[2023-03-17 05:47:43,598] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:47:43,599] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:47:43,599] [INFO] DQC Reference Directory: /var/lib/cwl/stg094077f0-2055-4355-874e-ef9029141927/dqc_reference
[2023-03-17 05:47:44,725] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:47:44,726] [INFO] Task started: Prodigal
[2023-03-17 05:47:44,726] [INFO] Running command: cat /var/lib/cwl/stga6dff31c-b84a-4d14-8240-0de71780d5df/OceanDNA-b26798.fa | prodigal -d OceanDNA-b26798/cds.fna -a OceanDNA-b26798/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:48:12,732] [INFO] Task succeeded: Prodigal
[2023-03-17 05:48:12,732] [INFO] Task started: HMMsearch
[2023-03-17 05:48:12,732] [INFO] Running command: hmmsearch --tblout OceanDNA-b26798/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg094077f0-2055-4355-874e-ef9029141927/dqc_reference/reference_markers.hmm OceanDNA-b26798/protein.faa > /dev/null
[2023-03-17 05:48:12,949] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:48:12,949] [INFO] Found 6/6 markers.
[2023-03-17 05:48:12,976] [INFO] Query marker FASTA was written to OceanDNA-b26798/markers.fasta
[2023-03-17 05:48:12,978] [INFO] Task started: Blastn
[2023-03-17 05:48:12,978] [INFO] Running command: blastn -query OceanDNA-b26798/markers.fasta -db /var/lib/cwl/stg094077f0-2055-4355-874e-ef9029141927/dqc_reference/reference_markers.fasta -out OceanDNA-b26798/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:48:14,098] [INFO] Task succeeded: Blastn
[2023-03-17 05:48:14,104] [INFO] Selected 13 target genomes.
[2023-03-17 05:48:14,105] [INFO] Target genome list was writen to OceanDNA-b26798/target_genomes.txt
[2023-03-17 05:48:14,113] [INFO] Task started: fastANI
[2023-03-17 05:48:14,113] [INFO] Running command: fastANI --query /var/lib/cwl/stga6dff31c-b84a-4d14-8240-0de71780d5df/OceanDNA-b26798.fa --refList OceanDNA-b26798/target_genomes.txt --output OceanDNA-b26798/fastani_result.tsv --threads 1
[2023-03-17 05:48:28,035] [INFO] Task succeeded: fastANI
[2023-03-17 05:48:28,036] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg094077f0-2055-4355-874e-ef9029141927/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:48:28,036] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg094077f0-2055-4355-874e-ef9029141927/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:48:28,095] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:48:28,095] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:48:28,095] [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 rhizophilum	strain=7209-2	GCA_004912145.1	1850373	1850373	type	True	87.9895	1219	1496	95	below_threshold
Rhizobium rosettiformans	strain=DSM 26376	GCA_014202175.1	1368430	1368430	type	True	85.2859	1119	1496	95	below_threshold
Rhizobium rosettiformans	strain=W3	GCA_004912135.1	1368430	1368430	type	True	85.2731	1100	1496	95	below_threshold
Rhizobium wuzhouense	strain=W44	GCA_003205195.1	1986026	1986026	type	True	83.7531	1004	1496	95	below_threshold
Rhizobium glycinendophyticum	strain=CL12	GCA_006443685.1	2589807	2589807	type	True	83.0801	963	1496	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	79.8175	605	1496	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	79.7182	688	1496	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	79.201	609	1496	95	below_threshold
Rhizobium changzhiense	strain=WYCCWR 11279	GCA_013087625.1	2692317	2692317	type	True	79.162	591	1496	95	below_threshold
Agrobacterium leguminum	strain=MOPV5	GCA_015704895.1	2792015	2792015	type	True	79.0897	531	1496	95	below_threshold
Rhizobium petrolearium	strain=DSM 26482	GCA_017873175.1	515361	515361	type	True	78.9978	558	1496	95	below_threshold
Agrobacterium rhizogenes	strain=NBRC 13257	GCA_000696095.1	359	359	type	True	78.8078	588	1496	95	below_threshold
Agrobacterium rhizogenes	strain=LMG150	GCA_007002985.1	359	359	type	True	78.7817	593	1496	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:48:28,100] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26798/tc_result.tsv
[2023-03-17 05:48:28,101] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:48:28,101] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:48:28,101] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg094077f0-2055-4355-874e-ef9029141927/dqc_reference/checkm_data
[2023-03-17 05:48:28,101] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:48:28,107] [INFO] Task started: CheckM
[2023-03-17 05:48:28,107] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26798/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26798/checkm_input OceanDNA-b26798/checkm_result
[2023-03-17 05:49:41,547] [INFO] Task succeeded: CheckM
[2023-03-17 05:49:41,548] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:49:41,583] [INFO] ===== Completeness check finished =====
[2023-03-17 05:49:41,584] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:49:41,584] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26798/markers.fasta)
[2023-03-17 05:49:41,585] [INFO] Task started: Blastn
[2023-03-17 05:49:41,585] [INFO] Running command: blastn -query OceanDNA-b26798/markers.fasta -db /var/lib/cwl/stg094077f0-2055-4355-874e-ef9029141927/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26798/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:49:43,753] [INFO] Task succeeded: Blastn
[2023-03-17 05:49:43,755] [INFO] Selected 12 target genomes.
[2023-03-17 05:49:43,755] [INFO] Target genome list was writen to OceanDNA-b26798/target_genomes_gtdb.txt
[2023-03-17 05:49:43,834] [INFO] Task started: fastANI
[2023-03-17 05:49:43,834] [INFO] Running command: fastANI --query /var/lib/cwl/stga6dff31c-b84a-4d14-8240-0de71780d5df/OceanDNA-b26798.fa --refList OceanDNA-b26798/target_genomes_gtdb.txt --output OceanDNA-b26798/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:49:56,956] [INFO] Task succeeded: fastANI
[2023-03-17 05:49:56,964] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:49:56,964] [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_004912145.1	s__Allorhizobium rhizophilum	87.9895	1219	1496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	95.70	95.70	0.88	0.88	2	-
GCA_900473745.1	s__Allorhizobium sp900473745	87.6558	1208	1496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900466945.1	s__Allorhizobium sp900466945	87.4899	1223	1496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002855515.1	s__Allorhizobium sp002855515	86.4533	1125	1496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156055.1	s__Allorhizobium sp900156055	85.4629	1093	1496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001713475.1	s__Allorhizobium sp001713475	85.3545	1120	1496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	98.17	97.98	0.95	0.89	6	-
GCF_000300855.1	s__Allorhizobium albertimagni	85.3258	1094	1496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004912135.1	s__Allorhizobium rosettiformans	85.2632	1101	1496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.40	95.42	0.87	0.84	7	-
GCF_016806065.1	s__Allorhizobium sp001724035	85.1571	1124	1496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	96.77	96.77	0.91	0.91	2	-
GCF_014237835.1	s__Allorhizobium sp014237835	84.6798	1081	1496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003205195.1	s__Allorhizobium wuzhouense	83.7624	1003	1496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	97.59	97.59	0.92	0.92	2	-
GCF_006443685.1	s__Allorhizobium glycinendophyticum	83.0892	962	1496	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:49:56,971] [INFO] GTDB search result was written to OceanDNA-b26798/result_gtdb.tsv
[2023-03-17 05:49:56,971] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:49:56,973] [INFO] DFAST_QC result json was written to OceanDNA-b26798/dqc_result.json
[2023-03-17 05:49:56,973] [INFO] DFAST_QC completed!
[2023-03-17 05:49:56,973] [INFO] Total running time: 0h2m13s