[2024-01-24 13:18:26,414] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:26,416] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:26,416] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4996a41-9778-4c8a-9ce1-6d8734eaaf11/dqc_reference
[2024-01-24 13:18:27,604] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:27,605] [INFO] Task started: Prodigal
[2024-01-24 13:18:27,606] [INFO] Running command: gunzip -c /var/lib/cwl/stga7529b20-8c2d-493e-9df1-e2c298eb9599/GCF_021168455.1_ASM2116845v1_genomic.fna.gz | prodigal -d GCF_021168455.1_ASM2116845v1_genomic.fna/cds.fna -a GCF_021168455.1_ASM2116845v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:41,687] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:41,688] [INFO] Task started: HMMsearch
[2024-01-24 13:18:41,688] [INFO] Running command: hmmsearch --tblout GCF_021168455.1_ASM2116845v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4996a41-9778-4c8a-9ce1-6d8734eaaf11/dqc_reference/reference_markers.hmm GCF_021168455.1_ASM2116845v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:41,936] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:41,938] [INFO] Found 6/6 markers.
[2024-01-24 13:18:41,978] [INFO] Query marker FASTA was written to GCF_021168455.1_ASM2116845v1_genomic.fna/markers.fasta
[2024-01-24 13:18:41,978] [INFO] Task started: Blastn
[2024-01-24 13:18:41,978] [INFO] Running command: blastn -query GCF_021168455.1_ASM2116845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4996a41-9778-4c8a-9ce1-6d8734eaaf11/dqc_reference/reference_markers.fasta -out GCF_021168455.1_ASM2116845v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:43,013] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:43,018] [INFO] Selected 23 target genomes.
[2024-01-24 13:18:43,018] [INFO] Target genome list was writen to GCF_021168455.1_ASM2116845v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:43,034] [INFO] Task started: fastANI
[2024-01-24 13:18:43,034] [INFO] Running command: fastANI --query /var/lib/cwl/stga7529b20-8c2d-493e-9df1-e2c298eb9599/GCF_021168455.1_ASM2116845v1_genomic.fna.gz --refList GCF_021168455.1_ASM2116845v1_genomic.fna/target_genomes.txt --output GCF_021168455.1_ASM2116845v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:08,269] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:08,270] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4996a41-9778-4c8a-9ce1-6d8734eaaf11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:08,270] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4996a41-9778-4c8a-9ce1-6d8734eaaf11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:08,289] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:19:08,290] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:19:08,290] [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
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	80.8509	699	1646	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	80.8141	744	1646	95	below_threshold
Shinella zoogloeoides	strain=DSM 287	GCA_009826855.1	352475	352475	type	True	80.7829	707	1646	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	80.5457	834	1646	95	below_threshold
Shinella granuli	strain=DSM 18401	GCA_004341885.1	323621	323621	type	True	80.5438	826	1646	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.4569	756	1646	95	below_threshold
Rhizobium giardinii	strain=H152	GCA_000379605.1	56731	56731	type	True	80.4345	807	1646	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	80.2408	714	1646	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	80.236	728	1646	95	below_threshold
Ensifer sesbaniae	strain=CCBAU 65729	GCA_013283665.1	1214071	1214071	type	True	80.1465	745	1646	95	below_threshold
Shinella kummerowiae	strain=CCBAU 25048	GCA_009827055.1	417745	417745	type	True	80.0754	756	1646	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	80.0285	772	1646	95	below_threshold
Pararhizobium antarcticum	strain=NAQVI 59	GCA_001885585.1	1798805	1798805	type	True	79.9509	766	1646	95	below_threshold
Rhizobium metallidurans	strain=DSM 26575	GCA_014196505.1	1265931	1265931	type	True	79.8583	685	1646	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	79.5986	706	1646	95	below_threshold
Rhizobium phaseoli	strain=ATCC 14482	GCA_003985125.1	396	396	type	True	79.5358	700	1646	95	below_threshold
Rhizobium chutanense	strain=C5	GCA_002531935.1	2035448	2035448	type	True	79.5054	751	1646	95	below_threshold
Rhizobium anhuiense	strain=CCBAU 23252	GCA_003985145.1	1184720	1184720	type	True	79.3969	747	1646	95	below_threshold
Rhizobium anhuiense	strain=CGMCC 1.12621	GCA_014638185.1	1184720	1184720	type	True	79.3843	750	1646	95	below_threshold
Rhizobium fabae	strain=CCBAU 33202	GCA_003985135.1	573179	573179	type	True	79.3166	697	1646	95	below_threshold
Neorhizobium galegae	strain=HAMBI 540	GCA_000731315.1	399	399	suspected-type	True	79.1339	681	1646	95	below_threshold
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	78.8334	567	1646	95	below_threshold
Agrobacterium salinitolerans	strain=YIC 5082	GCA_002008225.1	1183413	1183413	type	True	78.7402	544	1646	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:08,303] [INFO] DFAST Taxonomy check result was written to GCF_021168455.1_ASM2116845v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:08,303] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:08,303] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:08,304] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4996a41-9778-4c8a-9ce1-6d8734eaaf11/dqc_reference/checkm_data
[2024-01-24 13:19:08,305] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:08,351] [INFO] Task started: CheckM
[2024-01-24 13:19:08,351] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021168455.1_ASM2116845v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021168455.1_ASM2116845v1_genomic.fna/checkm_input GCF_021168455.1_ASM2116845v1_genomic.fna/checkm_result
[2024-01-24 13:19:52,479] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:52,481] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:52,505] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:52,505] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:52,505] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021168455.1_ASM2116845v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:52,506] [INFO] Task started: Blastn
[2024-01-24 13:19:52,506] [INFO] Running command: blastn -query GCF_021168455.1_ASM2116845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4996a41-9778-4c8a-9ce1-6d8734eaaf11/dqc_reference/reference_markers_gtdb.fasta -out GCF_021168455.1_ASM2116845v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:54,721] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:54,724] [INFO] Selected 6 target genomes.
[2024-01-24 13:19:54,724] [INFO] Target genome list was writen to GCF_021168455.1_ASM2116845v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:54,739] [INFO] Task started: fastANI
[2024-01-24 13:19:54,739] [INFO] Running command: fastANI --query /var/lib/cwl/stga7529b20-8c2d-493e-9df1-e2c298eb9599/GCF_021168455.1_ASM2116845v1_genomic.fna.gz --refList GCF_021168455.1_ASM2116845v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021168455.1_ASM2116845v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:02,576] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:02,583] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:02,583] [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_900467185.1	s__Pararhizobium sp900467185	95.7995	1473	1646	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003217095.1	s__Pararhizobium sp003217095	91.4118	1441	1646	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	95.84	95.04	0.89	0.86	9	-
GCF_900067135.1	s__Pararhizobium sp900067135	90.1278	1364	1646	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111275.1	s__Pararhizobium sp900111275	88.058	1336	1646	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424045.1	s__Pararhizobium sp001424045	88.0339	1277	1646	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	97.68	97.68	0.89	0.89	2	-
GCF_001424065.1	s__Pararhizobium sp001424065	85.7278	1176	1646	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pararhizobium	95.0	99.05	98.24	0.93	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:02,584] [INFO] GTDB search result was written to GCF_021168455.1_ASM2116845v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:02,585] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:02,588] [INFO] DFAST_QC result json was written to GCF_021168455.1_ASM2116845v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:02,588] [INFO] DFAST_QC completed!
[2024-01-24 13:20:02,589] [INFO] Total running time: 0h1m36s