[2024-01-25 19:59:20,516] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:59:20,518] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:59:20,518] [INFO] DQC Reference Directory: /var/lib/cwl/stga9ba2647-510a-4a29-8cd6-d5bee3b48e55/dqc_reference
[2024-01-25 19:59:21,649] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:59:21,650] [INFO] Task started: Prodigal
[2024-01-25 19:59:21,650] [INFO] Running command: gunzip -c /var/lib/cwl/stge4f356a2-eb9e-4836-990d-3927bc46dbed/GCF_017873135.1_ASM1787313v1_genomic.fna.gz | prodigal -d GCF_017873135.1_ASM1787313v1_genomic.fna/cds.fna -a GCF_017873135.1_ASM1787313v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:59:37,867] [INFO] Task succeeded: Prodigal
[2024-01-25 19:59:37,867] [INFO] Task started: HMMsearch
[2024-01-25 19:59:37,867] [INFO] Running command: hmmsearch --tblout GCF_017873135.1_ASM1787313v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9ba2647-510a-4a29-8cd6-d5bee3b48e55/dqc_reference/reference_markers.hmm GCF_017873135.1_ASM1787313v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:59:38,260] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:59:38,261] [INFO] Found 6/6 markers.
[2024-01-25 19:59:38,313] [INFO] Query marker FASTA was written to GCF_017873135.1_ASM1787313v1_genomic.fna/markers.fasta
[2024-01-25 19:59:38,314] [INFO] Task started: Blastn
[2024-01-25 19:59:38,314] [INFO] Running command: blastn -query GCF_017873135.1_ASM1787313v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9ba2647-510a-4a29-8cd6-d5bee3b48e55/dqc_reference/reference_markers.fasta -out GCF_017873135.1_ASM1787313v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:39,381] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:39,384] [INFO] Selected 26 target genomes.
[2024-01-25 19:59:39,384] [INFO] Target genome list was writen to GCF_017873135.1_ASM1787313v1_genomic.fna/target_genomes.txt
[2024-01-25 19:59:39,404] [INFO] Task started: fastANI
[2024-01-25 19:59:39,404] [INFO] Running command: fastANI --query /var/lib/cwl/stge4f356a2-eb9e-4836-990d-3927bc46dbed/GCF_017873135.1_ASM1787313v1_genomic.fna.gz --refList GCF_017873135.1_ASM1787313v1_genomic.fna/target_genomes.txt --output GCF_017873135.1_ASM1787313v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:00:12,000] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:12,001] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9ba2647-510a-4a29-8cd6-d5bee3b48e55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:00:12,002] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9ba2647-510a-4a29-8cd6-d5bee3b48e55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:00:12,016] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:00:12,016] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:00:12,016] [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 giardinii	strain=H152	GCA_000379605.1	56731	56731	type	True	84.8223	1296	2028	95	below_threshold
Pararhizobium antarcticum	strain=NAQVI 59	GCA_001885585.1	1798805	1798805	type	True	82.1539	1078	2028	95	below_threshold
Shinella zoogloeoides	strain=DSM 287	GCA_009826855.1	352475	352475	type	True	80.6825	780	2028	95	below_threshold
Ensifer sesbaniae	strain=CCBAU 65729	GCA_013283665.1	1214071	1214071	type	True	80.5903	960	2028	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	80.4706	947	2028	95	below_threshold
Shinella kummerowiae	strain=CCBAU 25048	GCA_009827055.1	417745	417745	type	True	80.3718	882	2028	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.2752	782	2028	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	80.2691	857	2028	95	below_threshold
Sinorhizobium fredii	strain=NBRC 14780	GCA_006539605.1	380	380	type	True	80.1907	875	2028	95	below_threshold
Sinorhizobium fredii	strain=USDA205	GCA_009601405.1	380	380	type	True	80.1737	890	2028	95	below_threshold
Rhizobium ecuadorense	strain=CNPSO 671	GCA_001187535.1	1671795	1671795	type	True	80.1686	822	2028	95	below_threshold
Sinorhizobium fredii	strain=USDA 205	GCA_001461695.1	380	380	type	True	80.1591	888	2028	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	80.0123	832	2028	95	below_threshold
Rhizobium chutanense	strain=C5	GCA_002531935.1	2035448	2035448	type	True	79.9994	864	2028	95	below_threshold
Rhizobium changzhiense	strain=WYCCWR 11279	GCA_013087625.1	2692317	2692317	type	True	79.9609	860	2028	95	below_threshold
Rhizobium sophorae	strain=CCBAU 03386	GCA_013087515.1	1535242	1535242	type	True	79.9399	892	2028	95	below_threshold
Rhizobium laguerreae	strain=FB206	GCA_002008165.1	1076926	1076926	type	True	79.9266	857	2028	95	below_threshold
Rhizobium fabae	strain=CCBAU 33202	GCA_003985135.1	573179	573179	type	True	79.9107	834	2028	95	below_threshold
Rhizobium fabae	strain=DSM 19331	GCA_014196235.1	573179	573179	type	True	79.9051	828	2028	95	below_threshold
Rhizobium laguerreae	strain=CECT 8280	GCA_014192445.1	1076926	1076926	type	True	79.8837	854	2028	95	below_threshold
Rhizobium etli	strain=CFN 42	GCA_000092045.1	29449	29449	suspected-type	True	79.7679	814	2028	95	below_threshold
Ensifer psoraleae	strain=CCBAU 65732	GCA_013283645.1	520838	520838	type	True	79.6922	862	2028	95	below_threshold
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	79.0751	619	2028	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	79.0135	625	2028	95	below_threshold
Rhizobium skierniewicense	strain=Ch11	GCA_023757665.1	984260	984260	type	True	77.79	418	2028	95	below_threshold
Rhizobium skierniewicense	strain=DSM 26438	GCA_014196515.1	984260	984260	type	True	77.7235	416	2028	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:00:12,017] [INFO] DFAST Taxonomy check result was written to GCF_017873135.1_ASM1787313v1_genomic.fna/tc_result.tsv
[2024-01-25 20:00:12,018] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:00:12,018] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:00:12,018] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9ba2647-510a-4a29-8cd6-d5bee3b48e55/dqc_reference/checkm_data
[2024-01-25 20:00:12,019] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:00:12,075] [INFO] Task started: CheckM
[2024-01-25 20:00:12,075] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017873135.1_ASM1787313v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017873135.1_ASM1787313v1_genomic.fna/checkm_input GCF_017873135.1_ASM1787313v1_genomic.fna/checkm_result
[2024-01-25 20:01:00,959] [INFO] Task succeeded: CheckM
[2024-01-25 20:01:00,961] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:01:00,980] [INFO] ===== Completeness check finished =====
[2024-01-25 20:01:00,980] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:01:00,980] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017873135.1_ASM1787313v1_genomic.fna/markers.fasta)
[2024-01-25 20:01:00,981] [INFO] Task started: Blastn
[2024-01-25 20:01:00,981] [INFO] Running command: blastn -query GCF_017873135.1_ASM1787313v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga9ba2647-510a-4a29-8cd6-d5bee3b48e55/dqc_reference/reference_markers_gtdb.fasta -out GCF_017873135.1_ASM1787313v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:02,995] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:02,998] [INFO] Selected 9 target genomes.
[2024-01-25 20:01:02,998] [INFO] Target genome list was writen to GCF_017873135.1_ASM1787313v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:01:03,006] [INFO] Task started: fastANI
[2024-01-25 20:01:03,006] [INFO] Running command: fastANI --query /var/lib/cwl/stge4f356a2-eb9e-4836-990d-3927bc46dbed/GCF_017873135.1_ASM1787313v1_genomic.fna.gz --refList GCF_017873135.1_ASM1787313v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017873135.1_ASM1787313v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:01:16,899] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:16,906] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:01:16,906] [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_017873135.1	s__Pararhizobium herbae	100.0	2028	2028	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001687365.1	s__Pararhizobium polonicum	88.8037	1448	2028	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745255.1	s__Pararhizobium sp000745255	87.5556	1521	2028	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	96.24	95.31	0.88	0.85	4	-
GCA_900468065.1	s__Pararhizobium sp900468065	85.9625	1325	2028	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900473045.1	s__Pararhizobium sp900473045	85.6996	1328	2028	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745575.1	s__Pararhizobium sp000745575	85.476	1360	2028	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	96.55	96.55	0.93	0.93	2	-
GCF_001426685.1	s__Pararhizobium sp001426685	85.4642	1282	2028	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900472175.1	s__Pararhizobium sp900472175	85.305	1295	2028	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426665.1	s__Pararhizobium sp001426665	84.9369	1313	2028	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	99.66	98.98	0.96	0.87	4	-
--------------------------------------------------------------------------------
[2024-01-25 20:01:16,907] [INFO] GTDB search result was written to GCF_017873135.1_ASM1787313v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:01:16,908] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:01:16,911] [INFO] DFAST_QC result json was written to GCF_017873135.1_ASM1787313v1_genomic.fna/dqc_result.json
[2024-01-25 20:01:16,911] [INFO] DFAST_QC completed!
[2024-01-25 20:01:16,911] [INFO] Total running time: 0h1m56s