DFAST_QC result json was written to GCA_018005775.1_ASM1800577v1_genomic.fna/dqc_result.json
[2023-06-19 08:50:41,670] [INFO] DFAST_QC completed!
[2023-06-19 08:50:41,670] [INFO] Total running time: 0h0m38s