[2024-01-24 10:57:25,176] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:25,179] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:25,179] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc9c95e1-5162-4a1d-b29e-4312afd05998/dqc_reference
[2024-01-24 10:57:26,459] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:26,460] [INFO] Task started: Prodigal
[2024-01-24 10:57:26,460] [INFO] Running command: gunzip -c /var/lib/cwl/stg27bd8eaf-a0fa-4956-ae20-58eb038364b9/GCF_022271405.1_ASM2227140v1_genomic.fna.gz | prodigal -d GCF_022271405.1_ASM2227140v1_genomic.fna/cds.fna -a GCF_022271405.1_ASM2227140v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:42,427] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:42,427] [INFO] Task started: HMMsearch
[2024-01-24 10:57:42,427] [INFO] Running command: hmmsearch --tblout GCF_022271405.1_ASM2227140v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc9c95e1-5162-4a1d-b29e-4312afd05998/dqc_reference/reference_markers.hmm GCF_022271405.1_ASM2227140v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:42,785] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:42,786] [INFO] Found 6/6 markers.
[2024-01-24 10:57:42,834] [INFO] Query marker FASTA was written to GCF_022271405.1_ASM2227140v1_genomic.fna/markers.fasta
[2024-01-24 10:57:42,834] [INFO] Task started: Blastn
[2024-01-24 10:57:42,835] [INFO] Running command: blastn -query GCF_022271405.1_ASM2227140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc9c95e1-5162-4a1d-b29e-4312afd05998/dqc_reference/reference_markers.fasta -out GCF_022271405.1_ASM2227140v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:43,858] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:43,861] [INFO] Selected 15 target genomes.
[2024-01-24 10:57:43,861] [INFO] Target genome list was writen to GCF_022271405.1_ASM2227140v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:43,881] [INFO] Task started: fastANI
[2024-01-24 10:57:43,881] [INFO] Running command: fastANI --query /var/lib/cwl/stg27bd8eaf-a0fa-4956-ae20-58eb038364b9/GCF_022271405.1_ASM2227140v1_genomic.fna.gz --refList GCF_022271405.1_ASM2227140v1_genomic.fna/target_genomes.txt --output GCF_022271405.1_ASM2227140v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:09,518] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:09,518] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc9c95e1-5162-4a1d-b29e-4312afd05998/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:09,519] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc9c95e1-5162-4a1d-b29e-4312afd05998/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:09,531] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:58:09,531] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:58:09,531] [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 pseudopalustris	strain=DSM 123	GCA_900110435.1	1513892	1513892	type	True	85.7152	1226	1792	95	below_threshold
Rhodopseudomonas pentothenatexigens	strain=JA575	GCA_900218015.1	999699	999699	type	True	85.3579	1255	1792	95	below_threshold
Rhodopseudomonas pentothenatexigens	strain=JA575	GCA_003385925.1	999699	999699	type	True	85.3473	1257	1792	95	below_threshold
Rhodopseudomonas rhenobacensis	strain=DSM 12706	GCA_014203125.1	87461	87461	type	True	82.7395	1014	1792	95	below_threshold
Rhodopseudomonas faecalis	strain=JCM 11668	GCA_003217325.1	99655	99655	type	True	81.581	850	1792	95	below_threshold
Bradyrhizobium ivorense	strain=CI-1B	GCA_900696085.2	2511166	2511166	type	True	81.3315	1005	1792	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_000379145.1	29448	29448	type	True	81.1923	988	1792	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	81.1456	993	1792	95	below_threshold
Bradyrhizobium pachyrhizi	strain=PAC 48	GCA_001189245.1	280333	280333	type	True	81.1437	983	1792	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	81.0925	933	1792	95	below_threshold
Bradyrhizobium acaciae	strain=10BB	GCA_020889785.1	2683706	2683706	type	True	81.0412	947	1792	95	below_threshold
Bradyrhizobium sediminis	strain=S2-20-1	GCA_018736085.1	2840469	2840469	type	True	80.9034	906	1792	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	80.7757	939	1792	95	below_threshold
Bradyrhizobium lablabi	strain=CCBAU 23086	GCA_001440475.1	722472	722472	suspected-type	True	80.3423	947	1792	95	below_threshold
Bradyrhizobium valentinum	strain=LmjM3	GCA_001440405.1	1518501	1518501	type	True	80.1851	872	1792	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:09,533] [INFO] DFAST Taxonomy check result was written to GCF_022271405.1_ASM2227140v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:09,534] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:09,534] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:09,534] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc9c95e1-5162-4a1d-b29e-4312afd05998/dqc_reference/checkm_data
[2024-01-24 10:58:09,536] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:09,589] [INFO] Task started: CheckM
[2024-01-24 10:58:09,590] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022271405.1_ASM2227140v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022271405.1_ASM2227140v1_genomic.fna/checkm_input GCF_022271405.1_ASM2227140v1_genomic.fna/checkm_result
[2024-01-24 10:58:53,968] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:53,969] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:53,985] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:53,985] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:53,985] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022271405.1_ASM2227140v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:53,986] [INFO] Task started: Blastn
[2024-01-24 10:58:53,986] [INFO] Running command: blastn -query GCF_022271405.1_ASM2227140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc9c95e1-5162-4a1d-b29e-4312afd05998/dqc_reference/reference_markers_gtdb.fasta -out GCF_022271405.1_ASM2227140v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:55,932] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:55,935] [INFO] Selected 12 target genomes.
[2024-01-24 10:58:55,935] [INFO] Target genome list was writen to GCF_022271405.1_ASM2227140v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:55,959] [INFO] Task started: fastANI
[2024-01-24 10:58:55,959] [INFO] Running command: fastANI --query /var/lib/cwl/stg27bd8eaf-a0fa-4956-ae20-58eb038364b9/GCF_022271405.1_ASM2227140v1_genomic.fna.gz --refList GCF_022271405.1_ASM2227140v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022271405.1_ASM2227140v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:14,298] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:14,309] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:59:14,309] [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_003591005.1	s__Rhodopseudomonas palustris_K	89.4862	1481	1792	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001295845.1	s__Rhodopseudomonas sp001295845	88.8773	1392	1792	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016215605.1	s__Rhodopseudomonas palustris_L	87.7638	1364	1792	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013365.1	s__Rhodopseudomonas palustris_J	86.9571	1359	1792	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110435.1	s__Rhodopseudomonas pseudopalustris	85.6996	1227	1792	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	98.41	98.34	0.90	0.86	3	-
GCF_900218015.1	s__Rhodopseudomonas pentothenatexigens	85.3361	1258	1792	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	100.00	100.00	1.00	1.00	3	-
GCF_003226555.1	s__Rhodopseudomonas palustris_I	85.1383	1271	1792	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000177255.2	s__Rhodopseudomonas palustris_G	85.0989	1240	1792	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	98.28	98.19	0.96	0.95	4	-
GCF_010907035.1	s__Rhodopseudomonas sp010907035	85.0816	1236	1792	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	85.0272	1294	1792	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	84.8938	1274	1792	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	97.90	97.49	0.94	0.92	8	-
GCF_000333455.1	s__Rhodopseudomonas sp000333455	84.4438	1011	1792	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:14,311] [INFO] GTDB search result was written to GCF_022271405.1_ASM2227140v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:14,311] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:14,315] [INFO] DFAST_QC result json was written to GCF_022271405.1_ASM2227140v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:14,315] [INFO] DFAST_QC completed!
[2024-01-24 10:59:14,315] [INFO] Total running time: 0h1m49s