[2024-01-24 13:46:01,172] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:01,174] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:01,174] [INFO] DQC Reference Directory: /var/lib/cwl/stg18486fe7-7676-4ac2-87c0-2509e9c9e327/dqc_reference
[2024-01-24 13:46:02,510] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:02,511] [INFO] Task started: Prodigal
[2024-01-24 13:46:02,511] [INFO] Running command: gunzip -c /var/lib/cwl/stgf376dd6b-5575-4baa-b64c-24b8dbf66c15/GCF_017488845.2_ASM1748884v2_genomic.fna.gz | prodigal -d GCF_017488845.2_ASM1748884v2_genomic.fna/cds.fna -a GCF_017488845.2_ASM1748884v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:27,059] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:27,060] [INFO] Task started: HMMsearch
[2024-01-24 13:46:27,060] [INFO] Running command: hmmsearch --tblout GCF_017488845.2_ASM1748884v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18486fe7-7676-4ac2-87c0-2509e9c9e327/dqc_reference/reference_markers.hmm GCF_017488845.2_ASM1748884v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:27,405] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:27,407] [INFO] Found 6/6 markers.
[2024-01-24 13:46:27,474] [INFO] Query marker FASTA was written to GCF_017488845.2_ASM1748884v2_genomic.fna/markers.fasta
[2024-01-24 13:46:27,474] [INFO] Task started: Blastn
[2024-01-24 13:46:27,474] [INFO] Running command: blastn -query GCF_017488845.2_ASM1748884v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg18486fe7-7676-4ac2-87c0-2509e9c9e327/dqc_reference/reference_markers.fasta -out GCF_017488845.2_ASM1748884v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:28,534] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:28,539] [INFO] Selected 24 target genomes.
[2024-01-24 13:46:28,539] [INFO] Target genome list was writen to GCF_017488845.2_ASM1748884v2_genomic.fna/target_genomes.txt
[2024-01-24 13:46:28,584] [INFO] Task started: fastANI
[2024-01-24 13:46:28,585] [INFO] Running command: fastANI --query /var/lib/cwl/stgf376dd6b-5575-4baa-b64c-24b8dbf66c15/GCF_017488845.2_ASM1748884v2_genomic.fna.gz --refList GCF_017488845.2_ASM1748884v2_genomic.fna/target_genomes.txt --output GCF_017488845.2_ASM1748884v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:56,634] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:56,635] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18486fe7-7676-4ac2-87c0-2509e9c9e327/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:56,636] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18486fe7-7676-4ac2-87c0-2509e9c9e327/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:56,656] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:46:56,656] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:46:56,656] [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
Ensifer sesbaniae	strain=CCBAU 65729	GCA_013283665.1	1214071	1214071	type	True	83.7361	1458	2695	95	below_threshold
Sinorhizobium fredii	strain=USDA205	GCA_009601405.1	380	380	type	True	81.7624	1089	2695	95	below_threshold
Sinorhizobium fredii	strain=NBRC 14780	GCA_006539605.1	380	380	type	True	81.7538	1052	2695	95	below_threshold
Sinorhizobium fredii	strain=USDA 205	GCA_001461695.1	380	380	type	True	81.6487	1102	2695	95	below_threshold
Sinorhizobium meliloti	strain=USDA1002	GCA_009601385.1	382	382	type	True	81.525	1126	2695	95	below_threshold
Sinorhizobium meliloti	strain=NBRC 14782	GCA_006539625.1	382	382	type	True	81.4664	1075	2695	95	below_threshold
Ensifer psoraleae	strain=CCBAU 65732	GCA_013283645.1	520838	520838	type	True	81.3336	1191	2695	95	below_threshold
Ensifer mexicanus	strain=ITTG R7	GCA_013488225.1	375549	375549	type	True	81.3239	1170	2695	95	below_threshold
Ensifer mexicanus	strain=DSM 18446	GCA_017873105.1	375549	375549	type	True	81.2897	1165	2695	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	80.8853	853	2695	95	below_threshold
Ensifer sojae	strain=CCBAU 05684	GCA_002288525.1	716925	716925	type	True	80.8632	970	2695	95	below_threshold
Shinella zoogloeoides	strain=DSM 287	GCA_009826855.1	352475	352475	type	True	80.7883	847	2695	95	below_threshold
Ensifer sojae	strain=CCBAU 05684	GCA_000261485.1	716925	716925	type	True	80.7611	939	2695	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.7139	835	2695	95	below_threshold
Sinorhizobium kostiense	strain=DSM 13372	GCA_017874595.1	76747	76747	type	True	80.5243	963	2695	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	80.4745	841	2695	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	80.3544	823	2695	95	below_threshold
Pararhizobium antarcticum	strain=NAQVI 59	GCA_001885585.1	1798805	1798805	type	True	79.8387	841	2695	95	below_threshold
Rhizobium pisi	strain=DSM 30132	GCA_003938655.1	574561	574561	type	True	79.4752	818	2695	95	below_threshold
Rhizobium fabae	strain=DSM 19331	GCA_014196235.1	573179	573179	type	True	79.4006	807	2695	95	below_threshold
Rhizobium fabae	strain=CCBAU 33202	GCA_003985135.1	573179	573179	type	True	79.3559	805	2695	95	below_threshold
Neorhizobium alkalisoli	strain=DSM 21826	GCA_002968635.1	528178	528178	type	True	78.8964	610	2695	95	below_threshold
Rhizobium skierniewicense	strain=Ch11	GCA_023757665.1	984260	984260	type	True	77.8495	383	2695	95	below_threshold
Rhizobium skierniewicense	strain=DSM 26438	GCA_014196515.1	984260	984260	type	True	77.7829	387	2695	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:56,659] [INFO] DFAST Taxonomy check result was written to GCF_017488845.2_ASM1748884v2_genomic.fna/tc_result.tsv
[2024-01-24 13:46:56,660] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:56,660] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:56,660] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18486fe7-7676-4ac2-87c0-2509e9c9e327/dqc_reference/checkm_data
[2024-01-24 13:46:56,661] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:56,743] [INFO] Task started: CheckM
[2024-01-24 13:46:56,744] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017488845.2_ASM1748884v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017488845.2_ASM1748884v2_genomic.fna/checkm_input GCF_017488845.2_ASM1748884v2_genomic.fna/checkm_result
[2024-01-24 13:48:06,057] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:06,059] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:06,088] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:06,089] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:06,089] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017488845.2_ASM1748884v2_genomic.fna/markers.fasta)
[2024-01-24 13:48:06,090] [INFO] Task started: Blastn
[2024-01-24 13:48:06,090] [INFO] Running command: blastn -query GCF_017488845.2_ASM1748884v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg18486fe7-7676-4ac2-87c0-2509e9c9e327/dqc_reference/reference_markers_gtdb.fasta -out GCF_017488845.2_ASM1748884v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:08,113] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:08,117] [INFO] Selected 7 target genomes.
[2024-01-24 13:48:08,117] [INFO] Target genome list was writen to GCF_017488845.2_ASM1748884v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:08,163] [INFO] Task started: fastANI
[2024-01-24 13:48:08,163] [INFO] Running command: fastANI --query /var/lib/cwl/stgf376dd6b-5575-4baa-b64c-24b8dbf66c15/GCF_017488845.2_ASM1748884v2_genomic.fna.gz --refList GCF_017488845.2_ASM1748884v2_genomic.fna/target_genomes_gtdb.txt --output GCF_017488845.2_ASM1748884v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:20,950] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:20,962] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:20,962] [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_000583045.1	s__Ensifer adhaerens_A	98.6483	2214	2695	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	98.74	98.60	0.88	0.84	14	conclusive
GCF_001695855.1	s__Ensifer sp001695855	90.3543	1778	2695	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	98.60	98.60	0.94	0.94	3	-
GCF_001270265.1	s__Ensifer adhaerens_B	90.2346	1890	2695	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002725.1	s__Ensifer sp002002725	89.1274	1805	2695	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	98.52	98.52	0.94	0.94	2	-
GCF_013371465.1	s__Ensifer sp013371465	88.7611	1795	2695	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013283195.1	s__Ensifer adhaerens_G	88.613	1807	2695	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	98.31	98.31	0.94	0.94	2	-
GCA_900469625.1	s__Ensifer sp900469625	87.4854	1685	2695	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	98.94	98.62	0.97	0.96	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:20,964] [INFO] GTDB search result was written to GCF_017488845.2_ASM1748884v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:20,964] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:20,968] [INFO] DFAST_QC result json was written to GCF_017488845.2_ASM1748884v2_genomic.fna/dqc_result.json
[2024-01-24 13:48:20,968] [INFO] DFAST_QC completed!
[2024-01-24 13:48:20,968] [INFO] Total running time: 0h2m20s