[2024-01-24 11:05:22,000] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:22,002] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:22,002] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f73d915-299c-4416-b6f6-88aab1ce98ab/dqc_reference
[2024-01-24 11:05:23,354] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:23,355] [INFO] Task started: Prodigal
[2024-01-24 11:05:23,355] [INFO] Running command: gunzip -c /var/lib/cwl/stg6835d396-f0b9-4dec-aa9b-89fb056f457e/GCF_002531855.1_ASM253185v1_genomic.fna.gz | prodigal -d GCF_002531855.1_ASM253185v1_genomic.fna/cds.fna -a GCF_002531855.1_ASM253185v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:44,647] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:44,647] [INFO] Task started: HMMsearch
[2024-01-24 11:05:44,647] [INFO] Running command: hmmsearch --tblout GCF_002531855.1_ASM253185v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f73d915-299c-4416-b6f6-88aab1ce98ab/dqc_reference/reference_markers.hmm GCF_002531855.1_ASM253185v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:45,042] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:45,043] [INFO] Found 6/6 markers.
[2024-01-24 11:05:45,099] [INFO] Query marker FASTA was written to GCF_002531855.1_ASM253185v1_genomic.fna/markers.fasta
[2024-01-24 11:05:45,099] [INFO] Task started: Blastn
[2024-01-24 11:05:45,099] [INFO] Running command: blastn -query GCF_002531855.1_ASM253185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f73d915-299c-4416-b6f6-88aab1ce98ab/dqc_reference/reference_markers.fasta -out GCF_002531855.1_ASM253185v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:46,065] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:46,069] [INFO] Selected 18 target genomes.
[2024-01-24 11:05:46,069] [INFO] Target genome list was writen to GCF_002531855.1_ASM253185v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:46,093] [INFO] Task started: fastANI
[2024-01-24 11:05:46,093] [INFO] Running command: fastANI --query /var/lib/cwl/stg6835d396-f0b9-4dec-aa9b-89fb056f457e/GCF_002531855.1_ASM253185v1_genomic.fna.gz --refList GCF_002531855.1_ASM253185v1_genomic.fna/target_genomes.txt --output GCF_002531855.1_ASM253185v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:17,058] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:17,058] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f73d915-299c-4416-b6f6-88aab1ce98ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:17,059] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f73d915-299c-4416-b6f6-88aab1ce98ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:17,073] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:06:17,073] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:17,073] [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 hidalgonense	strain=FH14	GCA_002531855.1	1538159	1538159	type	True	100.0	2351	2358	95	conclusive
Rhizobium hidalgonense	strain=FH14	GCA_002914525.1	1538159	1538159	type	True	100.0	2351	2358	95	conclusive
Rhizobium ecuadorense	strain=CNPSO 671	GCA_001187535.1	1671795	1671795	type	True	91.3237	1734	2358	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	90.9891	1832	2358	95	below_threshold
Rhizobium chutanense	strain=C5	GCA_002531935.1	2035448	2035448	type	True	90.902	1793	2358	95	below_threshold
Rhizobium anhuiense	strain=CGMCC 1.12621	GCA_014638185.1	1184720	1184720	type	True	89.0589	1700	2358	95	below_threshold
Rhizobium anhuiense	strain=CCBAU 23252	GCA_003985145.1	1184720	1184720	type	True	89.0526	1718	2358	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	88.8791	1747	2358	95	below_threshold
Rhizobium ruizarguesonis	strain=UPM1133	GCA_012349115.1	2081791	2081791	type	True	88.8194	1765	2358	95	below_threshold
Rhizobium changzhiense	strain=WYCCWR 11279	GCA_013087625.1	2692317	2692317	type	True	88.7978	1652	2358	95	below_threshold
Rhizobium sophorae	strain=CCBAU 03386	GCA_013087515.1	1535242	1535242	type	True	88.6337	1710	2358	95	below_threshold
Rhizobium laguerreae	strain=FB206	GCA_002008165.1	1076926	1076926	type	True	88.4495	1745	2358	95	below_threshold
Rhizobium laguerreae	strain=CECT 8280	GCA_014192445.1	1076926	1076926	type	True	88.4365	1741	2358	95	below_threshold
Rhizobium pisi	strain=DSM 30132	GCA_003938655.1	574561	574561	type	True	87.8997	1643	2358	95	below_threshold
Rhizobium fabae	strain=CCBAU 33202	GCA_003985135.1	573179	573179	type	True	87.8345	1634	2358	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	81.4132	1143	2358	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	80.3567	991	2358	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.0534	743	2358	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:17,075] [INFO] DFAST Taxonomy check result was written to GCF_002531855.1_ASM253185v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:17,075] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:17,076] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:17,076] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f73d915-299c-4416-b6f6-88aab1ce98ab/dqc_reference/checkm_data
[2024-01-24 11:06:17,077] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:17,146] [INFO] Task started: CheckM
[2024-01-24 11:06:17,146] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002531855.1_ASM253185v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002531855.1_ASM253185v1_genomic.fna/checkm_input GCF_002531855.1_ASM253185v1_genomic.fna/checkm_result
[2024-01-24 11:07:15,870] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:15,871] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:15,892] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:15,892] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:15,892] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002531855.1_ASM253185v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:15,893] [INFO] Task started: Blastn
[2024-01-24 11:07:15,893] [INFO] Running command: blastn -query GCF_002531855.1_ASM253185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f73d915-299c-4416-b6f6-88aab1ce98ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_002531855.1_ASM253185v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:17,885] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:17,888] [INFO] Selected 15 target genomes.
[2024-01-24 11:07:17,889] [INFO] Target genome list was writen to GCF_002531855.1_ASM253185v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:17,911] [INFO] Task started: fastANI
[2024-01-24 11:07:17,911] [INFO] Running command: fastANI --query /var/lib/cwl/stg6835d396-f0b9-4dec-aa9b-89fb056f457e/GCF_002531855.1_ASM253185v1_genomic.fna.gz --refList GCF_002531855.1_ASM253185v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002531855.1_ASM253185v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:44,866] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:44,883] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:44,883] [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_002914525.1	s__Rhizobium hidalgonense	100.0	2351	2358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.87	98.55	0.90	0.84	6	conclusive
GCF_000271845.1	s__Rhizobium leguminosarum_G	92.1916	1868	2358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187535.1	s__Rhizobium ecuadorense	91.3237	1734	2358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.51	98.31	0.89	0.89	4	-
GCF_000172795.2	s__Rhizobium sp000172795	91.0879	1718	2358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197615.1	s__Rhizobium esperanzae_A	91.0035	1634	2358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002531905.1	s__Rhizobium sp002531905	90.9486	1835	2358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.24	98.93	0.89	0.86	4	-
GCF_002531935.1	s__Rhizobium chutanense	90.9137	1791	2358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.76	96.76	0.89	0.89	2	-
GCF_002531755.2	s__Rhizobium acidisoli	90.8826	1875	2358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.96	96.40	0.88	0.80	8	-
GCF_001664485.1	s__Rhizobium sp001664485	90.8675	1846	2358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.08	96.02	0.91	0.83	8	-
GCF_014198335.1	s__Rhizobium leguminosarum_N	90.8477	1679	2358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.95	99.93	0.95	0.91	10	-
GCF_002531725.1	s__Rhizobium sp002531725	90.3408	1804	2358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000292525.1	s__Rhizobium sp000292525	89.684	1763	2358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876795.1	s__Rhizobium leguminosarum_P	89.6667	1757	2358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010668805.1	s__Rhizobium phaseoli_A	89.6328	1738	2358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003985145.1	s__Rhizobium anhuiense	89.0524	1718	2358	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.85	98.46	0.91	0.88	19	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:44,885] [INFO] GTDB search result was written to GCF_002531855.1_ASM253185v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:44,886] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:44,889] [INFO] DFAST_QC result json was written to GCF_002531855.1_ASM253185v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:44,890] [INFO] DFAST_QC completed!
[2024-01-24 11:07:44,890] [INFO] Total running time: 0h2m23s