[2023-03-19 03:38:32,421] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:38:32,421] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:38:32,421] [INFO] DQC Reference Directory: /var/lib/cwl/stg121cab48-253d-4bfb-911f-54d5d378f0cf/dqc_reference
[2023-03-19 03:38:33,503] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:38:33,504] [INFO] Task started: Prodigal
[2023-03-19 03:38:33,504] [INFO] Running command: cat /var/lib/cwl/stg329694ce-2c9f-4f00-b97f-a7d2fd2d99c6/OceanDNA-b26685.fa | prodigal -d OceanDNA-b26685/cds.fna -a OceanDNA-b26685/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:38:57,960] [INFO] Task succeeded: Prodigal
[2023-03-19 03:38:57,961] [INFO] Task started: HMMsearch
[2023-03-19 03:38:57,961] [INFO] Running command: hmmsearch --tblout OceanDNA-b26685/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg121cab48-253d-4bfb-911f-54d5d378f0cf/dqc_reference/reference_markers.hmm OceanDNA-b26685/protein.faa > /dev/null
[2023-03-19 03:38:58,158] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:38:58,159] [INFO] Found 6/6 markers.
[2023-03-19 03:38:58,181] [INFO] Query marker FASTA was written to OceanDNA-b26685/markers.fasta
[2023-03-19 03:38:58,181] [INFO] Task started: Blastn
[2023-03-19 03:38:58,181] [INFO] Running command: blastn -query OceanDNA-b26685/markers.fasta -db /var/lib/cwl/stg121cab48-253d-4bfb-911f-54d5d378f0cf/dqc_reference/reference_markers.fasta -out OceanDNA-b26685/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:38:58,812] [INFO] Task succeeded: Blastn
[2023-03-19 03:38:58,813] [INFO] Selected 16 target genomes.
[2023-03-19 03:38:58,813] [INFO] Target genome list was writen to OceanDNA-b26685/target_genomes.txt
[2023-03-19 03:38:58,820] [INFO] Task started: fastANI
[2023-03-19 03:38:58,820] [INFO] Running command: fastANI --query /var/lib/cwl/stg329694ce-2c9f-4f00-b97f-a7d2fd2d99c6/OceanDNA-b26685.fa --refList OceanDNA-b26685/target_genomes.txt --output OceanDNA-b26685/fastani_result.tsv --threads 1
[2023-03-19 03:39:10,916] [INFO] Task succeeded: fastANI
[2023-03-19 03:39:10,916] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg121cab48-253d-4bfb-911f-54d5d378f0cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:39:10,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg121cab48-253d-4bfb-911f-54d5d378f0cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:39:10,926] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:39:10,926] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 03:39:10,926] [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	83.0763	838	1258	95	below_threshold
Devosia ginsengisoli	strain=Gsoil 520	GCA_007859655.1	400770	400770	type	True	80.8236	739	1258	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	80.4316	649	1258	95	below_threshold
Devosia epidermidihirudinis	strain=E84	GCA_000971295.1	1293439	1293439	type	True	80.3539	628	1258	95	below_threshold
Devosia psychrophila	strain=Cr7-05	GCA_000971275.1	728005	728005	type	True	79.9445	666	1258	95	below_threshold
Devosia naphthalenivorans	strain=CM5-1	GCA_003056355.1	2082392	2082392	type	True	79.9103	602	1258	95	below_threshold
Devosia psychrophila	strain=CGMCC 1.10210	GCA_900112505.1	728005	728005	type	True	79.9089	685	1258	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	79.5705	621	1258	95	below_threshold
Devosia marina	strain=L53-10-65	GCA_009758415.1	2683198	2683198	type	True	79.207	582	1258	95	below_threshold
Devosia subaequoris	strain=HST3-14	GCA_024158985.1	395930	395930	type	True	79.117	545	1258	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	79.074	557	1258	95	below_threshold
Devosia sediminis	strain=MSA67	GCA_016411825.1	2798801	2798801	type	True	79.0596	568	1258	95	below_threshold
Devosia riboflavina	strain=IFO13584	GCA_000743575.1	46914	46914	type	True	78.8715	534	1258	95	below_threshold
Devosia rhizoryzae	strain=LEGU1	GCA_016698665.1	2774137	2774137	type	True	78.7399	455	1258	95	below_threshold
Mesorhizobium denitrificans	strain=LA-28	GCA_003403035.1	2294114	2294114	type	True	75.7709	83	1258	95	below_threshold
Paracoccus isoporae	strain=DSM 22220	GCA_900101865.1	591205	591205	type	True	75.7606	79	1258	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 03:39:10,926] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26685/tc_result.tsv
[2023-03-19 03:39:10,926] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:39:10,926] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:39:10,927] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg121cab48-253d-4bfb-911f-54d5d378f0cf/dqc_reference/checkm_data
[2023-03-19 03:39:10,927] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:39:11,205] [INFO] Task started: CheckM
[2023-03-19 03:39:11,205] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26685/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26685/checkm_input OceanDNA-b26685/checkm_result
[2023-03-19 03:40:12,313] [INFO] Task succeeded: CheckM
[2023-03-19 03:40:12,313] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:40:12,316] [INFO] ===== Completeness check finished =====
[2023-03-19 03:40:12,316] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:40:12,316] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26685/markers.fasta)
[2023-03-19 03:40:12,316] [INFO] Task started: Blastn
[2023-03-19 03:40:12,316] [INFO] Running command: blastn -query OceanDNA-b26685/markers.fasta -db /var/lib/cwl/stg121cab48-253d-4bfb-911f-54d5d378f0cf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26685/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:40:13,253] [INFO] Task succeeded: Blastn
[2023-03-19 03:40:13,254] [INFO] Selected 14 target genomes.
[2023-03-19 03:40:13,254] [INFO] Target genome list was writen to OceanDNA-b26685/target_genomes_gtdb.txt
[2023-03-19 03:40:13,267] [INFO] Task started: fastANI
[2023-03-19 03:40:13,267] [INFO] Running command: fastANI --query /var/lib/cwl/stg329694ce-2c9f-4f00-b97f-a7d2fd2d99c6/OceanDNA-b26685.fa --refList OceanDNA-b26685/target_genomes_gtdb.txt --output OceanDNA-b26685/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:40:24,776] [INFO] Task succeeded: fastANI
[2023-03-19 03:40:24,784] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:40:24,784] [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_018334155.1	s__Devosia sp018334155	98.5322	1162	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014926585.1	s__Devosia sp014926585	83.0816	837	1258	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	82.0969	785	1258	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	81.2702	775	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.99	99.98	0.99	0.98	4	-
GCF_007859655.1	s__Devosia ginsengisoli	80.8318	737	1258	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	80.8017	467	1258	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	80.7579	710	1258	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	80.5936	714	1258	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	80.4192	650	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971295.1	s__Devosia epidermidihirudinis	80.3583	625	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000971275.1	s__Devosia psychrophila	79.9493	665	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.97	99.97	0.98	0.98	2	-
GCF_003056355.1	s__Devosia naphthalenivorans	79.9107	602	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015234425.1	s__Devosia sp015234425	78.9649	537	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427875.1	s__Devosia sp001427875	78.7025	556	1258	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:40:24,784] [INFO] GTDB search result was written to OceanDNA-b26685/result_gtdb.tsv
[2023-03-19 03:40:24,784] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:40:24,786] [INFO] DFAST_QC result json was written to OceanDNA-b26685/dqc_result.json
[2023-03-19 03:40:24,786] [INFO] DFAST_QC completed!
[2023-03-19 03:40:24,786] [INFO] Total running time: 0h1m52s