[2024-01-24 14:05:33,825] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:33,827] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:33,827] [INFO] DQC Reference Directory: /var/lib/cwl/stgccd6be1c-ae1b-4ef2-8070-d9004c3addeb/dqc_reference
[2024-01-24 14:05:35,337] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:35,342] [INFO] Task started: Prodigal
[2024-01-24 14:05:35,342] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ea3b0d9-6f0c-4b53-b0ab-d21d3fced23a/GCF_017876115.1_ASM1787611v1_genomic.fna.gz | prodigal -d GCF_017876115.1_ASM1787611v1_genomic.fna/cds.fna -a GCF_017876115.1_ASM1787611v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:57,625] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:57,626] [INFO] Task started: HMMsearch
[2024-01-24 14:05:57,626] [INFO] Running command: hmmsearch --tblout GCF_017876115.1_ASM1787611v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgccd6be1c-ae1b-4ef2-8070-d9004c3addeb/dqc_reference/reference_markers.hmm GCF_017876115.1_ASM1787611v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:58,045] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:58,046] [INFO] Found 6/6 markers.
[2024-01-24 14:05:58,109] [INFO] Query marker FASTA was written to GCF_017876115.1_ASM1787611v1_genomic.fna/markers.fasta
[2024-01-24 14:05:58,109] [INFO] Task started: Blastn
[2024-01-24 14:05:58,109] [INFO] Running command: blastn -query GCF_017876115.1_ASM1787611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccd6be1c-ae1b-4ef2-8070-d9004c3addeb/dqc_reference/reference_markers.fasta -out GCF_017876115.1_ASM1787611v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:59,103] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:59,107] [INFO] Selected 15 target genomes.
[2024-01-24 14:05:59,107] [INFO] Target genome list was writen to GCF_017876115.1_ASM1787611v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:59,123] [INFO] Task started: fastANI
[2024-01-24 14:05:59,123] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ea3b0d9-6f0c-4b53-b0ab-d21d3fced23a/GCF_017876115.1_ASM1787611v1_genomic.fna.gz --refList GCF_017876115.1_ASM1787611v1_genomic.fna/target_genomes.txt --output GCF_017876115.1_ASM1787611v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:26,804] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:26,805] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgccd6be1c-ae1b-4ef2-8070-d9004c3addeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:26,805] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgccd6be1c-ae1b-4ef2-8070-d9004c3addeb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:26,818] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:26,818] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:26,819] [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	100.0	2298	2305	95	conclusive
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	86.9894	1498	2305	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	86.9322	1604	2305	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	86.9164	1614	2305	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	86.8353	1501	2305	95	below_threshold
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	86.8102	1636	2305	95	below_threshold
Azospirillum lipoferum	strain=59b	GCA_008364955.1	193	193	type	True	86.7211	1612	2305	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	86.7065	1653	2305	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	86.6721	1631	2305	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	86.5656	1508	2305	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	82.3581	1128	2305	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	82.2875	1231	2305	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	81.9172	1081	2305	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	78.1245	633	2305	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.6513	547	2305	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:26,820] [INFO] DFAST Taxonomy check result was written to GCF_017876115.1_ASM1787611v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:26,821] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:26,821] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:26,821] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgccd6be1c-ae1b-4ef2-8070-d9004c3addeb/dqc_reference/checkm_data
[2024-01-24 14:06:26,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:26,898] [INFO] Task started: CheckM
[2024-01-24 14:06:26,898] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017876115.1_ASM1787611v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017876115.1_ASM1787611v1_genomic.fna/checkm_input GCF_017876115.1_ASM1787611v1_genomic.fna/checkm_result
[2024-01-24 14:07:35,246] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:35,247] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.71%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:35,268] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:35,268] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:35,268] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017876115.1_ASM1787611v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:35,269] [INFO] Task started: Blastn
[2024-01-24 14:07:35,269] [INFO] Running command: blastn -query GCF_017876115.1_ASM1787611v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgccd6be1c-ae1b-4ef2-8070-d9004c3addeb/dqc_reference/reference_markers_gtdb.fasta -out GCF_017876115.1_ASM1787611v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:37,203] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:37,206] [INFO] Selected 13 target genomes.
[2024-01-24 14:07:37,207] [INFO] Target genome list was writen to GCF_017876115.1_ASM1787611v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:37,215] [INFO] Task started: fastANI
[2024-01-24 14:07:37,215] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ea3b0d9-6f0c-4b53-b0ab-d21d3fced23a/GCF_017876115.1_ASM1787611v1_genomic.fna.gz --refList GCF_017876115.1_ASM1787611v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017876115.1_ASM1787611v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:01,745] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:01,757] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:01,758] [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	100.0	2298	2305	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	87.0426	1700	2305	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116095.1	s__Azospirillum sp003116095	87.0379	1561	2305	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	86.971	1500	2305	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	98.65	97.30	0.92	0.84	3	-
GCF_001305595.1	s__Azospirillum thiophilum	86.9197	1614	2305	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900177515.1	s__Azospirillum oryzae_A	86.8958	1619	2305	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	86.8568	1610	2305	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	86.8372	1501	2305	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	86.7993	1535	2305	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008364955.1	s__Azospirillum lipoferum	86.7254	1611	2305	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	86.6928	1624	2305	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	86.6664	1634	2305	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.17	95.47	0.91	0.85	4	-
GCF_001639105.2	s__Azospirillum humicireducens	86.5387	1511	2305	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:01,766] [INFO] GTDB search result was written to GCF_017876115.1_ASM1787611v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:01,767] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:01,772] [INFO] DFAST_QC result json was written to GCF_017876115.1_ASM1787611v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:01,772] [INFO] DFAST_QC completed!
[2024-01-24 14:08:01,772] [INFO] Total running time: 0h2m28s