[2024-01-24 13:31:34,454] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:34,455] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:34,455] [INFO] DQC Reference Directory: /var/lib/cwl/stg12b008ec-dfdd-43cb-b386-6738421ebabc/dqc_reference
[2024-01-24 13:31:35,785] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:35,786] [INFO] Task started: Prodigal
[2024-01-24 13:31:35,786] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0d413d0-a6ab-4fed-96bc-781140d11226/GCF_001651855.1_ASM165185v1_genomic.fna.gz | prodigal -d GCF_001651855.1_ASM165185v1_genomic.fna/cds.fna -a GCF_001651855.1_ASM165185v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:56,025] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:56,025] [INFO] Task started: HMMsearch
[2024-01-24 13:31:56,025] [INFO] Running command: hmmsearch --tblout GCF_001651855.1_ASM165185v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12b008ec-dfdd-43cb-b386-6738421ebabc/dqc_reference/reference_markers.hmm GCF_001651855.1_ASM165185v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:56,449] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:56,450] [INFO] Found 6/6 markers.
[2024-01-24 13:31:56,554] [INFO] Query marker FASTA was written to GCF_001651855.1_ASM165185v1_genomic.fna/markers.fasta
[2024-01-24 13:31:56,555] [INFO] Task started: Blastn
[2024-01-24 13:31:56,555] [INFO] Running command: blastn -query GCF_001651855.1_ASM165185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12b008ec-dfdd-43cb-b386-6738421ebabc/dqc_reference/reference_markers.fasta -out GCF_001651855.1_ASM165185v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:57,794] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:57,797] [INFO] Selected 17 target genomes.
[2024-01-24 13:31:57,798] [INFO] Target genome list was writen to GCF_001651855.1_ASM165185v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:57,815] [INFO] Task started: fastANI
[2024-01-24 13:31:57,816] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0d413d0-a6ab-4fed-96bc-781140d11226/GCF_001651855.1_ASM165185v1_genomic.fna.gz --refList GCF_001651855.1_ASM165185v1_genomic.fna/target_genomes.txt --output GCF_001651855.1_ASM165185v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:21,715] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:21,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12b008ec-dfdd-43cb-b386-6738421ebabc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:21,716] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12b008ec-dfdd-43cb-b386-6738421ebabc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:21,737] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:32:21,737] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:32:21,737] [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
Sinorhizobium fredii	strain=NBRC 14780	GCA_006539605.1	380	380	type	True	88.2303	1513	2176	95	below_threshold
Sinorhizobium fredii	strain=USDA 205	GCA_001461695.1	380	380	type	True	88.1573	1550	2176	95	below_threshold
Sinorhizobium fredii	strain=USDA205	GCA_009601405.1	380	380	type	True	88.1043	1576	2176	95	below_threshold
Ensifer sojae	strain=CCBAU 05684	GCA_000261485.1	716925	716925	type	True	83.0314	1157	2176	95	below_threshold
Ensifer sojae	strain=CCBAU 05684	GCA_002288525.1	716925	716925	type	True	83.0311	1211	2176	95	below_threshold
Sinorhizobium kostiense	strain=DSM 13372	GCA_017874595.1	76747	76747	type	True	82.9169	1290	2176	95	below_threshold
Ensifer alkalisoli	strain=YIC4027	GCA_001723275.1	1752398	1752398	type	True	82.8735	1203	2176	95	below_threshold
Ensifer alkalisoli	strain=YIC4027	GCA_008932245.1	1752398	1752398	type	True	82.8195	1220	2176	95	below_threshold
Ensifer mexicanus	strain=ITTG R7	GCA_013488225.1	375549	375549	type	True	82.7978	1280	2176	95	below_threshold
Ensifer psoraleae	strain=CCBAU 65732	GCA_013283645.1	520838	520838	type	True	82.7564	1262	2176	95	below_threshold
Ensifer mexicanus	strain=DSM 18446	GCA_017873105.1	375549	375549	type	True	82.7227	1280	2176	95	below_threshold
Sinorhizobium arboris	strain=LMG 14919	GCA_000427465.1	76745	76745	type	True	82.5195	1258	2176	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	81.1402	803	2176	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	80.7965	914	2176	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	80.64	742	2176	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	80.2102	739	2176	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	80.1376	731	2176	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:21,739] [INFO] DFAST Taxonomy check result was written to GCF_001651855.1_ASM165185v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:21,739] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:21,740] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:21,740] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12b008ec-dfdd-43cb-b386-6738421ebabc/dqc_reference/checkm_data
[2024-01-24 13:32:21,741] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:21,803] [INFO] Task started: CheckM
[2024-01-24 13:32:21,803] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001651855.1_ASM165185v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001651855.1_ASM165185v1_genomic.fna/checkm_input GCF_001651855.1_ASM165185v1_genomic.fna/checkm_result
[2024-01-24 13:33:17,387] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:17,388] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:17,407] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:17,408] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:17,408] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001651855.1_ASM165185v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:17,408] [INFO] Task started: Blastn
[2024-01-24 13:33:17,408] [INFO] Running command: blastn -query GCF_001651855.1_ASM165185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12b008ec-dfdd-43cb-b386-6738421ebabc/dqc_reference/reference_markers_gtdb.fasta -out GCF_001651855.1_ASM165185v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:19,698] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:19,702] [INFO] Selected 8 target genomes.
[2024-01-24 13:33:19,702] [INFO] Target genome list was writen to GCF_001651855.1_ASM165185v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:19,721] [INFO] Task started: fastANI
[2024-01-24 13:33:19,722] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0d413d0-a6ab-4fed-96bc-781140d11226/GCF_001651855.1_ASM165185v1_genomic.fna.gz --refList GCF_001651855.1_ASM165185v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001651855.1_ASM165185v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:33,588] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:33,601] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:33,601] [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_001651855.1	s__Sinorhizobium americanum	100.0	2173	2176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	98.81	98.12	0.92	0.85	4	conclusive
GCF_002944405.1	s__Sinorhizobium fredii_C	93.0747	1757	2176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	98.60	98.35	0.89	0.83	7	-
GCF_000378985.1	s__Sinorhizobium sp000378985	89.199	1690	2176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001651865.1	s__Sinorhizobium glycinis	88.4421	1489	2176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000018545.1	s__Sinorhizobium fredii_A	88.1798	1594	2176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001461695.1	s__Sinorhizobium fredii	88.1573	1550	2176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	98.55	96.82	0.88	0.82	17	-
GCF_000265205.3	s__Sinorhizobium fredii_B	87.9341	1624	2176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	98.03	98.03	0.83	0.83	2	-
GCA_001704765.1	s__Sinorhizobium shofinae	87.6384	1322	2176	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:33,603] [INFO] GTDB search result was written to GCF_001651855.1_ASM165185v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:33,604] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:33,607] [INFO] DFAST_QC result json was written to GCF_001651855.1_ASM165185v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:33,607] [INFO] DFAST_QC completed!
[2024-01-24 13:33:33,607] [INFO] Total running time: 0h1m59s