[2024-01-24 12:14:34,091] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:34,094] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:34,094] [INFO] DQC Reference Directory: /var/lib/cwl/stgd093b09c-2fb6-40b8-a64e-edd578f73b86/dqc_reference
[2024-01-24 12:14:35,401] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,402] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,402] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe6f2041-25d2-45dd-8326-1f4c1454d4f3/GCF_015831345.1_ASM1583134v1_genomic.fna.gz | prodigal -d GCF_015831345.1_ASM1583134v1_genomic.fna/cds.fna -a GCF_015831345.1_ASM1583134v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:51,415] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:51,416] [INFO] Task started: HMMsearch
[2024-01-24 12:14:51,416] [INFO] Running command: hmmsearch --tblout GCF_015831345.1_ASM1583134v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd093b09c-2fb6-40b8-a64e-edd578f73b86/dqc_reference/reference_markers.hmm GCF_015831345.1_ASM1583134v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:51,763] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:51,765] [INFO] Found 6/6 markers.
[2024-01-24 12:14:51,810] [INFO] Query marker FASTA was written to GCF_015831345.1_ASM1583134v1_genomic.fna/markers.fasta
[2024-01-24 12:14:51,811] [INFO] Task started: Blastn
[2024-01-24 12:14:51,811] [INFO] Running command: blastn -query GCF_015831345.1_ASM1583134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd093b09c-2fb6-40b8-a64e-edd578f73b86/dqc_reference/reference_markers.fasta -out GCF_015831345.1_ASM1583134v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:52,964] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:52,969] [INFO] Selected 16 target genomes.
[2024-01-24 12:14:52,970] [INFO] Target genome list was writen to GCF_015831345.1_ASM1583134v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:52,979] [INFO] Task started: fastANI
[2024-01-24 12:14:52,979] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe6f2041-25d2-45dd-8326-1f4c1454d4f3/GCF_015831345.1_ASM1583134v1_genomic.fna.gz --refList GCF_015831345.1_ASM1583134v1_genomic.fna/target_genomes.txt --output GCF_015831345.1_ASM1583134v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:08,534] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:08,535] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd093b09c-2fb6-40b8-a64e-edd578f73b86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:08,535] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd093b09c-2fb6-40b8-a64e-edd578f73b86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:08,549] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:15:08,549] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:15:08,549] [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
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	82.0052	798	1506	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	81.717	727	1506	95	below_threshold
Ramlibacter henchirensis	strain=DSM 14656	GCA_004682015.1	204072	204072	type	True	81.5685	783	1506	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	81.5581	823	1506	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	81.5419	791	1506	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	81.4737	797	1506	95	below_threshold
Ramlibacter lithotrophicus	strain=RBP-1	GCA_012184415.1	2606681	2606681	type	True	81.3535	768	1506	95	below_threshold
Ramlibacter alkalitolerans	strain=KACC 19305	GCA_016722765.1	2039631	2039631	type	True	81.3488	827	1506	95	below_threshold
Ramlibacter monticola	strain=KACC 19175	GCA_016722785.1	1926872	1926872	type	True	81.306	833	1506	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	81.3018	865	1506	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	80.7942	712	1506	95	below_threshold
Caenimonas koreensis	strain=EMB320	GCA_009646335.1	367474	367474	type	True	80.7646	762	1506	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.255	628	1506	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	80.1923	735	1506	95	below_threshold
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	79.5413	326	1506	95	below_threshold
Melaminivora alkalimesophila	strain=DSM 26006	GCA_003182375.1	1165852	1165852	type	True	79.4521	470	1506	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:08,551] [INFO] DFAST Taxonomy check result was written to GCF_015831345.1_ASM1583134v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:08,552] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:08,552] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:08,552] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd093b09c-2fb6-40b8-a64e-edd578f73b86/dqc_reference/checkm_data
[2024-01-24 12:15:08,553] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:08,603] [INFO] Task started: CheckM
[2024-01-24 12:15:08,604] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015831345.1_ASM1583134v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015831345.1_ASM1583134v1_genomic.fna/checkm_input GCF_015831345.1_ASM1583134v1_genomic.fna/checkm_result
[2024-01-24 12:16:19,405] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:19,406] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:19,447] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:19,447] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:19,448] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015831345.1_ASM1583134v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:19,448] [INFO] Task started: Blastn
[2024-01-24 12:16:19,448] [INFO] Running command: blastn -query GCF_015831345.1_ASM1583134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd093b09c-2fb6-40b8-a64e-edd578f73b86/dqc_reference/reference_markers_gtdb.fasta -out GCF_015831345.1_ASM1583134v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:21,690] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:21,697] [INFO] Selected 18 target genomes.
[2024-01-24 12:16:21,697] [INFO] Target genome list was writen to GCF_015831345.1_ASM1583134v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:21,724] [INFO] Task started: fastANI
[2024-01-24 12:16:21,725] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe6f2041-25d2-45dd-8326-1f4c1454d4f3/GCF_015831345.1_ASM1583134v1_genomic.fna.gz --refList GCF_015831345.1_ASM1583134v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015831345.1_ASM1583134v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:40,429] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:40,449] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:40,450] [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_015831345.1	s__Ramlibacter sp015831345	100.0	1506	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003797765.1	s__Ramlibacter sp003797765	82.1526	893	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191525.1	s__Ramlibacter sp016191525	82.1304	847	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297445.1	s__Ramlibacter sp014297445	81.8542	894	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001580455.1	s__Ramlibacter tataouinensis_B	81.819	797	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155545.1	s__Ramlibacter soli	81.8149	825	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424545.1	s__Ramlibacter sp001424545	81.7924	835	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297465.1	s__Ramlibacter sp014297465	81.729	858	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015070875.1	s__Ramlibacter sp015070875	81.6691	774	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016641735.1	s__Ramlibacter sp016641735	81.5507	790	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013778345.1	s__Ramlibacter sp013778345	81.5501	824	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007833165.1	s__Ramlibacter sp007833165	81.4418	827	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213325.1	s__Ramlibacter sp016213325	81.3507	821	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012184415.1	s__Ramlibacter lithotrophicus	81.3476	769	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927085.1	s__Ramlibacter sp012927085	81.3207	862	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014376915.1	s__Ramlibacter sp014376915	81.0633	501	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013815685.1	s__Ramlibacter sp013815685	80.8416	690	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282995.1	s__Melaminivora alkalimesophila	79.5109	328	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Melaminivora	95.0	99.95	99.95	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:40,451] [INFO] GTDB search result was written to GCF_015831345.1_ASM1583134v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:40,452] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:40,455] [INFO] DFAST_QC result json was written to GCF_015831345.1_ASM1583134v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:40,456] [INFO] DFAST_QC completed!
[2024-01-24 12:16:40,456] [INFO] Total running time: 0h2m6s