[2024-01-25 20:03:20,485] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:03:20,486] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:03:20,486] [INFO] DQC Reference Directory: /var/lib/cwl/stgb34b1677-5da2-4f2e-909c-929a41fae08c/dqc_reference
[2024-01-25 20:03:21,609] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:03:21,609] [INFO] Task started: Prodigal
[2024-01-25 20:03:21,610] [INFO] Running command: gunzip -c /var/lib/cwl/stgb820cab8-2f60-4668-afe3-515b8d1c3c1e/GCF_003385925.1_ASM338592v1_genomic.fna.gz | prodigal -d GCF_003385925.1_ASM338592v1_genomic.fna/cds.fna -a GCF_003385925.1_ASM338592v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:03:35,144] [INFO] Task succeeded: Prodigal
[2024-01-25 20:03:35,144] [INFO] Task started: HMMsearch
[2024-01-25 20:03:35,144] [INFO] Running command: hmmsearch --tblout GCF_003385925.1_ASM338592v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb34b1677-5da2-4f2e-909c-929a41fae08c/dqc_reference/reference_markers.hmm GCF_003385925.1_ASM338592v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:03:35,421] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:03:35,422] [INFO] Found 6/6 markers.
[2024-01-25 20:03:35,468] [INFO] Query marker FASTA was written to GCF_003385925.1_ASM338592v1_genomic.fna/markers.fasta
[2024-01-25 20:03:35,469] [INFO] Task started: Blastn
[2024-01-25 20:03:35,469] [INFO] Running command: blastn -query GCF_003385925.1_ASM338592v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb34b1677-5da2-4f2e-909c-929a41fae08c/dqc_reference/reference_markers.fasta -out GCF_003385925.1_ASM338592v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:36,450] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:36,453] [INFO] Selected 13 target genomes.
[2024-01-25 20:03:36,453] [INFO] Target genome list was writen to GCF_003385925.1_ASM338592v1_genomic.fna/target_genomes.txt
[2024-01-25 20:03:36,463] [INFO] Task started: fastANI
[2024-01-25 20:03:36,464] [INFO] Running command: fastANI --query /var/lib/cwl/stgb820cab8-2f60-4668-afe3-515b8d1c3c1e/GCF_003385925.1_ASM338592v1_genomic.fna.gz --refList GCF_003385925.1_ASM338592v1_genomic.fna/target_genomes.txt --output GCF_003385925.1_ASM338592v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:03:57,237] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:57,238] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb34b1677-5da2-4f2e-909c-929a41fae08c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:03:57,238] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb34b1677-5da2-4f2e-909c-929a41fae08c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:03:57,246] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:03:57,246] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:03:57,247] [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
Rhodopseudomonas pentothenatexigens	strain=JA575	GCA_003385925.1	999699	999699	type	True	100.0	1760	1761	95	conclusive
Rhodopseudomonas pentothenatexigens	strain=JA575	GCA_900218015.1	999699	999699	type	True	100.0	1760	1761	95	conclusive
Rhodopseudomonas pseudopalustris	strain=DSM 123	GCA_900110435.1	1513892	1513892	type	True	84.752	1208	1761	95	below_threshold
Rhodopseudomonas rhenobacensis	strain=DSM 12706	GCA_014203125.1	87461	87461	type	True	82.9979	1010	1761	95	below_threshold
Rhodopseudomonas faecalis	strain=JCM 11668	GCA_003217325.1	99655	99655	type	True	81.8097	889	1761	95	below_threshold
Bradyrhizobium ivorense	strain=CI-1B	GCA_900696085.2	2511166	2511166	type	True	81.233	1001	1761	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	81.1689	974	1761	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	80.9898	922	1761	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	80.7056	974	1761	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	80.62	950	1761	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	80.5719	948	1761	95	below_threshold
Bradyrhizobium amphicarpaeae	strain=39S1MB	GCA_002266435.2	1404768	1404768	type	True	80.5596	989	1761	95	below_threshold
Bradyrhizobium jicamae	strain=PAC68	GCA_001440395.1	280332	280332	type	True	80.3792	898	1761	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:03:57,248] [INFO] DFAST Taxonomy check result was written to GCF_003385925.1_ASM338592v1_genomic.fna/tc_result.tsv
[2024-01-25 20:03:57,248] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:03:57,248] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:03:57,249] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb34b1677-5da2-4f2e-909c-929a41fae08c/dqc_reference/checkm_data
[2024-01-25 20:03:57,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:03:57,302] [INFO] Task started: CheckM
[2024-01-25 20:03:57,302] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003385925.1_ASM338592v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003385925.1_ASM338592v1_genomic.fna/checkm_input GCF_003385925.1_ASM338592v1_genomic.fna/checkm_result
[2024-01-25 20:04:42,253] [INFO] Task succeeded: CheckM
[2024-01-25 20:04:42,254] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:04:42,272] [INFO] ===== Completeness check finished =====
[2024-01-25 20:04:42,272] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:04:42,273] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003385925.1_ASM338592v1_genomic.fna/markers.fasta)
[2024-01-25 20:04:42,274] [INFO] Task started: Blastn
[2024-01-25 20:04:42,274] [INFO] Running command: blastn -query GCF_003385925.1_ASM338592v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb34b1677-5da2-4f2e-909c-929a41fae08c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003385925.1_ASM338592v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:44,285] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:44,288] [INFO] Selected 6 target genomes.
[2024-01-25 20:04:44,288] [INFO] Target genome list was writen to GCF_003385925.1_ASM338592v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:04:44,316] [INFO] Task started: fastANI
[2024-01-25 20:04:44,316] [INFO] Running command: fastANI --query /var/lib/cwl/stgb820cab8-2f60-4668-afe3-515b8d1c3c1e/GCF_003385925.1_ASM338592v1_genomic.fna.gz --refList GCF_003385925.1_ASM338592v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003385925.1_ASM338592v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:04:54,674] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:54,680] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:04:54,680] [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_900218015.1	s__Rhodopseudomonas pentothenatexigens	100.0	1760	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_000177255.2	s__Rhodopseudomonas palustris_G	91.2327	1463	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	98.28	98.19	0.96	0.95	4	-
GCF_003226555.1	s__Rhodopseudomonas palustris_I	90.9583	1520	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003031265.1	s__Rhodopseudomonas palustris_H	90.0759	1448	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	96.56	96.03	0.93	0.93	4	-
GCF_013415845.1	s__Rhodopseudomonas palustris_F	89.9802	1421	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	97.90	97.49	0.94	0.92	8	-
GCF_010907035.1	s__Rhodopseudomonas sp010907035	89.9767	1380	1761	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:04:54,681] [INFO] GTDB search result was written to GCF_003385925.1_ASM338592v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:04:54,682] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:04:54,684] [INFO] DFAST_QC result json was written to GCF_003385925.1_ASM338592v1_genomic.fna/dqc_result.json
[2024-01-25 20:04:54,685] [INFO] DFAST_QC completed!
[2024-01-25 20:04:54,685] [INFO] Total running time: 0h1m34s