[2024-01-24 11:43:37,684] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:37,686] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:37,686] [INFO] DQC Reference Directory: /var/lib/cwl/stge32a92ff-fe63-4915-a17d-57e66d4b9bd0/dqc_reference
[2024-01-24 11:43:38,928] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:38,929] [INFO] Task started: Prodigal
[2024-01-24 11:43:38,929] [INFO] Running command: gunzip -c /var/lib/cwl/stgadad1800-349d-4e98-8b70-b3e8ba063e14/GCF_016595245.1_ASM1659524v1_genomic.fna.gz | prodigal -d GCF_016595245.1_ASM1659524v1_genomic.fna/cds.fna -a GCF_016595245.1_ASM1659524v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:03,790] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:03,791] [INFO] Task started: HMMsearch
[2024-01-24 11:44:03,791] [INFO] Running command: hmmsearch --tblout GCF_016595245.1_ASM1659524v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge32a92ff-fe63-4915-a17d-57e66d4b9bd0/dqc_reference/reference_markers.hmm GCF_016595245.1_ASM1659524v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:04,436] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:04,438] [INFO] Found 6/6 markers.
[2024-01-24 11:44:04,548] [INFO] Query marker FASTA was written to GCF_016595245.1_ASM1659524v1_genomic.fna/markers.fasta
[2024-01-24 11:44:04,548] [INFO] Task started: Blastn
[2024-01-24 11:44:04,548] [INFO] Running command: blastn -query GCF_016595245.1_ASM1659524v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge32a92ff-fe63-4915-a17d-57e66d4b9bd0/dqc_reference/reference_markers.fasta -out GCF_016595245.1_ASM1659524v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:05,548] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:05,551] [INFO] Selected 14 target genomes.
[2024-01-24 11:44:05,552] [INFO] Target genome list was writen to GCF_016595245.1_ASM1659524v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:05,561] [INFO] Task started: fastANI
[2024-01-24 11:44:05,561] [INFO] Running command: fastANI --query /var/lib/cwl/stgadad1800-349d-4e98-8b70-b3e8ba063e14/GCF_016595245.1_ASM1659524v1_genomic.fna.gz --refList GCF_016595245.1_ASM1659524v1_genomic.fna/target_genomes.txt --output GCF_016595245.1_ASM1659524v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:33,863] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:33,864] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge32a92ff-fe63-4915-a17d-57e66d4b9bd0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:33,864] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge32a92ff-fe63-4915-a17d-57e66d4b9bd0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:33,876] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:44:33,876] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:44:33,876] [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 palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	91.0039	2060	2678	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	90.9546	2071	2678	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	90.9182	2026	2678	95	below_threshold
Azospirillum lipoferum	strain=59b	GCA_008364955.1	193	193	type	True	90.7819	2041	2678	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	90.699	1770	2678	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	89.546	1680	2678	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	89.4162	1789	2678	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	88.8619	1866	2678	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	88.8357	1862	2678	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	82.6716	1366	2678	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	82.5864	1237	2678	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	82.466	1188	2678	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	77.9747	706	2678	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.5169	600	2678	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:33,878] [INFO] DFAST Taxonomy check result was written to GCF_016595245.1_ASM1659524v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:33,879] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:33,879] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:33,879] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge32a92ff-fe63-4915-a17d-57e66d4b9bd0/dqc_reference/checkm_data
[2024-01-24 11:44:33,880] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:33,952] [INFO] Task started: CheckM
[2024-01-24 11:44:33,953] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016595245.1_ASM1659524v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016595245.1_ASM1659524v1_genomic.fna/checkm_input GCF_016595245.1_ASM1659524v1_genomic.fna/checkm_result
[2024-01-24 11:45:56,729] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:56,731] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:56,756] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:56,757] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:56,757] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016595245.1_ASM1659524v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:56,758] [INFO] Task started: Blastn
[2024-01-24 11:45:56,758] [INFO] Running command: blastn -query GCF_016595245.1_ASM1659524v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge32a92ff-fe63-4915-a17d-57e66d4b9bd0/dqc_reference/reference_markers_gtdb.fasta -out GCF_016595245.1_ASM1659524v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:58,497] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:58,501] [INFO] Selected 15 target genomes.
[2024-01-24 11:45:58,501] [INFO] Target genome list was writen to GCF_016595245.1_ASM1659524v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:58,512] [INFO] Task started: fastANI
[2024-01-24 11:45:58,512] [INFO] Running command: fastANI --query /var/lib/cwl/stgadad1800-349d-4e98-8b70-b3e8ba063e14/GCF_016595245.1_ASM1659524v1_genomic.fna.gz --refList GCF_016595245.1_ASM1659524v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016595245.1_ASM1659524v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:27,526] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:27,544] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:27,544] [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_016595245.1	s__Azospirillum sp016595245	100.0	2674	2678	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_013340935.1	s__Azospirillum melinis	90.9388	2022	2678	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	90.9068	2041	2678	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	90.7778	2042	2678	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	90.7454	1959	2678	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	90.7174	1769	2678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	98.65	97.30	0.92	0.84	3	-
GCF_004923315.1	s__Azospirillum sp003116065	90.6001	1958	2678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.27	96.11	0.89	0.85	4	-
GCF_004923295.1	s__Azospirillum sp003115975	90.4004	1876	2678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000283655.1	s__Azospirillum lipoferum_C	89.8648	1788	2678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003233655.1	s__Azospirillum ramasamyi	89.5457	1680	2678	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	89.3992	1792	2678	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	88.9027	1861	2678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005796225.1	s__Pseudarthrobacter sp005796225	75.0001	69	2678	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:27,545] [INFO] GTDB search result was written to GCF_016595245.1_ASM1659524v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:27,546] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:27,549] [INFO] DFAST_QC result json was written to GCF_016595245.1_ASM1659524v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:27,550] [INFO] DFAST_QC completed!
[2024-01-24 11:46:27,550] [INFO] Total running time: 0h2m50s