[2024-01-24 13:41:20,198] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:20,199] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:20,200] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0d1a0b6-fb9b-4d6a-8d60-b8bae59f3ecb/dqc_reference
[2024-01-24 13:41:21,610] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:21,611] [INFO] Task started: Prodigal
[2024-01-24 13:41:21,611] [INFO] Running command: gunzip -c /var/lib/cwl/stgcbd6833c-b100-4c35-998a-c484a051f4f7/GCF_016722895.1_ASM1672289v1_genomic.fna.gz | prodigal -d GCF_016722895.1_ASM1672289v1_genomic.fna/cds.fna -a GCF_016722895.1_ASM1672289v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:39,336] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:39,336] [INFO] Task started: HMMsearch
[2024-01-24 13:41:39,336] [INFO] Running command: hmmsearch --tblout GCF_016722895.1_ASM1672289v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0d1a0b6-fb9b-4d6a-8d60-b8bae59f3ecb/dqc_reference/reference_markers.hmm GCF_016722895.1_ASM1672289v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:39,718] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:39,719] [INFO] Found 6/6 markers.
[2024-01-24 13:41:39,765] [INFO] Query marker FASTA was written to GCF_016722895.1_ASM1672289v1_genomic.fna/markers.fasta
[2024-01-24 13:41:39,765] [INFO] Task started: Blastn
[2024-01-24 13:41:39,765] [INFO] Running command: blastn -query GCF_016722895.1_ASM1672289v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0d1a0b6-fb9b-4d6a-8d60-b8bae59f3ecb/dqc_reference/reference_markers.fasta -out GCF_016722895.1_ASM1672289v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:40,770] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:40,773] [INFO] Selected 19 target genomes.
[2024-01-24 13:41:40,774] [INFO] Target genome list was writen to GCF_016722895.1_ASM1672289v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:40,781] [INFO] Task started: fastANI
[2024-01-24 13:41:40,782] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbd6833c-b100-4c35-998a-c484a051f4f7/GCF_016722895.1_ASM1672289v1_genomic.fna.gz --refList GCF_016722895.1_ASM1672289v1_genomic.fna/target_genomes.txt --output GCF_016722895.1_ASM1672289v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:59,981] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:59,981] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0d1a0b6-fb9b-4d6a-8d60-b8bae59f3ecb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:59,981] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0d1a0b6-fb9b-4d6a-8d60-b8bae59f3ecb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:59,996] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:59,996] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:59,996] [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 rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	83.1052	909	1691	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	82.4526	747	1691	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	81.4466	704	1691	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	81.2595	797	1691	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	81.2313	677	1691	95	below_threshold
Ramlibacter henchirensis	strain=DSM 14656	GCA_004682015.1	204072	204072	type	True	81.0382	727	1691	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	80.8123	678	1691	95	below_threshold
Ramlibacter monticola	strain=KACC 19175	GCA_016722785.1	1926872	1926872	type	True	80.7078	742	1691	95	below_threshold
Ramlibacter alkalitolerans	strain=KACC 19305	GCA_016722765.1	2039631	2039631	type	True	80.5964	745	1691	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	80.5449	806	1691	95	below_threshold
Ramlibacter lithotrophicus	strain=RBP-1	GCA_012184415.1	2606681	2606681	type	True	80.2145	679	1691	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	80.1999	636	1691	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	79.8735	687	1691	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	79.6875	676	1691	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	79.6628	528	1691	95	below_threshold
Melaminivora jejuensis	strain=KCTC 32230	GCA_017811175.1	1267217	1267217	type	True	79.3228	509	1691	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	79.1741	453	1691	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_001298675.1	343013	343013	type	True	79.1601	456	1691	95	below_threshold
Ottowia oryzae	strain=KADR8-3	GCA_003008535.1	2109914	2109914	type	True	79.0506	473	1691	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:59,998] [INFO] DFAST Taxonomy check result was written to GCF_016722895.1_ASM1672289v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:59,998] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:59,999] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:59,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0d1a0b6-fb9b-4d6a-8d60-b8bae59f3ecb/dqc_reference/checkm_data
[2024-01-24 13:42:00,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:00,056] [INFO] Task started: CheckM
[2024-01-24 13:42:00,056] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016722895.1_ASM1672289v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016722895.1_ASM1672289v1_genomic.fna/checkm_input GCF_016722895.1_ASM1672289v1_genomic.fna/checkm_result
[2024-01-24 13:43:14,787] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:14,789] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:14,821] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:14,821] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:14,822] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016722895.1_ASM1672289v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:14,822] [INFO] Task started: Blastn
[2024-01-24 13:43:14,822] [INFO] Running command: blastn -query GCF_016722895.1_ASM1672289v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0d1a0b6-fb9b-4d6a-8d60-b8bae59f3ecb/dqc_reference/reference_markers_gtdb.fasta -out GCF_016722895.1_ASM1672289v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:16,809] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:16,814] [INFO] Selected 15 target genomes.
[2024-01-24 13:43:16,814] [INFO] Target genome list was writen to GCF_016722895.1_ASM1672289v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:16,848] [INFO] Task started: fastANI
[2024-01-24 13:43:16,848] [INFO] Running command: fastANI --query /var/lib/cwl/stgcbd6833c-b100-4c35-998a-c484a051f4f7/GCF_016722895.1_ASM1672289v1_genomic.fna.gz --refList GCF_016722895.1_ASM1672289v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016722895.1_ASM1672289v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:32,053] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:32,071] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:32,071] [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_016722895.1	s__Ramlibacter sp016722895	100.0	1686	1691	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_004681965.1	s__Ramlibacter rhizophilus	83.0651	913	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000215705.1	s__Ramlibacter tataouinensis	82.468	746	1691	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	81.7967	777	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014874145.1	s__Ramlibacter sp014874145	81.5331	779	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004681975.1	s__Ramlibacter sp004681975	81.4164	707	1691	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	81.256	796	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001580455.1	s__Ramlibacter tataouinensis_B	81.1086	655	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005503335.1	s__SCMQ01 sp005503335	80.8889	650	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCMQ01	95.0	99.99	99.99	1.00	1.00	3	-
GCA_016191525.1	s__Ramlibacter sp016191525	80.6921	664	1691	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	80.2155	679	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001476815.1	s__Pseudacidovorax intermedius_A	80.1206	675	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudacidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002434305.1	s__Pulveribacter sp002434305	79.8313	539	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pulveribacter	95.0	97.39	97.21	0.93	0.92	3	-
GCF_003797765.1	s__Ramlibacter sp003797765	79.7793	651	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003013695.1	s__Pulveribacter suum	79.5585	544	1691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pulveribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:32,073] [INFO] GTDB search result was written to GCF_016722895.1_ASM1672289v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:32,074] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:32,078] [INFO] DFAST_QC result json was written to GCF_016722895.1_ASM1672289v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:32,078] [INFO] DFAST_QC completed!
[2024-01-24 13:43:32,078] [INFO] Total running time: 0h2m12s