[2024-01-25 20:21:05,655] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:21:05,656] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:21:05,656] [INFO] DQC Reference Directory: /var/lib/cwl/stga538e542-00ab-4137-8201-50bdcb3723b1/dqc_reference
[2024-01-25 20:21:06,821] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:21:06,822] [INFO] Task started: Prodigal
[2024-01-25 20:21:06,822] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b166d95-49b5-4789-ab9c-29f8fd30a3eb/GCF_026343995.1_ASM2634399v1_genomic.fna.gz | prodigal -d GCF_026343995.1_ASM2634399v1_genomic.fna/cds.fna -a GCF_026343995.1_ASM2634399v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:21:20,278] [INFO] Task succeeded: Prodigal
[2024-01-25 20:21:20,279] [INFO] Task started: HMMsearch
[2024-01-25 20:21:20,279] [INFO] Running command: hmmsearch --tblout GCF_026343995.1_ASM2634399v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga538e542-00ab-4137-8201-50bdcb3723b1/dqc_reference/reference_markers.hmm GCF_026343995.1_ASM2634399v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:21:20,532] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:21:20,534] [INFO] Found 6/6 markers.
[2024-01-25 20:21:20,576] [INFO] Query marker FASTA was written to GCF_026343995.1_ASM2634399v1_genomic.fna/markers.fasta
[2024-01-25 20:21:20,577] [INFO] Task started: Blastn
[2024-01-25 20:21:20,577] [INFO] Running command: blastn -query GCF_026343995.1_ASM2634399v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga538e542-00ab-4137-8201-50bdcb3723b1/dqc_reference/reference_markers.fasta -out GCF_026343995.1_ASM2634399v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:21,464] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:21,467] [INFO] Selected 20 target genomes.
[2024-01-25 20:21:21,467] [INFO] Target genome list was writen to GCF_026343995.1_ASM2634399v1_genomic.fna/target_genomes.txt
[2024-01-25 20:21:21,475] [INFO] Task started: fastANI
[2024-01-25 20:21:21,475] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b166d95-49b5-4789-ab9c-29f8fd30a3eb/GCF_026343995.1_ASM2634399v1_genomic.fna.gz --refList GCF_026343995.1_ASM2634399v1_genomic.fna/target_genomes.txt --output GCF_026343995.1_ASM2634399v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:21:40,765] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:40,766] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga538e542-00ab-4137-8201-50bdcb3723b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:21:40,766] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga538e542-00ab-4137-8201-50bdcb3723b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:21:40,778] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:21:40,778] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:21:40,779] [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
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	82.0705	990	1723	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	81.4951	860	1723	95	below_threshold
Kaistia granuli	strain=Ko04	GCA_000380505.1	363259	363259	type	True	81.4246	829	1723	95	below_threshold
Kaistia soli	strain=DSM 19436	GCA_900129325.1	446684	446684	type	True	80.8642	868	1723	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	78.3423	430	1723	95	below_threshold
Methylobrevis pamukkalensis	strain=PK2	GCA_001720135.1	1439726	1439726	type	True	77.7487	371	1723	95	below_threshold
Azorhizobium caulinodans	strain=ORS 571	GCA_000010525.1	7	7	type	True	77.7391	307	1723	95	below_threshold
Bauldia litoralis	strain=ATCC 35022	GCA_900104485.1	665467	665467	type	True	77.7184	407	1723	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	77.6772	429	1723	95	below_threshold
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	77.6521	454	1723	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	77.6357	344	1723	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.5809	366	1723	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	77.5405	385	1723	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	77.3295	294	1723	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	77.3197	295	1723	95	below_threshold
Rhizobium tubonense	strain=CCBAU 85046	GCA_003240585.1	484088	484088	type	True	77.1022	263	1723	95	below_threshold
Enterovirga rhinocerotis	strain=DSM 25903	GCA_004363955.1	1339210	1339210	type	True	77.0467	294	1723	95	below_threshold
Afifella pfennigii	strain=DSM 17143	GCA_000688515.1	209897	209897	type	True	77.0003	277	1723	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	76.9669	320	1723	95	below_threshold
Phreatobacter stygius	strain=KCTC 52518	GCA_005144885.1	1940610	1940610	type	True	76.9619	374	1723	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:21:40,780] [INFO] DFAST Taxonomy check result was written to GCF_026343995.1_ASM2634399v1_genomic.fna/tc_result.tsv
[2024-01-25 20:21:40,780] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:21:40,780] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:21:40,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga538e542-00ab-4137-8201-50bdcb3723b1/dqc_reference/checkm_data
[2024-01-25 20:21:40,781] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:21:40,830] [INFO] Task started: CheckM
[2024-01-25 20:21:40,830] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026343995.1_ASM2634399v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026343995.1_ASM2634399v1_genomic.fna/checkm_input GCF_026343995.1_ASM2634399v1_genomic.fna/checkm_result
[2024-01-25 20:22:22,738] [INFO] Task succeeded: CheckM
[2024-01-25 20:22:22,739] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:22:22,765] [INFO] ===== Completeness check finished =====
[2024-01-25 20:22:22,766] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:22:22,768] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026343995.1_ASM2634399v1_genomic.fna/markers.fasta)
[2024-01-25 20:22:22,768] [INFO] Task started: Blastn
[2024-01-25 20:22:22,769] [INFO] Running command: blastn -query GCF_026343995.1_ASM2634399v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga538e542-00ab-4137-8201-50bdcb3723b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_026343995.1_ASM2634399v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:24,518] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:24,521] [INFO] Selected 10 target genomes.
[2024-01-25 20:22:24,521] [INFO] Target genome list was writen to GCF_026343995.1_ASM2634399v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:22:24,547] [INFO] Task started: fastANI
[2024-01-25 20:22:24,547] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b166d95-49b5-4789-ab9c-29f8fd30a3eb/GCF_026343995.1_ASM2634399v1_genomic.fna.gz --refList GCF_026343995.1_ASM2634399v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026343995.1_ASM2634399v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:22:35,094] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:35,102] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:22:35,102] [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_014196455.1	s__Kaistia hirudinis	82.074	989	1723	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	96.80	96.80	0.96	0.96	2	-
GCF_016629525.1	s__Kaistia sp016629525	81.6744	882	1723	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305815.1	s__Kaistia sp017305815	81.6572	633	1723	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307955.1	s__Kaistia sp017307955	81.5403	920	1723	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423225.1	s__Kaistia adipata	81.5067	858	1723	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000380505.1	s__Kaistia granuli	81.385	834	1723	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129325.1	s__Kaistia soli	80.8762	866	1723	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Kaistia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092925.1	s__Starkeya novella	77.641	434	1723	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304475.1	s__Phreatobacter sp017304475	77.0763	424	1723	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003164915.1	s__Roseiarcus sp003164915	76.3691	246	1723	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Roseiarcus	95.0	99.60	99.60	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:22:35,106] [INFO] GTDB search result was written to GCF_026343995.1_ASM2634399v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:22:35,106] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:22:35,111] [INFO] DFAST_QC result json was written to GCF_026343995.1_ASM2634399v1_genomic.fna/dqc_result.json
[2024-01-25 20:22:35,111] [INFO] DFAST_QC completed!
[2024-01-25 20:22:35,111] [INFO] Total running time: 0h1m29s