[2024-01-25 18:40:20,778] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:40:20,779] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:40:20,779] [INFO] DQC Reference Directory: /var/lib/cwl/stge57174f1-fae4-4ea5-ace5-f4aa9f4d1fbc/dqc_reference
[2024-01-25 18:40:21,934] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:40:21,935] [INFO] Task started: Prodigal
[2024-01-25 18:40:21,935] [INFO] Running command: gunzip -c /var/lib/cwl/stg77033227-7559-48fa-8361-0a1e3e5d7e06/GCF_013488225.1_ASM1348822v1_genomic.fna.gz | prodigal -d GCF_013488225.1_ASM1348822v1_genomic.fna/cds.fna -a GCF_013488225.1_ASM1348822v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:40:41,206] [INFO] Task succeeded: Prodigal
[2024-01-25 18:40:41,206] [INFO] Task started: HMMsearch
[2024-01-25 18:40:41,206] [INFO] Running command: hmmsearch --tblout GCF_013488225.1_ASM1348822v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge57174f1-fae4-4ea5-ace5-f4aa9f4d1fbc/dqc_reference/reference_markers.hmm GCF_013488225.1_ASM1348822v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:40:41,482] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:40:41,483] [INFO] Found 6/6 markers.
[2024-01-25 18:40:41,535] [INFO] Query marker FASTA was written to GCF_013488225.1_ASM1348822v1_genomic.fna/markers.fasta
[2024-01-25 18:40:41,535] [INFO] Task started: Blastn
[2024-01-25 18:40:41,535] [INFO] Running command: blastn -query GCF_013488225.1_ASM1348822v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge57174f1-fae4-4ea5-ace5-f4aa9f4d1fbc/dqc_reference/reference_markers.fasta -out GCF_013488225.1_ASM1348822v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:42,458] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:42,462] [INFO] Selected 14 target genomes.
[2024-01-25 18:40:42,462] [INFO] Target genome list was writen to GCF_013488225.1_ASM1348822v1_genomic.fna/target_genomes.txt
[2024-01-25 18:40:42,466] [INFO] Task started: fastANI
[2024-01-25 18:40:42,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg77033227-7559-48fa-8361-0a1e3e5d7e06/GCF_013488225.1_ASM1348822v1_genomic.fna.gz --refList GCF_013488225.1_ASM1348822v1_genomic.fna/target_genomes.txt --output GCF_013488225.1_ASM1348822v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:41:03,065] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:03,066] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge57174f1-fae4-4ea5-ace5-f4aa9f4d1fbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:41:03,066] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge57174f1-fae4-4ea5-ace5-f4aa9f4d1fbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:41:03,075] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:41:03,075] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:41:03,075] [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 mexicanus	strain=ITTG R7	GCA_013488225.1	375549	375549	type	True	100.0	2375	2378	95	conclusive
Ensifer mexicanus	strain=DSM 18446	GCA_017873105.1	375549	375549	type	True	99.9853	2329	2378	95	conclusive
Ensifer psoraleae	strain=CCBAU 65732	GCA_013283645.1	520838	520838	type	True	87.4642	1616	2378	95	below_threshold
Sinorhizobium fredii	strain=USDA 205	GCA_001461695.1	380	380	type	True	82.8008	1235	2378	95	below_threshold
Sinorhizobium fredii	strain=NBRC 14780	GCA_006539605.1	380	380	type	True	82.7851	1207	2378	95	below_threshold
Sinorhizobium meliloti	strain=NBRC 14782	GCA_006539625.1	382	382	type	True	82.1055	1174	2378	95	below_threshold
Sinorhizobium meliloti	strain=USDA1002	GCA_009601385.1	382	382	type	True	82.0792	1215	2378	95	below_threshold
Ensifer sesbaniae	strain=CCBAU 65729	GCA_013283665.1	1214071	1214071	type	True	81.8343	1187	2378	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.3558	788	2378	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	80.1333	727	2378	95	below_threshold
Rhizobium giardinii	strain=H152	GCA_000379605.1	56731	56731	type	True	80.0268	900	2378	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	79.9681	895	2378	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	79.7146	714	2378	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	79.5996	695	2378	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:41:03,078] [INFO] DFAST Taxonomy check result was written to GCF_013488225.1_ASM1348822v1_genomic.fna/tc_result.tsv
[2024-01-25 18:41:03,078] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:41:03,079] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:41:03,079] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge57174f1-fae4-4ea5-ace5-f4aa9f4d1fbc/dqc_reference/checkm_data
[2024-01-25 18:41:03,080] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:41:03,151] [INFO] Task started: CheckM
[2024-01-25 18:41:03,151] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013488225.1_ASM1348822v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013488225.1_ASM1348822v1_genomic.fna/checkm_input GCF_013488225.1_ASM1348822v1_genomic.fna/checkm_result
[2024-01-25 18:41:57,173] [INFO] Task succeeded: CheckM
[2024-01-25 18:41:57,174] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:41:57,203] [INFO] ===== Completeness check finished =====
[2024-01-25 18:41:57,203] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:41:57,203] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013488225.1_ASM1348822v1_genomic.fna/markers.fasta)
[2024-01-25 18:41:57,204] [INFO] Task started: Blastn
[2024-01-25 18:41:57,204] [INFO] Running command: blastn -query GCF_013488225.1_ASM1348822v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge57174f1-fae4-4ea5-ace5-f4aa9f4d1fbc/dqc_reference/reference_markers_gtdb.fasta -out GCF_013488225.1_ASM1348822v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:59,171] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:59,175] [INFO] Selected 11 target genomes.
[2024-01-25 18:41:59,175] [INFO] Target genome list was writen to GCF_013488225.1_ASM1348822v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:41:59,182] [INFO] Task started: fastANI
[2024-01-25 18:41:59,182] [INFO] Running command: fastANI --query /var/lib/cwl/stg77033227-7559-48fa-8361-0a1e3e5d7e06/GCF_013488225.1_ASM1348822v1_genomic.fna.gz --refList GCF_013488225.1_ASM1348822v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013488225.1_ASM1348822v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:42:18,632] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:18,640] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:42:18,640] [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_013488225.1	s__Sinorhizobium mexicanum	100.0	2374	2378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_009601505.1	s__Sinorhizobium terangae	89.8418	1660	2378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	99.98	99.98	0.98	0.98	2	-
GCF_004827385.1	s__Sinorhizobium sp004827385	89.7086	1655	2378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013283645.1	s__Sinorhizobium psoraleae	87.4596	1617	2378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001651875.1	s__Sinorhizobium saheli	83.0918	1206	2378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	99.97	99.97	0.96	0.96	2	-
GCF_000018545.1	s__Sinorhizobium fredii_A	82.8557	1263	2378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001704765.1	s__Sinorhizobium shofinae	82.6842	1044	2378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513895.1	s__Sinorhizobium sp000513895	82.6474	1278	2378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001270265.1	s__Ensifer adhaerens_B	81.558	1173	2378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900469625.1	s__Ensifer sp900469625	81.4823	1052	2378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	98.94	98.62	0.97	0.96	3	-
GCF_013371465.1	s__Ensifer sp013371465	81.3459	1079	2378	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Ensifer	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:42:18,641] [INFO] GTDB search result was written to GCF_013488225.1_ASM1348822v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:42:18,642] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:42:18,646] [INFO] DFAST_QC result json was written to GCF_013488225.1_ASM1348822v1_genomic.fna/dqc_result.json
[2024-01-25 18:42:18,646] [INFO] DFAST_QC completed!
[2024-01-25 18:42:18,646] [INFO] Total running time: 0h1m58s