[2024-01-24 13:12:38,293] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:38,295] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:38,296] [INFO] DQC Reference Directory: /var/lib/cwl/stge90f0bde-a02f-452a-8ac4-57d3b07bf06a/dqc_reference
[2024-01-24 13:12:39,731] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:39,732] [INFO] Task started: Prodigal
[2024-01-24 13:12:39,732] [INFO] Running command: gunzip -c /var/lib/cwl/stg0d74a1a6-ff20-464f-a12c-fc533dddf615/GCF_017874595.1_ASM1787459v1_genomic.fna.gz | prodigal -d GCF_017874595.1_ASM1787459v1_genomic.fna/cds.fna -a GCF_017874595.1_ASM1787459v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:58,442] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:58,442] [INFO] Task started: HMMsearch
[2024-01-24 13:12:58,442] [INFO] Running command: hmmsearch --tblout GCF_017874595.1_ASM1787459v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge90f0bde-a02f-452a-8ac4-57d3b07bf06a/dqc_reference/reference_markers.hmm GCF_017874595.1_ASM1787459v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:58,845] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:58,847] [INFO] Found 6/6 markers.
[2024-01-24 13:12:58,899] [INFO] Query marker FASTA was written to GCF_017874595.1_ASM1787459v1_genomic.fna/markers.fasta
[2024-01-24 13:12:58,899] [INFO] Task started: Blastn
[2024-01-24 13:12:58,900] [INFO] Running command: blastn -query GCF_017874595.1_ASM1787459v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge90f0bde-a02f-452a-8ac4-57d3b07bf06a/dqc_reference/reference_markers.fasta -out GCF_017874595.1_ASM1787459v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:59,877] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:59,881] [INFO] Selected 14 target genomes.
[2024-01-24 13:12:59,881] [INFO] Target genome list was writen to GCF_017874595.1_ASM1787459v1_genomic.fna/target_genomes.txt
[2024-01-24 13:12:59,887] [INFO] Task started: fastANI
[2024-01-24 13:12:59,887] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d74a1a6-ff20-464f-a12c-fc533dddf615/GCF_017874595.1_ASM1787459v1_genomic.fna.gz --refList GCF_017874595.1_ASM1787459v1_genomic.fna/target_genomes.txt --output GCF_017874595.1_ASM1787459v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:21,564] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:21,565] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge90f0bde-a02f-452a-8ac4-57d3b07bf06a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:21,565] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge90f0bde-a02f-452a-8ac4-57d3b07bf06a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:21,581] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:21,582] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:21,582] [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 kostiense	strain=DSM 13372	GCA_017874595.1	76747	76747	type	True	100.0	2094	2098	95	conclusive
Ensifer sojae	strain=CCBAU 05684	GCA_002288525.1	716925	716925	type	True	84.4945	1371	2098	95	below_threshold
Ensifer sojae	strain=CCBAU 05684	GCA_000261485.1	716925	716925	type	True	84.4806	1311	2098	95	below_threshold
Ensifer alkalisoli	strain=YIC4027	GCA_008932245.1	1752398	1752398	type	True	84.2032	1362	2098	95	below_threshold
Ensifer alkalisoli	strain=YIC4027	GCA_001723275.1	1752398	1752398	type	True	84.1344	1329	2098	95	below_threshold
Sinorhizobium fredii	strain=NBRC 14780	GCA_006539605.1	380	380	type	True	83.1742	1220	2098	95	below_threshold
Sinorhizobium fredii	strain=USDA 205	GCA_001461695.1	380	380	type	True	83.1482	1244	2098	95	below_threshold
Sinorhizobium fredii	strain=USDA205	GCA_009601405.1	380	380	type	True	83.1368	1288	2098	95	below_threshold
Ensifer psoraleae	strain=CCBAU 65732	GCA_013283645.1	520838	520838	type	True	82.1814	1241	2098	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.2401	740	2098	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	79.5561	674	2098	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	78.9328	700	2098	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	78.9311	581	2098	95	below_threshold
Rhizobium petrolearium	strain=DSM 26482	GCA_017873175.1	515361	515361	type	True	78.4543	546	2098	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:21,584] [INFO] DFAST Taxonomy check result was written to GCF_017874595.1_ASM1787459v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:21,585] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:21,585] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:21,585] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge90f0bde-a02f-452a-8ac4-57d3b07bf06a/dqc_reference/checkm_data
[2024-01-24 13:13:21,587] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:21,649] [INFO] Task started: CheckM
[2024-01-24 13:13:21,650] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017874595.1_ASM1787459v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017874595.1_ASM1787459v1_genomic.fna/checkm_input GCF_017874595.1_ASM1787459v1_genomic.fna/checkm_result
[2024-01-24 13:14:15,404] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:15,405] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:15,427] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:15,427] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:15,428] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017874595.1_ASM1787459v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:15,428] [INFO] Task started: Blastn
[2024-01-24 13:14:15,428] [INFO] Running command: blastn -query GCF_017874595.1_ASM1787459v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge90f0bde-a02f-452a-8ac4-57d3b07bf06a/dqc_reference/reference_markers_gtdb.fasta -out GCF_017874595.1_ASM1787459v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:17,295] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:17,299] [INFO] Selected 13 target genomes.
[2024-01-24 13:14:17,299] [INFO] Target genome list was writen to GCF_017874595.1_ASM1787459v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:17,309] [INFO] Task started: fastANI
[2024-01-24 13:14:17,310] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d74a1a6-ff20-464f-a12c-fc533dddf615/GCF_017874595.1_ASM1787459v1_genomic.fna.gz --refList GCF_017874595.1_ASM1787459v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017874595.1_ASM1787459v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:36,034] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:36,047] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:36,047] [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_017874595.1	s__Sinorhizobium kostiense	100.0	2094	2098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001854885.1	s__Sinorhizobium sp001854885	84.9785	1382	2098	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	84.504	1370	2098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_008932245.1	s__Sinorhizobium alkalisoli	84.2197	1361	2098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	98.95	98.95	0.93	0.93	2	-
GCF_001651875.1	s__Sinorhizobium saheli	83.6651	1270	2098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	99.97	99.97	0.96	0.96	2	-
GCF_001651865.1	s__Sinorhizobium glycinis	83.5432	1289	2098	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	83.2934	1338	2098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378985.1	s__Sinorhizobium sp000378985	83.204	1308	2098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002944405.1	s__Sinorhizobium fredii_C	83.1877	1252	2098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	98.60	98.35	0.89	0.83	7	-
GCF_001461695.1	s__Sinorhizobium fredii	83.1546	1242	2098	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	83.102	1346	2098	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	83.0113	1074	2098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001651855.1	s__Sinorhizobium americanum	82.9721	1301	2098	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Sinorhizobium	95.0	98.81	98.12	0.92	0.85	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:36,049] [INFO] GTDB search result was written to GCF_017874595.1_ASM1787459v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:36,049] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:36,053] [INFO] DFAST_QC result json was written to GCF_017874595.1_ASM1787459v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:36,053] [INFO] DFAST_QC completed!
[2024-01-24 13:14:36,053] [INFO] Total running time: 0h1m58s