[2024-01-24 15:10:49,501] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:49,502] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:49,503] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9d78cbf-67bc-481a-91ee-4d8569714b65/dqc_reference
[2024-01-24 15:10:50,788] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:50,789] [INFO] Task started: Prodigal
[2024-01-24 15:10:50,789] [INFO] Running command: gunzip -c /var/lib/cwl/stg24d6d0c8-ff78-45c0-92bc-ec1d6577091f/GCF_017352135.1_ASM1735213v1_genomic.fna.gz | prodigal -d GCF_017352135.1_ASM1735213v1_genomic.fna/cds.fna -a GCF_017352135.1_ASM1735213v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:10,796] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:10,797] [INFO] Task started: HMMsearch
[2024-01-24 15:11:10,797] [INFO] Running command: hmmsearch --tblout GCF_017352135.1_ASM1735213v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9d78cbf-67bc-481a-91ee-4d8569714b65/dqc_reference/reference_markers.hmm GCF_017352135.1_ASM1735213v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:11,145] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:11,146] [INFO] Found 6/6 markers.
[2024-01-24 15:11:11,225] [INFO] Query marker FASTA was written to GCF_017352135.1_ASM1735213v1_genomic.fna/markers.fasta
[2024-01-24 15:11:11,226] [INFO] Task started: Blastn
[2024-01-24 15:11:11,226] [INFO] Running command: blastn -query GCF_017352135.1_ASM1735213v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9d78cbf-67bc-481a-91ee-4d8569714b65/dqc_reference/reference_markers.fasta -out GCF_017352135.1_ASM1735213v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:12,261] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:12,265] [INFO] Selected 17 target genomes.
[2024-01-24 15:11:12,265] [INFO] Target genome list was writen to GCF_017352135.1_ASM1735213v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:12,272] [INFO] Task started: fastANI
[2024-01-24 15:11:12,273] [INFO] Running command: fastANI --query /var/lib/cwl/stg24d6d0c8-ff78-45c0-92bc-ec1d6577091f/GCF_017352135.1_ASM1735213v1_genomic.fna.gz --refList GCF_017352135.1_ASM1735213v1_genomic.fna/target_genomes.txt --output GCF_017352135.1_ASM1735213v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:40,704] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:40,705] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9d78cbf-67bc-481a-91ee-4d8569714b65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:40,705] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9d78cbf-67bc-481a-91ee-4d8569714b65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:40,718] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:11:40,719] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:40,719] [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
Rhizobium lentis	strain=BLR27	GCA_017352135.1	1138194	1138194	type	True	100.0	2138	2138	95	conclusive
Rhizobium lentis	strain=BLR27	GCA_019684715.1	1138194	1138194	type	True	99.9938	2112	2138	95	conclusive
Rhizobium bangladeshense	strain=BLR175	GCA_019684215.1	1138189	1138189	type	True	89.6378	1777	2138	95	below_threshold
Rhizobium bangladeshense	strain=BLR175	GCA_017357245.1	1138189	1138189	type	True	89.6342	1772	2138	95	below_threshold
Rhizobium aethiopicum	strain=HBR26	GCA_900094625.1	1138170	1138170	type	True	89.283	1685	2138	95	below_threshold
Rhizobium esperanzae	strain=CNPSo 668	GCA_002204185.1	1967781	1967781	suspected-type	True	89.0309	1629	2138	95	below_threshold
Rhizobium etli	strain=CFN 42	GCA_000092045.1	29449	29449	suspected-type	True	88.721	1668	2138	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	88.6864	1642	2138	95	below_threshold
Rhizobium sophoriradicis	strain=CCBAU 03470	GCA_003939025.1	1535245	1535245	type	True	88.2047	1650	2138	95	below_threshold
Rhizobium phaseoli	strain=ATCC 14482	GCA_003985125.1	396	396	type	True	88.1781	1622	2138	95	below_threshold
Rhizobium anhuiense	strain=CGMCC 1.12621	GCA_014638185.1	1184720	1184720	type	True	87.8128	1661	2138	95	below_threshold
Rhizobium pisi	strain=DSM 30132	GCA_003938655.1	574561	574561	type	True	87.631	1562	2138	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	87.4056	1597	2138	95	below_threshold
Rhizobium viscosum	strain=DSM 7307	GCA_014873945.1	1673	1673	type	True	82.9397	1279	2138	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	81.373	1137	2138	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	80.4471	936	2138	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	79.8197	715	2138	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:40,721] [INFO] DFAST Taxonomy check result was written to GCF_017352135.1_ASM1735213v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:40,722] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:40,722] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:40,722] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9d78cbf-67bc-481a-91ee-4d8569714b65/dqc_reference/checkm_data
[2024-01-24 15:11:40,723] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:40,789] [INFO] Task started: CheckM
[2024-01-24 15:11:40,789] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017352135.1_ASM1735213v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017352135.1_ASM1735213v1_genomic.fna/checkm_input GCF_017352135.1_ASM1735213v1_genomic.fna/checkm_result
[2024-01-24 15:12:36,362] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:36,364] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:36,388] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:36,388] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:36,388] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017352135.1_ASM1735213v1_genomic.fna/markers.fasta)
[2024-01-24 15:12:36,389] [INFO] Task started: Blastn
[2024-01-24 15:12:36,389] [INFO] Running command: blastn -query GCF_017352135.1_ASM1735213v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9d78cbf-67bc-481a-91ee-4d8569714b65/dqc_reference/reference_markers_gtdb.fasta -out GCF_017352135.1_ASM1735213v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:38,406] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:38,410] [INFO] Selected 15 target genomes.
[2024-01-24 15:12:38,410] [INFO] Target genome list was writen to GCF_017352135.1_ASM1735213v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:38,422] [INFO] Task started: fastANI
[2024-01-24 15:12:38,422] [INFO] Running command: fastANI --query /var/lib/cwl/stg24d6d0c8-ff78-45c0-92bc-ec1d6577091f/GCF_017352135.1_ASM1735213v1_genomic.fna.gz --refList GCF_017352135.1_ASM1735213v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017352135.1_ASM1735213v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:13:03,709] [INFO] Task succeeded: fastANI
[2024-01-24 15:13:03,727] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:13:03,728] [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_017352135.1	s__Rhizobium lentis	100.0	2138	2138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017357245.1	s__Rhizobium bangladeshense	89.632	1772	2138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.42	98.08	0.93	0.91	5	-
GCF_017948245.1	s__Rhizobium sp017948245	89.6261	1801	2138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197535.1	s__Rhizobium aethiopicum_A	89.5748	1656	2138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.98	99.98	0.98	0.98	2	-
GCF_900094625.1	s__Rhizobium aethiopicum	89.283	1685	2138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.33	98.33	0.89	0.89	2	-
GCF_002117485.1	s__Rhizobium sp002117485	89.2738	1716	2138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.28	97.20	0.87	0.86	3	-
GCF_002204185.1	s__Rhizobium esperanzae	89.0241	1629	2138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.10	96.05	0.88	0.87	12	-
GCF_000092045.1	s__Rhizobium etli	88.718	1667	2138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.53	98.53	0.90	0.89	3	-
GCF_002531955.1	s__Rhizobium sp002531955	88.6997	1639	2138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.59	95.76	0.89	0.85	5	-
GCF_002211285.1	s__Rhizobium sp002211285	88.6231	1546	2138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003939025.1	s__Rhizobium sophoriradicis	88.1959	1653	2138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.45	97.30	0.92	0.88	16	-
GCF_003985125.1	s__Rhizobium phaseoli	88.1789	1621	2138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.51	96.92	0.91	0.87	41	-
GCF_000009265.1	s__Rhizobium leguminosarum_L	87.6786	1664	2138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.59	95.46	0.90	0.82	60	-
GCF_003938655.1	s__Rhizobium pisi	87.6403	1561	2138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.78	97.55	0.94	0.90	5	-
GCF_000769405.2	s__Rhizobium leguminosarum_E	87.4991	1608	2138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.71	96.49	0.91	0.87	37	-
--------------------------------------------------------------------------------
[2024-01-24 15:13:03,729] [INFO] GTDB search result was written to GCF_017352135.1_ASM1735213v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:13:03,730] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:13:03,742] [INFO] DFAST_QC result json was written to GCF_017352135.1_ASM1735213v1_genomic.fna/dqc_result.json
[2024-01-24 15:13:03,742] [INFO] DFAST_QC completed!
[2024-01-24 15:13:03,742] [INFO] Total running time: 0h2m14s