[2024-01-24 13:12:55,852] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:55,885] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:55,885] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3274504-8ec8-4a52-bdd0-55b6f8a76265/dqc_reference
[2024-01-24 13:12:57,301] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:57,302] [INFO] Task started: Prodigal
[2024-01-24 13:12:57,302] [INFO] Running command: gunzip -c /var/lib/cwl/stg2594e502-6d09-4541-be64-824413372734/GCF_000769405.2_CC275e2020_genomic.fna.gz | prodigal -d GCF_000769405.2_CC275e2020_genomic.fna/cds.fna -a GCF_000769405.2_CC275e2020_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:19,293] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:19,293] [INFO] Task started: HMMsearch
[2024-01-24 13:13:19,293] [INFO] Running command: hmmsearch --tblout GCF_000769405.2_CC275e2020_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3274504-8ec8-4a52-bdd0-55b6f8a76265/dqc_reference/reference_markers.hmm GCF_000769405.2_CC275e2020_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:19,674] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:19,676] [INFO] Found 6/6 markers.
[2024-01-24 13:13:19,731] [INFO] Query marker FASTA was written to GCF_000769405.2_CC275e2020_genomic.fna/markers.fasta
[2024-01-24 13:13:19,732] [INFO] Task started: Blastn
[2024-01-24 13:13:19,732] [INFO] Running command: blastn -query GCF_000769405.2_CC275e2020_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3274504-8ec8-4a52-bdd0-55b6f8a76265/dqc_reference/reference_markers.fasta -out GCF_000769405.2_CC275e2020_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:20,813] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:20,816] [INFO] Selected 16 target genomes.
[2024-01-24 13:13:20,817] [INFO] Target genome list was writen to GCF_000769405.2_CC275e2020_genomic.fna/target_genomes.txt
[2024-01-24 13:13:20,823] [INFO] Task started: fastANI
[2024-01-24 13:13:20,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg2594e502-6d09-4541-be64-824413372734/GCF_000769405.2_CC275e2020_genomic.fna.gz --refList GCF_000769405.2_CC275e2020_genomic.fna/target_genomes.txt --output GCF_000769405.2_CC275e2020_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:49,472] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:49,473] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3274504-8ec8-4a52-bdd0-55b6f8a76265/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:49,473] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3274504-8ec8-4a52-bdd0-55b6f8a76265/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:49,490] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:13:49,490] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:13:49,490] [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 indicum	strain=JKLM 12A2	GCA_005862305.2	2583231	2583231	type	True	93.9078	1980	2369	95	below_threshold
Rhizobium ruizarguesonis	strain=UPM1133	GCA_012349115.1	2081791	2081791	type	True	93.6157	1952	2369	95	below_threshold
Rhizobium leguminosarum	strain=USDA 2370	GCA_003058385.1	384	384	suspected-type	True	93.3965	1963	2369	95	below_threshold
Rhizobium leguminosarum	strain=DSM 106839	GCA_014202125.1	384	384	suspected-type	True	93.3897	1968	2369	95	below_threshold
Rhizobium leguminosarum	strain=USDA 2370	GCA_002008365.1	384	384	suspected-type	True	93.3643	1957	2369	95	below_threshold
Rhizobium indigoferae	strain=CCBAU 71042	GCA_013087605.1	158891	158891	type	True	93.3003	1917	2369	95	below_threshold
Rhizobium changzhiense	strain=WYCCWR 11279	GCA_013087625.1	2692317	2692317	type	True	93.0748	1811	2369	95	below_threshold
Rhizobium laguerreae	strain=CECT 8280	GCA_014192445.1	1076926	1076926	type	True	92.9866	1883	2369	95	below_threshold
Rhizobium laguerreae	strain=FB206	GCA_002008165.1	1076926	1076926	type	True	92.9796	1879	2369	95	below_threshold
Rhizobium sophorae	strain=CCBAU 03386	GCA_013087515.1	1535242	1535242	type	True	92.9474	1912	2369	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	89.0218	1765	2369	95	below_threshold
Rhizobium hidalgonense	strain=FH14	GCA_002531855.1	1538159	1538159	type	True	88.6711	1714	2369	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	87.9613	1599	2369	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	81.5362	1190	2369	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	80.2219	1021	2369	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.0562	752	2369	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:49,493] [INFO] DFAST Taxonomy check result was written to GCF_000769405.2_CC275e2020_genomic.fna/tc_result.tsv
[2024-01-24 13:13:49,493] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:49,494] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:49,494] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3274504-8ec8-4a52-bdd0-55b6f8a76265/dqc_reference/checkm_data
[2024-01-24 13:13:49,495] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:49,558] [INFO] Task started: CheckM
[2024-01-24 13:13:49,559] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000769405.2_CC275e2020_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000769405.2_CC275e2020_genomic.fna/checkm_input GCF_000769405.2_CC275e2020_genomic.fna/checkm_result
[2024-01-24 13:14:48,541] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:48,543] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:48,563] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:48,563] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:48,563] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000769405.2_CC275e2020_genomic.fna/markers.fasta)
[2024-01-24 13:14:48,564] [INFO] Task started: Blastn
[2024-01-24 13:14:48,564] [INFO] Running command: blastn -query GCF_000769405.2_CC275e2020_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3274504-8ec8-4a52-bdd0-55b6f8a76265/dqc_reference/reference_markers_gtdb.fasta -out GCF_000769405.2_CC275e2020_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:50,656] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:50,661] [INFO] Selected 13 target genomes.
[2024-01-24 13:14:50,661] [INFO] Target genome list was writen to GCF_000769405.2_CC275e2020_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:50,678] [INFO] Task started: fastANI
[2024-01-24 13:14:50,678] [INFO] Running command: fastANI --query /var/lib/cwl/stg2594e502-6d09-4541-be64-824413372734/GCF_000769405.2_CC275e2020_genomic.fna.gz --refList GCF_000769405.2_CC275e2020_genomic.fna/target_genomes_gtdb.txt --output GCF_000769405.2_CC275e2020_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:16,878] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:16,890] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:16,890] [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_000769405.2	s__Rhizobium leguminosarum_E	100.0	2367	2369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.71	96.49	0.91	0.87	37	conclusive
GCF_000023185.1	s__Rhizobium leguminosarum_J	94.7504	1970	2369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.61	97.68	0.92	0.88	6	-
GCF_002953715.1	s__Rhizobium leguminosarum_K	94.2108	1969	2369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	95.64	95.51	0.85	0.83	10	-
GCF_001657485.1	s__Rhizobium sp001657485	94.0158	2015	2369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.95	97.95	0.90	0.90	2	-
GCF_005862305.2	s__Rhizobium indicum	93.9057	1981	2369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.44	95.15	0.91	0.82	6	-
GCF_000009265.1	s__Rhizobium leguminosarum_L	93.8429	2017	2369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.59	95.46	0.90	0.82	60	-
GCF_012349115.1	s__Rhizobium ruizarguesonis	93.6157	1952	2369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.01	96.15	0.89	0.84	170	-
GCF_004123835.1	s__Rhizobium leguminosarum_M	93.452	1864	2369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002008365.1	s__Rhizobium leguminosarum	93.3512	1959	2369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.98	97.38	0.91	0.86	85	-
GCF_001652265.1	s__Rhizobium leguminosarum_D	93.0826	1880	2369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.67	97.67	0.88	0.88	3	-
GCF_002008165.1	s__Rhizobium laguerreae	92.9653	1881	2369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.33	95.04	0.87	0.82	51	-
GCF_013087515.1	s__Rhizobium sophorae	92.9472	1912	2369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.85	95.49	0.87	0.83	6	-
GCF_000371905.1	s__Rhizobium leguminosarum_I	92.7227	1871	2369	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.88	97.75	0.91	0.88	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:16,892] [INFO] GTDB search result was written to GCF_000769405.2_CC275e2020_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:16,892] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:16,897] [INFO] DFAST_QC result json was written to GCF_000769405.2_CC275e2020_genomic.fna/dqc_result.json
[2024-01-24 13:15:16,898] [INFO] DFAST_QC completed!
[2024-01-24 13:15:16,898] [INFO] Total running time: 0h2m21s