[2024-01-25 17:51:35,528] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:51:35,529] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:51:35,529] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f75615a-6261-4fb4-951b-cf319141f8fe/dqc_reference
[2024-01-25 17:51:36,641] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:51:36,641] [INFO] Task started: Prodigal
[2024-01-25 17:51:36,641] [INFO] Running command: gunzip -c /var/lib/cwl/stg398ce766-6cfb-46eb-8351-e6efb26e8ed7/GCF_030814895.1_ASM3081489v1_genomic.fna.gz | prodigal -d GCF_030814895.1_ASM3081489v1_genomic.fna/cds.fna -a GCF_030814895.1_ASM3081489v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:51:55,684] [INFO] Task succeeded: Prodigal
[2024-01-25 17:51:55,684] [INFO] Task started: HMMsearch
[2024-01-25 17:51:55,684] [INFO] Running command: hmmsearch --tblout GCF_030814895.1_ASM3081489v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f75615a-6261-4fb4-951b-cf319141f8fe/dqc_reference/reference_markers.hmm GCF_030814895.1_ASM3081489v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:51:56,013] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:51:56,014] [INFO] Found 6/6 markers.
[2024-01-25 17:51:56,068] [INFO] Query marker FASTA was written to GCF_030814895.1_ASM3081489v1_genomic.fna/markers.fasta
[2024-01-25 17:51:56,068] [INFO] Task started: Blastn
[2024-01-25 17:51:56,068] [INFO] Running command: blastn -query GCF_030814895.1_ASM3081489v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f75615a-6261-4fb4-951b-cf319141f8fe/dqc_reference/reference_markers.fasta -out GCF_030814895.1_ASM3081489v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:57,019] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:57,024] [INFO] Selected 15 target genomes.
[2024-01-25 17:51:57,024] [INFO] Target genome list was writen to GCF_030814895.1_ASM3081489v1_genomic.fna/target_genomes.txt
[2024-01-25 17:51:57,051] [INFO] Task started: fastANI
[2024-01-25 17:51:57,051] [INFO] Running command: fastANI --query /var/lib/cwl/stg398ce766-6cfb-46eb-8351-e6efb26e8ed7/GCF_030814895.1_ASM3081489v1_genomic.fna.gz --refList GCF_030814895.1_ASM3081489v1_genomic.fna/target_genomes.txt --output GCF_030814895.1_ASM3081489v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:52:23,923] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:23,924] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f75615a-6261-4fb4-951b-cf319141f8fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:52:23,925] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f75615a-6261-4fb4-951b-cf319141f8fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:52:23,934] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:52:23,934] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:52:23,934] [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 picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	99.9976	2301	2308	95	conclusive
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	87.0458	1586	2308	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	86.9923	1596	2308	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	86.9824	1501	2308	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	86.8686	1496	2308	95	below_threshold
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	86.8478	1634	2308	95	below_threshold
Azospirillum lipoferum	strain=59b	GCA_008364955.1	193	193	type	True	86.7479	1615	2308	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	86.7172	1636	2308	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	86.6703	1659	2308	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	86.549	1520	2308	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	82.3147	1146	2308	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	82.2602	1239	2308	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	81.9308	1078	2308	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	78.1332	633	2308	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.652	545	2308	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:52:23,936] [INFO] DFAST Taxonomy check result was written to GCF_030814895.1_ASM3081489v1_genomic.fna/tc_result.tsv
[2024-01-25 17:52:23,936] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:52:23,936] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:52:23,936] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f75615a-6261-4fb4-951b-cf319141f8fe/dqc_reference/checkm_data
[2024-01-25 17:52:23,937] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:52:24,003] [INFO] Task started: CheckM
[2024-01-25 17:52:24,003] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030814895.1_ASM3081489v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030814895.1_ASM3081489v1_genomic.fna/checkm_input GCF_030814895.1_ASM3081489v1_genomic.fna/checkm_result
[2024-01-25 17:53:32,785] [INFO] Task succeeded: CheckM
[2024-01-25 17:53:32,787] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.71%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:53:32,825] [INFO] ===== Completeness check finished =====
[2024-01-25 17:53:32,825] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:53:32,825] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030814895.1_ASM3081489v1_genomic.fna/markers.fasta)
[2024-01-25 17:53:32,826] [INFO] Task started: Blastn
[2024-01-25 17:53:32,826] [INFO] Running command: blastn -query GCF_030814895.1_ASM3081489v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f75615a-6261-4fb4-951b-cf319141f8fe/dqc_reference/reference_markers_gtdb.fasta -out GCF_030814895.1_ASM3081489v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:53:34,889] [INFO] Task succeeded: Blastn
[2024-01-25 17:53:34,892] [INFO] Selected 13 target genomes.
[2024-01-25 17:53:34,892] [INFO] Target genome list was writen to GCF_030814895.1_ASM3081489v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:53:34,903] [INFO] Task started: fastANI
[2024-01-25 17:53:34,903] [INFO] Running command: fastANI --query /var/lib/cwl/stg398ce766-6cfb-46eb-8351-e6efb26e8ed7/GCF_030814895.1_ASM3081489v1_genomic.fna.gz --refList GCF_030814895.1_ASM3081489v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030814895.1_ASM3081489v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:53:59,963] [INFO] Task succeeded: fastANI
[2024-01-25 17:53:59,971] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:53:59,971] [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_017876115.1	s__Azospirillum picis	99.9976	2301	2308	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_016595245.1	s__Azospirillum sp016595245	87.1328	1684	2308	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	87.0136	1593	2308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008364795.1	s__Azospirillum oryzae	87.0071	1498	2308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	98.65	97.30	0.92	0.84	3	-
GCF_003116095.1	s__Azospirillum sp003116095	87.0049	1576	2308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177515.1	s__Azospirillum oryzae_A	86.9951	1617	2308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004923315.1	s__Azospirillum sp003116065	86.943	1609	2308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.27	96.11	0.89	0.85	4	-
GCF_003233655.1	s__Azospirillum ramasamyi	86.8857	1495	2308	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	86.836	1542	2308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013340935.1	s__Azospirillum melinis	86.7507	1631	2308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.17	95.47	0.91	0.85	4	-
GCF_008364955.1	s__Azospirillum lipoferum	86.7456	1614	2308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116035.1	s__Azospirillum sp003116035	86.6726	1625	2308	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001639105.2	s__Azospirillum humicireducens	86.5367	1521	2308	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 17:53:59,973] [INFO] GTDB search result was written to GCF_030814895.1_ASM3081489v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:53:59,973] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:53:59,976] [INFO] DFAST_QC result json was written to GCF_030814895.1_ASM3081489v1_genomic.fna/dqc_result.json
[2024-01-25 17:53:59,976] [INFO] DFAST_QC completed!
[2024-01-25 17:53:59,976] [INFO] Total running time: 0h2m24s