[2024-01-25 19:56:05,669] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:56:05,670] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:56:05,671] [INFO] DQC Reference Directory: /var/lib/cwl/stgf75b4f5d-9f57-4f58-969b-7ee4528b5da7/dqc_reference
[2024-01-25 19:56:06,863] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:56:06,864] [INFO] Task started: Prodigal
[2024-01-25 19:56:06,864] [INFO] Running command: gunzip -c /var/lib/cwl/stg427bbc49-9e6d-4d1e-b985-2d3c741dfc57/GCF_003989665.1_ASM398966v1_genomic.fna.gz | prodigal -d GCF_003989665.1_ASM398966v1_genomic.fna/cds.fna -a GCF_003989665.1_ASM398966v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:56:25,396] [INFO] Task succeeded: Prodigal
[2024-01-25 19:56:25,396] [INFO] Task started: HMMsearch
[2024-01-25 19:56:25,396] [INFO] Running command: hmmsearch --tblout GCF_003989665.1_ASM398966v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf75b4f5d-9f57-4f58-969b-7ee4528b5da7/dqc_reference/reference_markers.hmm GCF_003989665.1_ASM398966v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:56:25,703] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:56:25,704] [INFO] Found 6/6 markers.
[2024-01-25 19:56:25,758] [INFO] Query marker FASTA was written to GCF_003989665.1_ASM398966v1_genomic.fna/markers.fasta
[2024-01-25 19:56:25,758] [INFO] Task started: Blastn
[2024-01-25 19:56:25,758] [INFO] Running command: blastn -query GCF_003989665.1_ASM398966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf75b4f5d-9f57-4f58-969b-7ee4528b5da7/dqc_reference/reference_markers.fasta -out GCF_003989665.1_ASM398966v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:26,795] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:26,798] [INFO] Selected 17 target genomes.
[2024-01-25 19:56:26,798] [INFO] Target genome list was writen to GCF_003989665.1_ASM398966v1_genomic.fna/target_genomes.txt
[2024-01-25 19:56:26,809] [INFO] Task started: fastANI
[2024-01-25 19:56:26,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg427bbc49-9e6d-4d1e-b985-2d3c741dfc57/GCF_003989665.1_ASM398966v1_genomic.fna.gz --refList GCF_003989665.1_ASM398966v1_genomic.fna/target_genomes.txt --output GCF_003989665.1_ASM398966v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:56:58,120] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:58,120] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf75b4f5d-9f57-4f58-969b-7ee4528b5da7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:56:58,121] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf75b4f5d-9f57-4f58-969b-7ee4528b5da7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:56:58,132] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:56:58,132] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:56:58,132] [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 doebereinerae	strain=GSF71	GCA_003989665.1	92933	92933	type	True	100.0	2285	2289	95	conclusive
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	89.0831	1726	2289	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	85.1792	1541	2289	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	85.1266	1550	2289	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	84.9307	1405	2289	95	below_threshold
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	84.8537	1555	2289	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	84.8296	1509	2289	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	84.8288	1489	2289	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	84.6649	1377	2289	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	84.4727	1411	2289	95	below_threshold
Azospirillum lipoferum	strain=59b	GCA_008364955.1	193	193	type	True	84.4218	1468	2289	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	84.0066	1232	2289	95	below_threshold
Azospirillum griseum	strain=L-25-5 w-1	GCA_003966125.1	2496639	2496639	type	True	83.3844	1158	2289	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	83.1004	1323	2289	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	83.0928	1205	2289	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	77.4112	491	2289	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.8214	403	2289	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:56:58,133] [INFO] DFAST Taxonomy check result was written to GCF_003989665.1_ASM398966v1_genomic.fna/tc_result.tsv
[2024-01-25 19:56:58,134] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:56:58,134] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:56:58,134] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf75b4f5d-9f57-4f58-969b-7ee4528b5da7/dqc_reference/checkm_data
[2024-01-25 19:56:58,135] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:56:58,200] [INFO] Task started: CheckM
[2024-01-25 19:56:58,200] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003989665.1_ASM398966v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003989665.1_ASM398966v1_genomic.fna/checkm_input GCF_003989665.1_ASM398966v1_genomic.fna/checkm_result
[2024-01-25 19:58:09,729] [INFO] Task succeeded: CheckM
[2024-01-25 19:58:09,730] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:58:09,749] [INFO] ===== Completeness check finished =====
[2024-01-25 19:58:09,749] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:58:09,750] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003989665.1_ASM398966v1_genomic.fna/markers.fasta)
[2024-01-25 19:58:09,750] [INFO] Task started: Blastn
[2024-01-25 19:58:09,750] [INFO] Running command: blastn -query GCF_003989665.1_ASM398966v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf75b4f5d-9f57-4f58-969b-7ee4528b5da7/dqc_reference/reference_markers_gtdb.fasta -out GCF_003989665.1_ASM398966v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:11,833] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:11,835] [INFO] Selected 13 target genomes.
[2024-01-25 19:58:11,835] [INFO] Target genome list was writen to GCF_003989665.1_ASM398966v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:58:11,872] [INFO] Task started: fastANI
[2024-01-25 19:58:11,872] [INFO] Running command: fastANI --query /var/lib/cwl/stg427bbc49-9e6d-4d1e-b985-2d3c741dfc57/GCF_003989665.1_ASM398966v1_genomic.fna.gz --refList GCF_003989665.1_ASM398966v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003989665.1_ASM398966v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:58:39,375] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:39,384] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:58:39,384] [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_003989665.1	s__Azospirillum doebereinerae	100.0	2285	2289	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_017876095.1	s__Azospirillum agricola	89.0681	1727	2289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	96.88	96.88	0.87	0.87	2	-
GCF_003116095.1	s__Azospirillum sp003116095	85.7269	1502	2289	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	85.1358	1551	2289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003233655.1	s__Azospirillum ramasamyi	84.929	1404	2289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595245.1	s__Azospirillum sp016595245	84.8338	1525	2289	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	84.8006	1494	2289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.17	95.47	0.91	0.85	4	-
GCF_003116035.1	s__Azospirillum sp003116035	84.6947	1539	2289	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	84.4887	1409	2289	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	84.4554	1419	2289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000010725.1	s__Azospirillum lipoferum_B	84.3508	1407	2289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003130795.1	s__Azospirillum thermophilum	83.4627	1319	2289	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966125.1	s__Azospirillum griseum	83.3982	1156	2289	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 19:58:39,386] [INFO] GTDB search result was written to GCF_003989665.1_ASM398966v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:58:39,386] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:58:39,389] [INFO] DFAST_QC result json was written to GCF_003989665.1_ASM398966v1_genomic.fna/dqc_result.json
[2024-01-25 19:58:39,389] [INFO] DFAST_QC completed!
[2024-01-25 19:58:39,389] [INFO] Total running time: 0h2m34s