[2023-03-14 12:25:41,508] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:25:41,508] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:25:41,508] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a63bd17-863b-4cbe-9f2e-70ce53279686/dqc_reference
[2023-03-14 12:25:42,738] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:25:42,738] [INFO] Task started: Prodigal
[2023-03-14 12:25:42,738] [INFO] Running command: cat /var/lib/cwl/stg84e8f81e-e85b-4f29-bc80-fde956f1b835/OceanDNA-b26784.fa | prodigal -d OceanDNA-b26784/cds.fna -a OceanDNA-b26784/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:26:12,158] [INFO] Task succeeded: Prodigal
[2023-03-14 12:26:12,158] [INFO] Task started: HMMsearch
[2023-03-14 12:26:12,159] [INFO] Running command: hmmsearch --tblout OceanDNA-b26784/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a63bd17-863b-4cbe-9f2e-70ce53279686/dqc_reference/reference_markers.hmm OceanDNA-b26784/protein.faa > /dev/null
[2023-03-14 12:26:12,395] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:26:12,395] [INFO] Found 6/6 markers.
[2023-03-14 12:26:12,436] [INFO] Query marker FASTA was written to OceanDNA-b26784/markers.fasta
[2023-03-14 12:26:12,437] [INFO] Task started: Blastn
[2023-03-14 12:26:12,438] [INFO] Running command: blastn -query OceanDNA-b26784/markers.fasta -db /var/lib/cwl/stg0a63bd17-863b-4cbe-9f2e-70ce53279686/dqc_reference/reference_markers.fasta -out OceanDNA-b26784/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:26:13,390] [INFO] Task succeeded: Blastn
[2023-03-14 12:26:13,391] [INFO] Selected 19 target genomes.
[2023-03-14 12:26:13,391] [INFO] Target genome list was writen to OceanDNA-b26784/target_genomes.txt
[2023-03-14 12:26:13,406] [INFO] Task started: fastANI
[2023-03-14 12:26:13,406] [INFO] Running command: fastANI --query /var/lib/cwl/stg84e8f81e-e85b-4f29-bc80-fde956f1b835/OceanDNA-b26784.fa --refList OceanDNA-b26784/target_genomes.txt --output OceanDNA-b26784/fastani_result.tsv --threads 1
[2023-03-14 12:26:31,783] [INFO] Task succeeded: fastANI
[2023-03-14 12:26:31,783] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a63bd17-863b-4cbe-9f2e-70ce53279686/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:26:31,783] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a63bd17-863b-4cbe-9f2e-70ce53279686/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:26:31,794] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:26:31,795] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:26:31,795] [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
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	82.06	946	1582	95	below_threshold
Oricola thermophila	strain=MEBiC13590	GCA_013358405.1	2742145	2742145	type	True	80.0029	685	1582	95	below_threshold
Oricola cellulosilytica	strain=JCM 19534	GCA_019966575.1	1429082	1429082	type	True	78.8324	413	1582	95	below_threshold
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	78.1099	392	1582	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	78.0222	322	1582	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	77.9793	362	1582	95	below_threshold
Aquibium carbonis	strain=B2.3	GCA_003970795.1	2495581	2495581	type	True	77.8508	371	1582	95	below_threshold
Mesorhizobium metallidurans	strain=STM 2683	GCA_000350085.1	489722	489722	type	True	77.8325	389	1582	95	below_threshold
Mesorhizobium erdmanii	strain=USDA 3471	GCA_000472705.1	1777866	1777866	type	True	77.796	391	1582	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	77.7701	367	1582	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	77.7586	418	1582	95	below_threshold
Aquamicrobium lusatiense	strain=DSM 11099	GCA_014201615.1	89772	89772	type	True	77.718	284	1582	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	77.7144	383	1582	95	below_threshold
Mesorhizobium waimense	strain=ICMP19557	GCA_003601975.1	1300307	1300307	type	True	77.7045	406	1582	95	below_threshold
Mesorhizobium comanense	strain=3P27G6	GCA_005503535.1	2502215	2502215	type	True	77.653	403	1582	95	below_threshold
Mesorhizobium neociceri	strain=CCANP35	GCA_013520985.1	1307853	1307853	type	True	77.5968	422	1582	95	below_threshold
Phyllobacterium calauticae	strain=R2-JL	GCA_019991125.1	2817027	2817027	type	True	77.0763	274	1582	95	below_threshold
Kaistia hirudinis	strain=DSM 25966	GCA_014196455.1	1293440	1293440	type	True	76.9341	288	1582	95	below_threshold
Phyllobacterium bourgognense	strain=31-25a	GCA_003337575.1	314236	314236	type	True	76.6483	163	1582	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:26:31,795] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26784/tc_result.tsv
[2023-03-14 12:26:31,795] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:26:31,795] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:26:31,795] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a63bd17-863b-4cbe-9f2e-70ce53279686/dqc_reference/checkm_data
[2023-03-14 12:26:31,796] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:26:31,831] [INFO] Task started: CheckM
[2023-03-14 12:26:31,831] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26784/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26784/checkm_input OceanDNA-b26784/checkm_result
[2023-03-14 12:27:42,896] [INFO] Task succeeded: CheckM
[2023-03-14 12:27:42,897] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:27:42,900] [INFO] ===== Completeness check finished =====
[2023-03-14 12:27:42,900] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:27:42,900] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26784/markers.fasta)
[2023-03-14 12:27:42,901] [INFO] Task started: Blastn
[2023-03-14 12:27:42,901] [INFO] Running command: blastn -query OceanDNA-b26784/markers.fasta -db /var/lib/cwl/stg0a63bd17-863b-4cbe-9f2e-70ce53279686/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26784/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:27:44,825] [INFO] Task succeeded: Blastn
[2023-03-14 12:27:44,825] [INFO] Selected 8 target genomes.
[2023-03-14 12:27:44,826] [INFO] Target genome list was writen to OceanDNA-b26784/target_genomes_gtdb.txt
[2023-03-14 12:27:44,830] [INFO] Task started: fastANI
[2023-03-14 12:27:44,830] [INFO] Running command: fastANI --query /var/lib/cwl/stg84e8f81e-e85b-4f29-bc80-fde956f1b835/OceanDNA-b26784.fa --refList OceanDNA-b26784/target_genomes_gtdb.txt --output OceanDNA-b26784/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:27:52,538] [INFO] Task succeeded: fastANI
[2023-03-14 12:27:52,544] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:27:52,544] [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
GCA_002706335.1	s__Oricola sp002706335	99.9655	1571	1582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002698425.1	s__Oricola sp002698425	88.8092	1161	1582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904745.1	s__Oricola sp014904745	81.4081	875	1582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013358405.1	s__Oricola thermophila	80.0059	684	1582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331745.1	s__Oricola cellulosilytica	78.8618	418	1582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149475.2	s__Roseitalea stylonematis	78.1716	433	1582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Roseitalea	95.0	98.99	98.97	0.96	0.95	13	-
GCF_014640615.1	s__Paramesorhizobium endophyticum	77.8271	283	1582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_A;f__Rhizobiaceae_A;g__Paramesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801285.1	s__Mesorhizobium composti	77.6905	386	1582	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	96.99	96.99	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-14 12:27:52,544] [INFO] GTDB search result was written to OceanDNA-b26784/result_gtdb.tsv
[2023-03-14 12:27:52,545] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:27:52,546] [INFO] DFAST_QC result json was written to OceanDNA-b26784/dqc_result.json
[2023-03-14 12:27:52,546] [INFO] DFAST_QC completed!
[2023-03-14 12:27:52,546] [INFO] Total running time: 0h2m11s