[2024-01-24 12:27:19,532] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:27:19,534] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:27:19,535] [INFO] DQC Reference Directory: /var/lib/cwl/stg53d44728-3c68-4537-afb2-84f2349b4748/dqc_reference
[2024-01-24 12:27:20,748] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:27:20,749] [INFO] Task started: Prodigal
[2024-01-24 12:27:20,749] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f1c782c-e7cb-46e7-9c48-9e6c37a20f80/GCF_008932245.1_ASM893224v1_genomic.fna.gz | prodigal -d GCF_008932245.1_ASM893224v1_genomic.fna/cds.fna -a GCF_008932245.1_ASM893224v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:27:38,915] [INFO] Task succeeded: Prodigal
[2024-01-24 12:27:38,915] [INFO] Task started: HMMsearch
[2024-01-24 12:27:38,916] [INFO] Running command: hmmsearch --tblout GCF_008932245.1_ASM893224v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53d44728-3c68-4537-afb2-84f2349b4748/dqc_reference/reference_markers.hmm GCF_008932245.1_ASM893224v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:27:39,239] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:27:39,240] [INFO] Found 6/6 markers.
[2024-01-24 12:27:39,289] [INFO] Query marker FASTA was written to GCF_008932245.1_ASM893224v1_genomic.fna/markers.fasta
[2024-01-24 12:27:39,290] [INFO] Task started: Blastn
[2024-01-24 12:27:39,290] [INFO] Running command: blastn -query GCF_008932245.1_ASM893224v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53d44728-3c68-4537-afb2-84f2349b4748/dqc_reference/reference_markers.fasta -out GCF_008932245.1_ASM893224v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:27:40,294] [INFO] Task succeeded: Blastn
[2024-01-24 12:27:40,299] [INFO] Selected 11 target genomes.
[2024-01-24 12:27:40,299] [INFO] Target genome list was writen to GCF_008932245.1_ASM893224v1_genomic.fna/target_genomes.txt
[2024-01-24 12:27:40,320] [INFO] Task started: fastANI
[2024-01-24 12:27:40,320] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f1c782c-e7cb-46e7-9c48-9e6c37a20f80/GCF_008932245.1_ASM893224v1_genomic.fna.gz --refList GCF_008932245.1_ASM893224v1_genomic.fna/target_genomes.txt --output GCF_008932245.1_ASM893224v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:27:54,476] [INFO] Task succeeded: fastANI
[2024-01-24 12:27:54,477] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53d44728-3c68-4537-afb2-84f2349b4748/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:27:54,478] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53d44728-3c68-4537-afb2-84f2349b4748/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:27:54,492] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:27:54,492] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:27:54,492] [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 alkalisoli	strain=YIC4027	GCA_008932245.1	1752398	1752398	type	True	100.0	2039	2042	95	conclusive
Ensifer alkalisoli	strain=YIC4027	GCA_001723275.1	1752398	1752398	type	True	98.916	1828	2042	95	conclusive
Ensifer sojae	strain=CCBAU 05684	GCA_002288525.1	716925	716925	type	True	89.4774	1505	2042	95	below_threshold
Ensifer sojae	strain=CCBAU 05684	GCA_000261485.1	716925	716925	type	True	89.4116	1435	2042	95	below_threshold
Sinorhizobium kostiense	strain=DSM 13372	GCA_017874595.1	76747	76747	type	True	84.302	1354	2042	95	below_threshold
Sinorhizobium fredii	strain=USDA 205	GCA_001461695.1	380	380	type	True	83.1399	1250	2042	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.3807	755	2042	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	80.2711	824	2042	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	80.2522	700	2042	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	79.7624	675	2042	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	78.9884	650	2042	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:27:54,494] [INFO] DFAST Taxonomy check result was written to GCF_008932245.1_ASM893224v1_genomic.fna/tc_result.tsv
[2024-01-24 12:27:54,494] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:27:54,494] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:27:54,494] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53d44728-3c68-4537-afb2-84f2349b4748/dqc_reference/checkm_data
[2024-01-24 12:27:54,495] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:27:54,552] [INFO] Task started: CheckM
[2024-01-24 12:27:54,552] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008932245.1_ASM893224v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008932245.1_ASM893224v1_genomic.fna/checkm_input GCF_008932245.1_ASM893224v1_genomic.fna/checkm_result
[2024-01-24 12:28:45,771] [INFO] Task succeeded: CheckM
[2024-01-24 12:28:45,772] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:28:45,800] [INFO] ===== Completeness check finished =====
[2024-01-24 12:28:45,801] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:28:45,801] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008932245.1_ASM893224v1_genomic.fna/markers.fasta)
[2024-01-24 12:28:45,801] [INFO] Task started: Blastn
[2024-01-24 12:28:45,802] [INFO] Running command: blastn -query GCF_008932245.1_ASM893224v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53d44728-3c68-4537-afb2-84f2349b4748/dqc_reference/reference_markers_gtdb.fasta -out GCF_008932245.1_ASM893224v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:28:47,804] [INFO] Task succeeded: Blastn
[2024-01-24 12:28:47,809] [INFO] Selected 9 target genomes.
[2024-01-24 12:28:47,809] [INFO] Target genome list was writen to GCF_008932245.1_ASM893224v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:28:47,914] [INFO] Task started: fastANI
[2024-01-24 12:28:47,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f1c782c-e7cb-46e7-9c48-9e6c37a20f80/GCF_008932245.1_ASM893224v1_genomic.fna.gz --refList GCF_008932245.1_ASM893224v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008932245.1_ASM893224v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:29:01,378] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:01,390] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:29:01,391] [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_008932245.1	s__Sinorhizobium alkalisoli	100.0	2039	2042	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	98.95	98.95	0.93	0.93	2	conclusive
GCF_001854885.1	s__Sinorhizobium sp001854885	93.7456	1555	2042	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002288525.1	s__Sinorhizobium sojae	89.4921	1502	2042	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017874595.1	s__Sinorhizobium kostiense	84.302	1354	2042	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	83.6412	1274	2042	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	99.97	99.97	0.96	0.96	2	-
GCF_000378985.1	s__Sinorhizobium sp000378985	83.3547	1277	2042	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	83.3385	1325	2042	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	83.2962	1244	2042	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	82.9002	1103	2042	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 12:29:01,392] [INFO] GTDB search result was written to GCF_008932245.1_ASM893224v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:29:01,393] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:29:01,396] [INFO] DFAST_QC result json was written to GCF_008932245.1_ASM893224v1_genomic.fna/dqc_result.json
[2024-01-24 12:29:01,396] [INFO] DFAST_QC completed!
[2024-01-24 12:29:01,396] [INFO] Total running time: 0h1m42s