[2023-03-15 07:52:40,278] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:52:40,278] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:52:40,278] [INFO] DQC Reference Directory: /var/lib/cwl/stg568021bf-2d24-47e8-9f4a-24d703ed50db/dqc_reference
[2023-03-15 07:52:41,476] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:52:41,476] [INFO] Task started: Prodigal
[2023-03-15 07:52:41,476] [INFO] Running command: cat /var/lib/cwl/stg54633ff2-cca9-401d-a9ad-54ab2cd22297/OceanDNA-b26680.fa | prodigal -d OceanDNA-b26680/cds.fna -a OceanDNA-b26680/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:53:03,706] [INFO] Task succeeded: Prodigal
[2023-03-15 07:53:03,707] [INFO] Task started: HMMsearch
[2023-03-15 07:53:03,707] [INFO] Running command: hmmsearch --tblout OceanDNA-b26680/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg568021bf-2d24-47e8-9f4a-24d703ed50db/dqc_reference/reference_markers.hmm OceanDNA-b26680/protein.faa > /dev/null
[2023-03-15 07:53:03,959] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:53:03,960] [INFO] Found 6/6 markers.
[2023-03-15 07:53:03,981] [INFO] Query marker FASTA was written to OceanDNA-b26680/markers.fasta
[2023-03-15 07:53:03,982] [INFO] Task started: Blastn
[2023-03-15 07:53:03,982] [INFO] Running command: blastn -query OceanDNA-b26680/markers.fasta -db /var/lib/cwl/stg568021bf-2d24-47e8-9f4a-24d703ed50db/dqc_reference/reference_markers.fasta -out OceanDNA-b26680/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:53:04,826] [INFO] Task succeeded: Blastn
[2023-03-15 07:53:04,827] [INFO] Selected 15 target genomes.
[2023-03-15 07:53:04,827] [INFO] Target genome list was writen to OceanDNA-b26680/target_genomes.txt
[2023-03-15 07:53:04,836] [INFO] Task started: fastANI
[2023-03-15 07:53:04,836] [INFO] Running command: fastANI --query /var/lib/cwl/stg54633ff2-cca9-401d-a9ad-54ab2cd22297/OceanDNA-b26680.fa --refList OceanDNA-b26680/target_genomes.txt --output OceanDNA-b26680/fastani_result.tsv --threads 1
[2023-03-15 07:53:17,359] [INFO] Task succeeded: fastANI
[2023-03-15 07:53:17,360] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg568021bf-2d24-47e8-9f4a-24d703ed50db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:53:17,360] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg568021bf-2d24-47e8-9f4a-24d703ed50db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:53:17,369] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:53:17,369] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 07:53:17,370] [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	87.9998	950	1147	95	below_threshold
Devosia ginsengisoli	strain=Gsoil 520	GCA_007859655.1	400770	400770	type	True	82.3836	774	1147	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	81.3248	701	1147	95	below_threshold
Devosia limi	strain=DSM 17137	GCA_000970435.1	288995	288995	type	True	81.153	662	1147	95	below_threshold
Devosia limi	strain=DSM 17137	GCA_900128975.1	288995	288995	type	True	81.0998	680	1147	95	below_threshold
Devosia psychrophila	strain=Cr7-05	GCA_000971275.1	728005	728005	type	True	81.047	674	1147	95	below_threshold
Devosia psychrophila	strain=CGMCC 1.10210	GCA_900112505.1	728005	728005	type	True	80.9765	703	1147	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	80.9193	658	1147	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	80.5392	682	1147	95	below_threshold
Devosia naphthalenivorans	strain=CM5-1	GCA_003056355.1	2082392	2082392	type	True	80.4576	629	1147	95	below_threshold
Devosia equisanguinis	strain=CIP 111628	GCA_900631955.1	2490941	2490941	type	True	80.3378	633	1147	95	below_threshold
Devosia chinhatensis	strain=IPL18	GCA_000969445.1	429727	429727	type	True	80.0675	574	1147	95	below_threshold
Devosia submarina	strain=JCM 18935	GCA_003056345.1	1173082	1173082	type	True	79.886	555	1147	95	below_threshold
Devosia subaequoris	strain=HST3-14	GCA_024158985.1	395930	395930	type	True	79.5018	581	1147	95	below_threshold
Devosia rhizoryzae	strain=LEGU1	GCA_016698665.1	2774137	2774137	type	True	79.424	534	1147	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:53:17,370] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26680/tc_result.tsv
[2023-03-15 07:53:17,370] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:53:17,370] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:53:17,370] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg568021bf-2d24-47e8-9f4a-24d703ed50db/dqc_reference/checkm_data
[2023-03-15 07:53:17,371] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:53:17,377] [INFO] Task started: CheckM
[2023-03-15 07:53:17,377] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26680/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26680/checkm_input OceanDNA-b26680/checkm_result
[2023-03-15 07:54:12,182] [INFO] Task succeeded: CheckM
[2023-03-15 07:54:12,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:54:12,186] [INFO] ===== Completeness check finished =====
[2023-03-15 07:54:12,186] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:54:12,186] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26680/markers.fasta)
[2023-03-15 07:54:12,186] [INFO] Task started: Blastn
[2023-03-15 07:54:12,186] [INFO] Running command: blastn -query OceanDNA-b26680/markers.fasta -db /var/lib/cwl/stg568021bf-2d24-47e8-9f4a-24d703ed50db/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26680/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:54:13,824] [INFO] Task succeeded: Blastn
[2023-03-15 07:54:13,825] [INFO] Selected 14 target genomes.
[2023-03-15 07:54:13,825] [INFO] Target genome list was writen to OceanDNA-b26680/target_genomes_gtdb.txt
[2023-03-15 07:54:13,836] [INFO] Task started: fastANI
[2023-03-15 07:54:13,836] [INFO] Running command: fastANI --query /var/lib/cwl/stg54633ff2-cca9-401d-a9ad-54ab2cd22297/OceanDNA-b26680.fa --refList OceanDNA-b26680/target_genomes_gtdb.txt --output OceanDNA-b26680/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:54:26,020] [INFO] Task succeeded: fastANI
[2023-03-15 07:54:26,029] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:54:26,029] [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	87.9714	952	1147	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	83.6765	838	1147	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	83.0847	799	1147	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	82.562	770	1147	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	82.3909	772	1147	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	82.2933	766	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427605.1	s__Devosia sp001427605	82.2732	741	1147	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	82.2676	737	1147	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	82.1698	765	1147	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	81.734	482	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900470445.1	s__Devosia sp900470445	81.5327	731	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	95.41	95.41	0.81	0.81	2	-
GCF_016698645.1	s__Devosia sp016698645	81.319	703	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128975.1	s__Devosia limi	81.1092	679	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.98	99.98	0.97	0.97	2	-
GCF_001650025.1	s__Devosia elaeis	80.9292	657	1147	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:54:26,029] [INFO] GTDB search result was written to OceanDNA-b26680/result_gtdb.tsv
[2023-03-15 07:54:26,029] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:54:26,031] [INFO] DFAST_QC result json was written to OceanDNA-b26680/dqc_result.json
[2023-03-15 07:54:26,031] [INFO] DFAST_QC completed!
[2023-03-15 07:54:26,031] [INFO] Total running time: 0h1m46s