[2024-01-24 13:57:57,569] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:57,571] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:57,571] [INFO] DQC Reference Directory: /var/lib/cwl/stg5da6e7b0-ae80-4bce-a176-40b73d51b4f9/dqc_reference
[2024-01-24 13:57:58,882] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:58,883] [INFO] Task started: Prodigal
[2024-01-24 13:57:58,883] [INFO] Running command: gunzip -c /var/lib/cwl/stg05effa1d-d7ce-45c5-a6f3-a51988135d14/GCF_003590795.1_ASM359079v1_genomic.fna.gz | prodigal -d GCF_003590795.1_ASM359079v1_genomic.fna/cds.fna -a GCF_003590795.1_ASM359079v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:20,496] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:20,496] [INFO] Task started: HMMsearch
[2024-01-24 13:58:20,496] [INFO] Running command: hmmsearch --tblout GCF_003590795.1_ASM359079v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5da6e7b0-ae80-4bce-a176-40b73d51b4f9/dqc_reference/reference_markers.hmm GCF_003590795.1_ASM359079v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:20,862] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:20,863] [INFO] Found 6/6 markers.
[2024-01-24 13:58:20,928] [INFO] Query marker FASTA was written to GCF_003590795.1_ASM359079v1_genomic.fna/markers.fasta
[2024-01-24 13:58:20,929] [INFO] Task started: Blastn
[2024-01-24 13:58:20,929] [INFO] Running command: blastn -query GCF_003590795.1_ASM359079v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5da6e7b0-ae80-4bce-a176-40b73d51b4f9/dqc_reference/reference_markers.fasta -out GCF_003590795.1_ASM359079v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:21,952] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:22,171] [INFO] Selected 14 target genomes.
[2024-01-24 13:58:22,172] [INFO] Target genome list was writen to GCF_003590795.1_ASM359079v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:22,220] [INFO] Task started: fastANI
[2024-01-24 13:58:22,220] [INFO] Running command: fastANI --query /var/lib/cwl/stg05effa1d-d7ce-45c5-a6f3-a51988135d14/GCF_003590795.1_ASM359079v1_genomic.fna.gz --refList GCF_003590795.1_ASM359079v1_genomic.fna/target_genomes.txt --output GCF_003590795.1_ASM359079v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:45,298] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:45,298] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5da6e7b0-ae80-4bce-a176-40b73d51b4f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:45,299] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5da6e7b0-ae80-4bce-a176-40b73d51b4f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:45,310] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:45,310] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:45,311] [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 cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	100.0	2146	2149	95	conclusive
Azospirillum griseum	strain=L-25-5 w-1	GCA_003966125.1	2496639	2496639	type	True	87.1936	1462	2149	95	below_threshold
Azospirillum doebereinerae	strain=GSF71	GCA_003989665.1	92933	92933	type	True	84.1624	1223	2149	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	84.0381	1295	2149	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	82.833	1228	2149	95	below_threshold
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	82.7376	1272	2149	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	82.4475	1207	2149	95	below_threshold
Azospirillum lipoferum	strain=59b	GCA_008364955.1	193	193	type	True	82.4215	1256	2149	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	82.0372	1068	2149	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	81.0326	1014	2149	95	below_threshold
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	81.0309	846	2149	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	81.0267	958	2149	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	77.084	421	2149	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.3509	330	2149	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:45,312] [INFO] DFAST Taxonomy check result was written to GCF_003590795.1_ASM359079v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:45,313] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:45,313] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:45,313] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5da6e7b0-ae80-4bce-a176-40b73d51b4f9/dqc_reference/checkm_data
[2024-01-24 13:58:45,314] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:45,379] [INFO] Task started: CheckM
[2024-01-24 13:58:45,379] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003590795.1_ASM359079v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003590795.1_ASM359079v1_genomic.fna/checkm_input GCF_003590795.1_ASM359079v1_genomic.fna/checkm_result
[2024-01-24 14:00:13,239] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:13,240] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:13,259] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:13,260] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:13,260] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003590795.1_ASM359079v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:13,260] [INFO] Task started: Blastn
[2024-01-24 14:00:13,260] [INFO] Running command: blastn -query GCF_003590795.1_ASM359079v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5da6e7b0-ae80-4bce-a176-40b73d51b4f9/dqc_reference/reference_markers_gtdb.fasta -out GCF_003590795.1_ASM359079v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:15,207] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:15,211] [INFO] Selected 11 target genomes.
[2024-01-24 14:00:15,211] [INFO] Target genome list was writen to GCF_003590795.1_ASM359079v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:15,245] [INFO] Task started: fastANI
[2024-01-24 14:00:15,245] [INFO] Running command: fastANI --query /var/lib/cwl/stg05effa1d-d7ce-45c5-a6f3-a51988135d14/GCF_003590795.1_ASM359079v1_genomic.fna.gz --refList GCF_003590795.1_ASM359079v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003590795.1_ASM359079v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:35,696] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:35,708] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:35,708] [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_003590795.1	s__Azospirillum sp003590795	100.0	2146	2149	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_003966125.1	s__Azospirillum griseum	87.2074	1461	2149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003989665.1	s__Azospirillum doebereinerae	84.1537	1225	2149	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	83.9757	1303	2149	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	83.3527	1287	2149	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	82.7434	1251	2149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008364955.1	s__Azospirillum lipoferum	82.4433	1252	2149	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	82.4274	1209	2149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003349955.1	s__Azospirillum brasilense_B	80.9245	948	2149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.36	95.36	0.89	0.89	2	-
GCF_014192915.1	s__Azospirillum sp014192915	80.8009	999	2149	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903904605.1	s__CAIYYX01 sp903904605	75.191	95	2149	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__CAIYYX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:35,710] [INFO] GTDB search result was written to GCF_003590795.1_ASM359079v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:35,710] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:35,717] [INFO] DFAST_QC result json was written to GCF_003590795.1_ASM359079v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:35,717] [INFO] DFAST_QC completed!
[2024-01-24 14:00:35,717] [INFO] Total running time: 0h2m38s