[2023-06-28 16:08:01,012] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:08:01,014] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:08:01,014] [INFO] DQC Reference Directory: /var/lib/cwl/stg26e78bc0-1b54-453b-85e0-69125e98a833/dqc_reference
[2023-06-28 16:08:02,306] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:08:02,307] [INFO] Task started: Prodigal
[2023-06-28 16:08:02,307] [INFO] Running command: gunzip -c /var/lib/cwl/stga9d95418-cbe9-4473-84f4-218b5efe5630/GCA_012517325.1_ASM1251732v1_genomic.fna.gz | prodigal -d GCA_012517325.1_ASM1251732v1_genomic.fna/cds.fna -a GCA_012517325.1_ASM1251732v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:08:16,431] [INFO] Task succeeded: Prodigal
[2023-06-28 16:08:16,432] [INFO] Task started: HMMsearch
[2023-06-28 16:08:16,432] [INFO] Running command: hmmsearch --tblout GCA_012517325.1_ASM1251732v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26e78bc0-1b54-453b-85e0-69125e98a833/dqc_reference/reference_markers.hmm GCA_012517325.1_ASM1251732v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:08:16,745] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:08:16,747] [INFO] Found 6/6 markers.
[2023-06-28 16:08:16,810] [INFO] Query marker FASTA was written to GCA_012517325.1_ASM1251732v1_genomic.fna/markers.fasta
[2023-06-28 16:08:16,811] [INFO] Task started: Blastn
[2023-06-28 16:08:16,811] [INFO] Running command: blastn -query GCA_012517325.1_ASM1251732v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26e78bc0-1b54-453b-85e0-69125e98a833/dqc_reference/reference_markers.fasta -out GCA_012517325.1_ASM1251732v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:08:17,580] [INFO] Task succeeded: Blastn
[2023-06-28 16:08:17,585] [INFO] Selected 30 target genomes.
[2023-06-28 16:08:17,585] [INFO] Target genome list was writen to GCA_012517325.1_ASM1251732v1_genomic.fna/target_genomes.txt
[2023-06-28 16:08:17,590] [INFO] Task started: fastANI
[2023-06-28 16:08:17,591] [INFO] Running command: fastANI --query /var/lib/cwl/stga9d95418-cbe9-4473-84f4-218b5efe5630/GCA_012517325.1_ASM1251732v1_genomic.fna.gz --refList GCA_012517325.1_ASM1251732v1_genomic.fna/target_genomes.txt --output GCA_012517325.1_ASM1251732v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:08:44,349] [INFO] Task succeeded: fastANI
[2023-06-28 16:08:44,349] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26e78bc0-1b54-453b-85e0-69125e98a833/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:08:44,350] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26e78bc0-1b54-453b-85e0-69125e98a833/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:08:44,371] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:08:44,371] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 16:08:44,371] [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
Desulfuromonas versatilis	strain=NIT-T3	GCA_019704135.1	2802975	2802975	type	True	75.5247	61	1683	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	75.2393	69	1683	95	below_threshold
Bradyrhizobium neotropicale	strain=BR 10247	GCA_001641695.1	1497615	1497615	type	True	75.1911	78	1683	95	below_threshold
Rudaea cellulosilytica	strain=DSM 22992	GCA_000378125.1	540746	540746	type	True	75.1248	50	1683	95	below_threshold
Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis	strain=AM401	GCA_006636215.1	2590453	2590453	type	True	75.1156	73	1683	95	below_threshold
Pseudomonas knackmussii	strain=B13	GCA_000689415.1	65741	65741	type	True	75.1118	85	1683	95	below_threshold
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	75.0598	87	1683	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	75.0552	89	1683	95	below_threshold
Myxococcus fulvus	strain=NBRC 100333	GCA_007991095.1	33	33	type	True	75.0263	84	1683	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	75.0137	79	1683	95	below_threshold
Solimonas terrae	strain=KIS83-12	GCA_011067135.1	1396819	1396819	type	True	74.9908	74	1683	95	below_threshold
Sphingomonas jatrophae	strain=S5-249	GCA_900113315.1	1166337	1166337	type	True	74.952	53	1683	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	74.9204	125	1683	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	74.9006	91	1683	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	74.9006	127	1683	95	below_threshold
Rugamonas aquatica	strain=FT29W	GCA_009380215.1	2743357	2743357	type	True	74.8766	114	1683	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	74.8745	57	1683	95	below_threshold
Rugamonas rivuli	strain=FT103W	GCA_009380165.1	2743358	2743358	type	True	74.8556	104	1683	95	below_threshold
Massilia polaris	strain=RP-1-19	GCA_012927275.1	2728846	2728846	type	True	74.8482	58	1683	95	below_threshold
Nocardia beijingensis	strain=NBRC 16342	GCA_001612785.1	95162	95162	type	True	74.8322	114	1683	95	below_threshold
Kribbella solani	strain=DSM 17294	GCA_014205295.1	236067	236067	type	True	74.644	92	1683	95	below_threshold
Amycolatopsis coloradensis	strain=DSM 44225	GCA_001953865.1	76021	76021	type	True	74.5619	97	1683	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 16:08:44,373] [INFO] DFAST Taxonomy check result was written to GCA_012517325.1_ASM1251732v1_genomic.fna/tc_result.tsv
[2023-06-28 16:08:44,374] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:08:44,374] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:08:44,374] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26e78bc0-1b54-453b-85e0-69125e98a833/dqc_reference/checkm_data
[2023-06-28 16:08:44,375] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:08:44,424] [INFO] Task started: CheckM
[2023-06-28 16:08:44,425] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_012517325.1_ASM1251732v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_012517325.1_ASM1251732v1_genomic.fna/checkm_input GCA_012517325.1_ASM1251732v1_genomic.fna/checkm_result
[2023-06-28 16:09:26,950] [INFO] Task succeeded: CheckM
[2023-06-28 16:09:26,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:09:26,976] [INFO] ===== Completeness check finished =====
[2023-06-28 16:09:26,977] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:09:26,977] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_012517325.1_ASM1251732v1_genomic.fna/markers.fasta)
[2023-06-28 16:09:26,977] [INFO] Task started: Blastn
[2023-06-28 16:09:26,978] [INFO] Running command: blastn -query GCA_012517325.1_ASM1251732v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26e78bc0-1b54-453b-85e0-69125e98a833/dqc_reference/reference_markers_gtdb.fasta -out GCA_012517325.1_ASM1251732v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:09:28,300] [INFO] Task succeeded: Blastn
[2023-06-28 16:09:28,305] [INFO] Selected 24 target genomes.
[2023-06-28 16:09:28,305] [INFO] Target genome list was writen to GCA_012517325.1_ASM1251732v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:09:28,356] [INFO] Task started: fastANI
[2023-06-28 16:09:28,357] [INFO] Running command: fastANI --query /var/lib/cwl/stga9d95418-cbe9-4473-84f4-218b5efe5630/GCA_012517325.1_ASM1251732v1_genomic.fna.gz --refList GCA_012517325.1_ASM1251732v1_genomic.fna/target_genomes_gtdb.txt --output GCA_012517325.1_ASM1251732v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:09:47,267] [INFO] Task succeeded: fastANI
[2023-06-28 16:09:47,284] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 16:09:47,285] [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
GCA_012517325.1	s__JAAYVF01 sp012517325	100.0	1675	1683	d__Bacteria;p__FEN-1099;c__FEN-1099;o__FEN-1099;f__FEN-1099;g__JAAYVF01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003170555.1	s__FEN-1099 sp003170555	76.5139	312	1683	d__Bacteria;p__FEN-1099;c__FEN-1099;o__FEN-1099;f__FEN-1099;g__FEN-1099	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018333835.1	s__Silanimonas sp018333835	75.0476	67	1683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Silanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016586165.1	s__Dyella sp016586165	75.0268	57	1683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218825.1	s__JACRCV01 sp016218825	75.0092	125	1683	d__Bacteria;p__Myxococcota;c__XYA12-FULL-58-9;o__XYA12-FULL-58-9;f__XYA12-FULL-58-9;g__JACRCV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011067135.1	s__Solimonas terrae	74.9962	73	1683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428385.1	s__Rhodanobacter sp001428385	74.9741	58	1683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284255.1	s__Rubrivivax gelatinosus_A	74.9635	140	1683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	98.28	98.28	0.94	0.94	2	-
GCF_000335475.2	s__Cystobacter fuscus	74.9266	75	1683	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Cystobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016904885.1	s__Melittangium primigenium	74.9104	83	1683	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Melittangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148905.1	s__Fulvimonas soli	74.8964	128	1683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Fulvimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCA_017848855.1	s__Rhodanobacter denitrificans_B	74.8945	87	1683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000953855.2	s__Mizugakiibacter sediminis	74.8802	132	1683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Mizugakiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305135.1	s__Dokdonella_A sp017305135	74.8794	63	1683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302215.1	s__Dokdonella sp017302215	74.7997	70	1683	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:09:47,305] [INFO] GTDB search result was written to GCA_012517325.1_ASM1251732v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:09:47,306] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:09:47,313] [INFO] DFAST_QC result json was written to GCA_012517325.1_ASM1251732v1_genomic.fna/dqc_result.json
[2023-06-28 16:09:47,313] [INFO] DFAST_QC completed!
[2023-06-28 16:09:47,314] [INFO] Total running time: 0h1m46s