[2024-01-25 19:10:05,766] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:10:05,767] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:10:05,768] [INFO] DQC Reference Directory: /var/lib/cwl/stgda68e94c-dc3d-4717-8197-f1c8f5722cf7/dqc_reference
[2024-01-25 19:10:06,951] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:10:06,951] [INFO] Task started: Prodigal
[2024-01-25 19:10:06,952] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8510a05-42f9-4819-8300-634a85853b2c/GCF_003939025.1_ASM393902v1_genomic.fna.gz | prodigal -d GCF_003939025.1_ASM393902v1_genomic.fna/cds.fna -a GCF_003939025.1_ASM393902v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:10:24,101] [INFO] Task succeeded: Prodigal
[2024-01-25 19:10:24,101] [INFO] Task started: HMMsearch
[2024-01-25 19:10:24,101] [INFO] Running command: hmmsearch --tblout GCF_003939025.1_ASM393902v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda68e94c-dc3d-4717-8197-f1c8f5722cf7/dqc_reference/reference_markers.hmm GCF_003939025.1_ASM393902v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:10:24,388] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:10:24,389] [INFO] Found 6/6 markers.
[2024-01-25 19:10:24,440] [INFO] Query marker FASTA was written to GCF_003939025.1_ASM393902v1_genomic.fna/markers.fasta
[2024-01-25 19:10:24,441] [INFO] Task started: Blastn
[2024-01-25 19:10:24,441] [INFO] Running command: blastn -query GCF_003939025.1_ASM393902v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda68e94c-dc3d-4717-8197-f1c8f5722cf7/dqc_reference/reference_markers.fasta -out GCF_003939025.1_ASM393902v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:25,433] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:25,436] [INFO] Selected 13 target genomes.
[2024-01-25 19:10:25,436] [INFO] Target genome list was writen to GCF_003939025.1_ASM393902v1_genomic.fna/target_genomes.txt
[2024-01-25 19:10:25,442] [INFO] Task started: fastANI
[2024-01-25 19:10:25,443] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8510a05-42f9-4819-8300-634a85853b2c/GCF_003939025.1_ASM393902v1_genomic.fna.gz --refList GCF_003939025.1_ASM393902v1_genomic.fna/target_genomes.txt --output GCF_003939025.1_ASM393902v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:10:47,018] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:47,019] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda68e94c-dc3d-4717-8197-f1c8f5722cf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:10:47,019] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda68e94c-dc3d-4717-8197-f1c8f5722cf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:10:47,027] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:10:47,028] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:10:47,028] [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
Rhizobium sophoriradicis	strain=CCBAU 03470	GCA_003939025.1	1535245	1535245	type	True	100.0	2181	2188	95	conclusive
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	93.5872	1849	2188	95	below_threshold
Rhizobium phaseoli	strain=ATCC 14482	GCA_003985125.1	396	396	type	True	92.217	1812	2188	95	below_threshold
Rhizobium binae	strain=BLR195	GCA_017357225.1	1138190	1138190	type	True	91.0086	1630	2188	95	below_threshold
Rhizobium binae	strain=BLR195	GCA_019684455.1	1138190	1138190	type	True	90.8894	1646	2188	95	below_threshold
Rhizobium etli	strain=CFN 42	GCA_000092045.1	29449	29449	suspected-type	True	89.8996	1741	2188	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	89.1805	1671	2188	95	below_threshold
Rhizobium esperanzae	strain=CNPSo 668	GCA_002204185.1	1967781	1967781	suspected-type	True	88.9586	1688	2188	95	below_threshold
Rhizobium anhuiense	strain=CGMCC 1.12621	GCA_014638185.1	1184720	1184720	type	True	87.9666	1648	2188	95	below_threshold
Rhizobium anhuiense	strain=CCBAU 23252	GCA_003985145.1	1184720	1184720	type	True	87.9208	1656	2188	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	81.4272	1120	2188	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	80.4963	949	2188	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.0775	742	2188	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:10:47,030] [INFO] DFAST Taxonomy check result was written to GCF_003939025.1_ASM393902v1_genomic.fna/tc_result.tsv
[2024-01-25 19:10:47,030] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:10:47,030] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:10:47,031] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda68e94c-dc3d-4717-8197-f1c8f5722cf7/dqc_reference/checkm_data
[2024-01-25 19:10:47,031] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:10:47,094] [INFO] Task started: CheckM
[2024-01-25 19:10:47,094] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003939025.1_ASM393902v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003939025.1_ASM393902v1_genomic.fna/checkm_input GCF_003939025.1_ASM393902v1_genomic.fna/checkm_result
[2024-01-25 19:11:35,673] [INFO] Task succeeded: CheckM
[2024-01-25 19:11:35,674] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:11:35,696] [INFO] ===== Completeness check finished =====
[2024-01-25 19:11:35,696] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:11:35,697] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003939025.1_ASM393902v1_genomic.fna/markers.fasta)
[2024-01-25 19:11:35,697] [INFO] Task started: Blastn
[2024-01-25 19:11:35,698] [INFO] Running command: blastn -query GCF_003939025.1_ASM393902v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda68e94c-dc3d-4717-8197-f1c8f5722cf7/dqc_reference/reference_markers_gtdb.fasta -out GCF_003939025.1_ASM393902v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:37,734] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:37,737] [INFO] Selected 12 target genomes.
[2024-01-25 19:11:37,737] [INFO] Target genome list was writen to GCF_003939025.1_ASM393902v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:11:37,749] [INFO] Task started: fastANI
[2024-01-25 19:11:37,749] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8510a05-42f9-4819-8300-634a85853b2c/GCF_003939025.1_ASM393902v1_genomic.fna.gz --refList GCF_003939025.1_ASM393902v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003939025.1_ASM393902v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:11:59,014] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:59,022] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:11:59,023] [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_003939025.1	s__Rhizobium sophoriradicis	100.0	2180	2188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.45	97.30	0.92	0.88	16	conclusive
GCF_002531955.1	s__Rhizobium sp002531955	93.5835	1859	2188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.59	95.76	0.89	0.85	5	-
GCF_001662075.1	s__Rhizobium bangladeshense_B	92.814	1765	2188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200175.1	s__Rhizobium lentis_A	92.2227	1773	2188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.99	99.97	0.99	0.98	4	-
GCF_003985125.1	s__Rhizobium phaseoli	92.2183	1812	2188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.51	96.92	0.91	0.87	41	-
GCF_017357225.1	s__Rhizobium binae	91.0055	1631	2188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001664485.1	s__Rhizobium sp001664485	89.5389	1742	2188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.08	96.02	0.91	0.83	8	-
GCF_002531825.1	s__Rhizobium sp002531825	89.3663	1664	2188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002531905.1	s__Rhizobium sp002531905	89.3403	1698	2188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.24	98.93	0.89	0.86	4	-
GCF_002211305.1	s__Rhizobium sp002211305	88.8888	1630	2188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.97	96.97	0.89	0.89	2	-
GCF_002531755.2	s__Rhizobium acidisoli	88.7946	1691	2188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.96	96.40	0.88	0.80	8	-
GCF_003985145.1	s__Rhizobium anhuiense	87.9251	1655	2188	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.85	98.46	0.91	0.88	19	-
--------------------------------------------------------------------------------
[2024-01-25 19:11:59,024] [INFO] GTDB search result was written to GCF_003939025.1_ASM393902v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:11:59,024] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:11:59,027] [INFO] DFAST_QC result json was written to GCF_003939025.1_ASM393902v1_genomic.fna/dqc_result.json
[2024-01-25 19:11:59,027] [INFO] DFAST_QC completed!
[2024-01-25 19:11:59,027] [INFO] Total running time: 0h1m53s