[2023-03-17 10:35:02,805] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:35:02,805] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:35:02,806] [INFO] DQC Reference Directory: /var/lib/cwl/stg51a95f35-0179-4872-a492-d2738faf655a/dqc_reference
[2023-03-17 10:35:04,550] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:35:04,551] [INFO] Task started: Prodigal
[2023-03-17 10:35:04,551] [INFO] Running command: cat /var/lib/cwl/stgf2dd01c4-408a-4d0c-910f-3a5cc5e05418/OceanDNA-b26682.fa | prodigal -d OceanDNA-b26682/cds.fna -a OceanDNA-b26682/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:35:21,528] [INFO] Task succeeded: Prodigal
[2023-03-17 10:35:21,529] [INFO] Task started: HMMsearch
[2023-03-17 10:35:21,529] [INFO] Running command: hmmsearch --tblout OceanDNA-b26682/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51a95f35-0179-4872-a492-d2738faf655a/dqc_reference/reference_markers.hmm OceanDNA-b26682/protein.faa > /dev/null
[2023-03-17 10:35:21,728] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:35:21,729] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf2dd01c4-408a-4d0c-910f-3a5cc5e05418/OceanDNA-b26682.fa]
[2023-03-17 10:35:21,755] [INFO] Query marker FASTA was written to OceanDNA-b26682/markers.fasta
[2023-03-17 10:35:21,755] [INFO] Task started: Blastn
[2023-03-17 10:35:21,755] [INFO] Running command: blastn -query OceanDNA-b26682/markers.fasta -db /var/lib/cwl/stg51a95f35-0179-4872-a492-d2738faf655a/dqc_reference/reference_markers.fasta -out OceanDNA-b26682/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:35:22,581] [INFO] Task succeeded: Blastn
[2023-03-17 10:35:22,582] [INFO] Selected 13 target genomes.
[2023-03-17 10:35:22,583] [INFO] Target genome list was writen to OceanDNA-b26682/target_genomes.txt
[2023-03-17 10:35:22,590] [INFO] Task started: fastANI
[2023-03-17 10:35:22,590] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2dd01c4-408a-4d0c-910f-3a5cc5e05418/OceanDNA-b26682.fa --refList OceanDNA-b26682/target_genomes.txt --output OceanDNA-b26682/fastani_result.tsv --threads 1
[2023-03-17 10:35:31,730] [INFO] Task succeeded: fastANI
[2023-03-17 10:35:31,731] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51a95f35-0179-4872-a492-d2738faf655a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:35:31,731] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51a95f35-0179-4872-a492-d2738faf655a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:35:31,740] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:35:31,740] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 10:35:31,740] [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
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	87.6218	588	813	95	below_threshold
Devosia ginsengisoli	strain=Gsoil 520	GCA_007859655.1	400770	400770	type	True	81.7279	474	813	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	81.0353	423	813	95	below_threshold
Devosia psychrophila	strain=CGMCC 1.10210	GCA_900112505.1	728005	728005	type	True	80.8841	449	813	95	below_threshold
Devosia psychrophila	strain=Cr7-05	GCA_000971275.1	728005	728005	type	True	80.8434	444	813	95	below_threshold
Devosia limi	strain=DSM 17137	GCA_900128975.1	288995	288995	type	True	80.7999	430	813	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	80.3509	414	813	95	below_threshold
Devosia naphthalenivorans	strain=CM5-1	GCA_003056355.1	2082392	2082392	type	True	80.2946	391	813	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	80.1999	443	813	95	below_threshold
Devosia faecipullorum	strain=CC-YST696	GCA_015158295.1	2755039	2755039	type	True	79.7572	349	813	95	below_threshold
Devosia marina	strain=L53-10-65	GCA_009758415.1	2683198	2683198	type	True	79.5465	370	813	95	below_threshold
Devosia subaequoris	strain=HST3-14	GCA_024158985.1	395930	395930	type	True	79.4435	345	813	95	below_threshold
Devosia rhizoryzae	strain=LEGU1	GCA_016698665.1	2774137	2774137	type	True	79.1009	339	813	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 10:35:31,741] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26682/tc_result.tsv
[2023-03-17 10:35:31,741] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:35:31,741] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:35:31,741] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51a95f35-0179-4872-a492-d2738faf655a/dqc_reference/checkm_data
[2023-03-17 10:35:31,742] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:35:31,765] [INFO] Task started: CheckM
[2023-03-17 10:35:31,765] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26682/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26682/checkm_input OceanDNA-b26682/checkm_result
[2023-03-17 10:36:16,127] [INFO] Task succeeded: CheckM
[2023-03-17 10:36:16,127] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:36:16,130] [INFO] ===== Completeness check finished =====
[2023-03-17 10:36:16,130] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:36:16,130] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26682/markers.fasta)
[2023-03-17 10:36:16,131] [INFO] Task started: Blastn
[2023-03-17 10:36:16,131] [INFO] Running command: blastn -query OceanDNA-b26682/markers.fasta -db /var/lib/cwl/stg51a95f35-0179-4872-a492-d2738faf655a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26682/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:36:17,668] [INFO] Task succeeded: Blastn
[2023-03-17 10:36:17,669] [INFO] Selected 10 target genomes.
[2023-03-17 10:36:17,669] [INFO] Target genome list was writen to OceanDNA-b26682/target_genomes_gtdb.txt
[2023-03-17 10:36:17,832] [INFO] Task started: fastANI
[2023-03-17 10:36:17,832] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2dd01c4-408a-4d0c-910f-3a5cc5e05418/OceanDNA-b26682.fa --refList OceanDNA-b26682/target_genomes_gtdb.txt --output OceanDNA-b26682/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:36:25,367] [INFO] Task succeeded: fastANI
[2023-03-17 10:36:25,374] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 10:36:25,374] [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_014926585.1	s__Devosia sp014926585	87.6572	586	813	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222805.1	s__Devosia sp005222805	83.03	501	813	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018828145.1	s__Devosia sp018828145	82.5076	502	813	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.99	99.98	0.99	0.98	4	-
GCF_018334155.1	s__Devosia sp018334155	82.1273	470	813	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426345.1	s__Devosia sp001426345	81.9107	464	813	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860165.1	s__Devosia sp014860165	81.8124	473	813	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859655.1	s__Devosia ginsengisoli	81.7526	472	813	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110945.1	s__Devosia sp900110945	81.4161	472	813	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018820005.1	s__Devosia sp018820005	81.2148	316	813	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016698645.1	s__Devosia sp016698645	81.0735	420	813	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 10:36:25,374] [INFO] GTDB search result was written to OceanDNA-b26682/result_gtdb.tsv
[2023-03-17 10:36:25,374] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:36:25,376] [INFO] DFAST_QC result json was written to OceanDNA-b26682/dqc_result.json
[2023-03-17 10:36:25,376] [INFO] DFAST_QC completed!
[2023-03-17 10:36:25,376] [INFO] Total running time: 0h1m23s