[2024-01-25 19:02:20,459] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:02:20,461] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:02:20,462] [INFO] DQC Reference Directory: /var/lib/cwl/stg76120862-debf-4511-97a6-2b780622b0e9/dqc_reference
[2024-01-25 19:02:21,634] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:02:21,635] [INFO] Task started: Prodigal
[2024-01-25 19:02:21,635] [INFO] Running command: gunzip -c /var/lib/cwl/stg46feebf0-330c-4c32-855c-d7ce3734b46f/GCF_030159855.1_ASM3015985v1_genomic.fna.gz | prodigal -d GCF_030159855.1_ASM3015985v1_genomic.fna/cds.fna -a GCF_030159855.1_ASM3015985v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:02:34,811] [INFO] Task succeeded: Prodigal
[2024-01-25 19:02:34,811] [INFO] Task started: HMMsearch
[2024-01-25 19:02:34,812] [INFO] Running command: hmmsearch --tblout GCF_030159855.1_ASM3015985v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76120862-debf-4511-97a6-2b780622b0e9/dqc_reference/reference_markers.hmm GCF_030159855.1_ASM3015985v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:02:35,056] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:02:35,057] [INFO] Found 6/6 markers.
[2024-01-25 19:02:35,095] [INFO] Query marker FASTA was written to GCF_030159855.1_ASM3015985v1_genomic.fna/markers.fasta
[2024-01-25 19:02:35,096] [INFO] Task started: Blastn
[2024-01-25 19:02:35,096] [INFO] Running command: blastn -query GCF_030159855.1_ASM3015985v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76120862-debf-4511-97a6-2b780622b0e9/dqc_reference/reference_markers.fasta -out GCF_030159855.1_ASM3015985v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:35,824] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:35,827] [INFO] Selected 17 target genomes.
[2024-01-25 19:02:35,827] [INFO] Target genome list was writen to GCF_030159855.1_ASM3015985v1_genomic.fna/target_genomes.txt
[2024-01-25 19:02:35,835] [INFO] Task started: fastANI
[2024-01-25 19:02:35,835] [INFO] Running command: fastANI --query /var/lib/cwl/stg46feebf0-330c-4c32-855c-d7ce3734b46f/GCF_030159855.1_ASM3015985v1_genomic.fna.gz --refList GCF_030159855.1_ASM3015985v1_genomic.fna/target_genomes.txt --output GCF_030159855.1_ASM3015985v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:02:50,717] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:50,717] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76120862-debf-4511-97a6-2b780622b0e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:02:50,718] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76120862-debf-4511-97a6-2b780622b0e9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:02:50,728] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:02:50,728] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:02:50,728] [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 ginsengisoli	strain=Gsoil 520	GCA_007859655.1	400770	400770	type	True	82.3661	886	1540	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	81.6984	779	1540	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	81.4736	750	1540	95	below_threshold
Devosia limi	strain=DSM 17137	GCA_900128975.1	288995	288995	type	True	81.443	767	1540	95	below_threshold
Devosia limi	strain=DSM 17137	GCA_000970435.1	288995	288995	type	True	81.4409	747	1540	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	80.9187	721	1540	95	below_threshold
Devosia naphthalenivorans	strain=CM5-1	GCA_003056355.1	2082392	2082392	type	True	80.7561	700	1540	95	below_threshold
Devosia epidermidihirudinis	strain=E84	GCA_000971295.1	1293439	1293439	type	True	80.7182	698	1540	95	below_threshold
Devosia psychrophila	strain=CGMCC 1.10210	GCA_900112505.1	728005	728005	type	True	80.7001	742	1540	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	80.5083	705	1540	95	below_threshold
Devosia equisanguinis	strain=CIP 111628	GCA_900631955.1	2490941	2490941	type	True	80.4241	670	1540	95	below_threshold
Devosia sediminis	strain=MSA67	GCA_016411825.1	2798801	2798801	type	True	80.2853	688	1540	95	below_threshold
Devosia faecipullorum	strain=CC-YST696	GCA_015158295.1	2755039	2755039	type	True	80.2298	603	1540	95	below_threshold
Devosia chinhatensis	strain=IPL18	GCA_000969445.1	429727	429727	type	True	80.0136	609	1540	95	below_threshold
Devosia rhizoryzae	strain=LEGU1	GCA_016698665.1	2774137	2774137	type	True	79.8458	596	1540	95	below_threshold
Devosia soli	strain=GH2-10	GCA_000970455.1	361041	361041	type	True	79.5774	627	1540	95	below_threshold
Devosia subaequoris	strain=HST3-14	GCA_024158985.1	395930	395930	type	True	79.5376	590	1540	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:02:50,730] [INFO] DFAST Taxonomy check result was written to GCF_030159855.1_ASM3015985v1_genomic.fna/tc_result.tsv
[2024-01-25 19:02:50,730] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:02:50,730] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:02:50,730] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76120862-debf-4511-97a6-2b780622b0e9/dqc_reference/checkm_data
[2024-01-25 19:02:50,731] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:02:50,775] [INFO] Task started: CheckM
[2024-01-25 19:02:50,775] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030159855.1_ASM3015985v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030159855.1_ASM3015985v1_genomic.fna/checkm_input GCF_030159855.1_ASM3015985v1_genomic.fna/checkm_result
[2024-01-25 19:03:29,039] [INFO] Task succeeded: CheckM
[2024-01-25 19:03:29,040] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:03:29,057] [INFO] ===== Completeness check finished =====
[2024-01-25 19:03:29,057] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:03:29,058] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030159855.1_ASM3015985v1_genomic.fna/markers.fasta)
[2024-01-25 19:03:29,058] [INFO] Task started: Blastn
[2024-01-25 19:03:29,058] [INFO] Running command: blastn -query GCF_030159855.1_ASM3015985v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76120862-debf-4511-97a6-2b780622b0e9/dqc_reference/reference_markers_gtdb.fasta -out GCF_030159855.1_ASM3015985v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:03:30,309] [INFO] Task succeeded: Blastn
[2024-01-25 19:03:30,312] [INFO] Selected 16 target genomes.
[2024-01-25 19:03:30,312] [INFO] Target genome list was writen to GCF_030159855.1_ASM3015985v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:03:30,330] [INFO] Task started: fastANI
[2024-01-25 19:03:30,331] [INFO] Running command: fastANI --query /var/lib/cwl/stg46feebf0-330c-4c32-855c-d7ce3734b46f/GCF_030159855.1_ASM3015985v1_genomic.fna.gz --refList GCF_030159855.1_ASM3015985v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030159855.1_ASM3015985v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:03:46,145] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:46,156] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:03:46,156] [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_900470445.1	s__Devosia sp900470445	87.2608	1095	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	95.41	95.41	0.81	0.81	2	-
GCF_000735585.1	s__Devosia sp000735585	87.2343	1046	1540	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	82.5083	818	1540	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	82.4193	879	1540	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	82.3513	815	1540	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	82.1739	812	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.99	99.98	0.99	0.98	4	-
GCA_014860165.1	s__Devosia sp014860165	81.9756	813	1540	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	81.8463	813	1540	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	81.7751	770	1540	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	81.4512	752	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650025.1	s__Devosia elaeis	80.9292	720	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056355.1	s__Devosia naphthalenivorans	80.7454	702	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900631955.1	s__Devosia sp001899045	80.4	674	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	98.09	98.08	0.92	0.92	4	-
GCF_016411825.1	s__Devosia sp016411825	80.2871	687	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018334155.1	s__Devosia sp018334155	80.2669	695	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744655.1	s__Devosia sp017744655	80.0701	716	1540	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:03:46,157] [INFO] GTDB search result was written to GCF_030159855.1_ASM3015985v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:03:46,158] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:03:46,161] [INFO] DFAST_QC result json was written to GCF_030159855.1_ASM3015985v1_genomic.fna/dqc_result.json
[2024-01-25 19:03:46,161] [INFO] DFAST_QC completed!
[2024-01-25 19:03:46,161] [INFO] Total running time: 0h1m26s