[2024-01-25 19:58:35,437] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:58:35,439] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:58:35,439] [INFO] DQC Reference Directory: /var/lib/cwl/stge33ee538-fdeb-4732-8229-887fdee6e3fb/dqc_reference
[2024-01-25 19:58:36,563] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:58:36,564] [INFO] Task started: Prodigal
[2024-01-25 19:58:36,564] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b61dcfb-fa39-4ee4-934f-c63414f3bb77/GCF_003130795.1_ASM313079v1_genomic.fna.gz | prodigal -d GCF_003130795.1_ASM313079v1_genomic.fna/cds.fna -a GCF_003130795.1_ASM313079v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:58:53,334] [INFO] Task succeeded: Prodigal
[2024-01-25 19:58:53,334] [INFO] Task started: HMMsearch
[2024-01-25 19:58:53,334] [INFO] Running command: hmmsearch --tblout GCF_003130795.1_ASM313079v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge33ee538-fdeb-4732-8229-887fdee6e3fb/dqc_reference/reference_markers.hmm GCF_003130795.1_ASM313079v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:58:53,734] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:58:53,735] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6b61dcfb-fa39-4ee4-934f-c63414f3bb77/GCF_003130795.1_ASM313079v1_genomic.fna.gz]
[2024-01-25 19:58:53,786] [INFO] Query marker FASTA was written to GCF_003130795.1_ASM313079v1_genomic.fna/markers.fasta
[2024-01-25 19:58:53,787] [INFO] Task started: Blastn
[2024-01-25 19:58:53,787] [INFO] Running command: blastn -query GCF_003130795.1_ASM313079v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge33ee538-fdeb-4732-8229-887fdee6e3fb/dqc_reference/reference_markers.fasta -out GCF_003130795.1_ASM313079v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:54,784] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:54,786] [INFO] Selected 19 target genomes.
[2024-01-25 19:58:54,787] [INFO] Target genome list was writen to GCF_003130795.1_ASM313079v1_genomic.fna/target_genomes.txt
[2024-01-25 19:58:54,816] [INFO] Task started: fastANI
[2024-01-25 19:58:54,816] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b61dcfb-fa39-4ee4-934f-c63414f3bb77/GCF_003130795.1_ASM313079v1_genomic.fna.gz --refList GCF_003130795.1_ASM313079v1_genomic.fna/target_genomes.txt --output GCF_003130795.1_ASM313079v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:59:28,025] [INFO] Task succeeded: fastANI
[2024-01-25 19:59:28,025] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge33ee538-fdeb-4732-8229-887fdee6e3fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:59:28,025] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge33ee538-fdeb-4732-8229-887fdee6e3fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:59:28,037] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:59:28,037] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:59:28,037] [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
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	100.0	2251	2255	95	conclusive
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	84.0535	1371	2255	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	83.7701	1278	2255	95	below_threshold
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	83.7666	1398	2255	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	83.481	1363	2255	95	below_threshold
Azospirillum lipoferum	strain=59b	GCA_008364955.1	193	193	type	True	83.4579	1375	2255	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	83.4395	1355	2255	95	below_threshold
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	83.2992	1073	2255	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	83.2883	1259	2255	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	83.2872	1353	2255	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	83.2673	1268	2255	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	83.1809	1292	2255	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	83.1394	1285	2255	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	83.1257	1211	2255	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	83.0455	1246	2255	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	82.8305	1217	2255	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	81.5744	1079	2255	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	78.3555	717	2255	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	77.3792	541	2255	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:59:28,039] [INFO] DFAST Taxonomy check result was written to GCF_003130795.1_ASM313079v1_genomic.fna/tc_result.tsv
[2024-01-25 19:59:28,040] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:59:28,040] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:59:28,040] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge33ee538-fdeb-4732-8229-887fdee6e3fb/dqc_reference/checkm_data
[2024-01-25 19:59:28,041] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:59:28,107] [INFO] Task started: CheckM
[2024-01-25 19:59:28,107] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003130795.1_ASM313079v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003130795.1_ASM313079v1_genomic.fna/checkm_input GCF_003130795.1_ASM313079v1_genomic.fna/checkm_result
[2024-01-25 20:00:36,747] [INFO] Task succeeded: CheckM
[2024-01-25 20:00:36,749] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 5.01%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2024-01-25 20:00:36,769] [INFO] ===== Completeness check finished =====
[2024-01-25 20:00:36,770] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:00:36,770] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003130795.1_ASM313079v1_genomic.fna/markers.fasta)
[2024-01-25 20:00:36,771] [INFO] Task started: Blastn
[2024-01-25 20:00:36,771] [INFO] Running command: blastn -query GCF_003130795.1_ASM313079v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge33ee538-fdeb-4732-8229-887fdee6e3fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_003130795.1_ASM313079v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:38,689] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:38,692] [INFO] Selected 18 target genomes.
[2024-01-25 20:00:38,692] [INFO] Target genome list was writen to GCF_003130795.1_ASM313079v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:00:38,704] [INFO] Task started: fastANI
[2024-01-25 20:00:38,704] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b61dcfb-fa39-4ee4-934f-c63414f3bb77/GCF_003130795.1_ASM313079v1_genomic.fna.gz --refList GCF_003130795.1_ASM313079v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003130795.1_ASM313079v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:01:12,254] [INFO] Task succeeded: fastANI
[2024-01-25 20:01:12,265] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:01:12,265] [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_003130795.1	s__Azospirillum thermophilum	100.0	2252	2255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003116095.1	s__Azospirillum sp003116095	84.2279	1442	2255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876095.1	s__Azospirillum agricola	84.013	1375	2255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	96.88	96.88	0.87	0.87	2	-
GCF_003233655.1	s__Azospirillum ramasamyi	83.8033	1278	2255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000283655.1	s__Azospirillum lipoferum_C	83.7617	1383	2255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305595.1	s__Azospirillum thiophilum	83.7453	1360	2255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008364825.1	s__Azospirillum sp008364825	83.7197	1344	2255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.23	95.23	0.77	0.77	2	-
GCF_003116035.1	s__Azospirillum sp003116035	83.7014	1376	2255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008364795.1	s__Azospirillum oryzae	83.6188	1310	2255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	98.65	97.30	0.92	0.84	3	-
GCF_003119115.1	s__Azospirillum sp003119115	83.5311	1301	2255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.55	95.10	0.94	0.88	3	-
GCF_016595245.1	s__Azospirillum sp016595245	83.5293	1370	2255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004923295.1	s__Azospirillum sp003115975	83.4817	1353	2255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003349955.1	s__Azospirillum brasilense_B	83.274	1226	2255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.36	95.36	0.89	0.89	2	-
GCF_001315015.1	s__Azospirillum brasilense	83.2387	1249	2255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0321	99.35	95.17	0.92	0.83	16	-
GCF_003119195.2	s__Azospirillum baldaniorum	83.1773	1294	2255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0321	97.20	95.48	0.90	0.83	11	-
GCF_007827815.1	s__Azospirillum brasilense_C	83.1048	1302	2255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.36	95.98	0.93	0.90	3	-
GCF_008365405.1	s__Azospirillum brasilense_D	83.0289	1248	2255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017876165.1	s__Azospirillum soli	82.8279	1215	2255	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:01:12,266] [INFO] GTDB search result was written to GCF_003130795.1_ASM313079v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:01:12,267] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:01:12,277] [INFO] DFAST_QC result json was written to GCF_003130795.1_ASM313079v1_genomic.fna/dqc_result.json
[2024-01-25 20:01:12,277] [INFO] DFAST_QC completed!
[2024-01-25 20:01:12,277] [INFO] Total running time: 0h2m37s