[2024-01-24 13:57:55,967] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:55,979] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:55,979] [INFO] DQC Reference Directory: /var/lib/cwl/stg4def5cd4-0929-485d-a842-9e84efc118dd/dqc_reference
[2024-01-24 13:57:57,241] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:57,242] [INFO] Task started: Prodigal
[2024-01-24 13:57:57,242] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d5aa8eb-8205-47a0-93ee-231064e1d7c3/GCF_003056355.1_ASM305635v1_genomic.fna.gz | prodigal -d GCF_003056355.1_ASM305635v1_genomic.fna/cds.fna -a GCF_003056355.1_ASM305635v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:11,954] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:11,955] [INFO] Task started: HMMsearch
[2024-01-24 13:58:11,955] [INFO] Running command: hmmsearch --tblout GCF_003056355.1_ASM305635v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4def5cd4-0929-485d-a842-9e84efc118dd/dqc_reference/reference_markers.hmm GCF_003056355.1_ASM305635v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:12,261] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:12,262] [INFO] Found 6/6 markers.
[2024-01-24 13:58:12,305] [INFO] Query marker FASTA was written to GCF_003056355.1_ASM305635v1_genomic.fna/markers.fasta
[2024-01-24 13:58:12,306] [INFO] Task started: Blastn
[2024-01-24 13:58:12,306] [INFO] Running command: blastn -query GCF_003056355.1_ASM305635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4def5cd4-0929-485d-a842-9e84efc118dd/dqc_reference/reference_markers.fasta -out GCF_003056355.1_ASM305635v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:13,255] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:13,258] [INFO] Selected 14 target genomes.
[2024-01-24 13:58:13,258] [INFO] Target genome list was writen to GCF_003056355.1_ASM305635v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:13,266] [INFO] Task started: fastANI
[2024-01-24 13:58:13,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d5aa8eb-8205-47a0-93ee-231064e1d7c3/GCF_003056355.1_ASM305635v1_genomic.fna.gz --refList GCF_003056355.1_ASM305635v1_genomic.fna/target_genomes.txt --output GCF_003056355.1_ASM305635v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:25,822] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:25,823] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4def5cd4-0929-485d-a842-9e84efc118dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:25,823] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4def5cd4-0929-485d-a842-9e84efc118dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:25,835] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:25,835] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:25,835] [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 naphthalenivorans	strain=CM5-1	GCA_003056355.1	2082392	2082392	type	True	100.0	1467	1472	95	conclusive
Devosia submarina	strain=JCM 18935	GCA_003056345.1	1173082	1173082	type	True	82.0743	790	1472	95	below_threshold
Devosia ginsengisoli	strain=Gsoil 520	GCA_007859655.1	400770	400770	type	True	81.4539	755	1472	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	81.0009	706	1472	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	80.8169	674	1472	95	below_threshold
Devosia limi	strain=DSM 17137	GCA_900128975.1	288995	288995	type	True	80.8083	682	1472	95	below_threshold
Devosia limi	strain=DSM 17137	GCA_000970435.1	288995	288995	type	True	80.7497	673	1472	95	below_threshold
Devosia psychrophila	strain=CGMCC 1.10210	GCA_900112505.1	728005	728005	type	True	80.6771	705	1472	95	below_threshold
Devosia psychrophila	strain=Cr7-05	GCA_000971275.1	728005	728005	type	True	80.5887	695	1472	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	79.7491	595	1472	95	below_threshold
Devosia rhizoryzae	strain=LEGU1	GCA_016698665.1	2774137	2774137	type	True	79.5251	568	1472	95	below_threshold
Devosia subaequoris	strain=HST3-14	GCA_024158985.1	395930	395930	type	True	79.0747	489	1472	95	below_threshold
Cucumibacter marinus	strain=DSM 18995	GCA_000429865.1	1121252	1121252	type	True	76.9928	206	1472	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	76.7715	157	1472	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:25,837] [INFO] DFAST Taxonomy check result was written to GCF_003056355.1_ASM305635v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:25,837] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:25,837] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:25,838] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4def5cd4-0929-485d-a842-9e84efc118dd/dqc_reference/checkm_data
[2024-01-24 13:58:25,839] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:25,883] [INFO] Task started: CheckM
[2024-01-24 13:58:25,883] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003056355.1_ASM305635v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003056355.1_ASM305635v1_genomic.fna/checkm_input GCF_003056355.1_ASM305635v1_genomic.fna/checkm_result
[2024-01-24 13:59:09,568] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:09,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:09,589] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:09,589] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:09,590] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003056355.1_ASM305635v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:09,590] [INFO] Task started: Blastn
[2024-01-24 13:59:09,590] [INFO] Running command: blastn -query GCF_003056355.1_ASM305635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4def5cd4-0929-485d-a842-9e84efc118dd/dqc_reference/reference_markers_gtdb.fasta -out GCF_003056355.1_ASM305635v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:11,001] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:11,005] [INFO] Selected 11 target genomes.
[2024-01-24 13:59:11,006] [INFO] Target genome list was writen to GCF_003056355.1_ASM305635v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:11,014] [INFO] Task started: fastANI
[2024-01-24 13:59:11,014] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d5aa8eb-8205-47a0-93ee-231064e1d7c3/GCF_003056355.1_ASM305635v1_genomic.fna.gz --refList GCF_003056355.1_ASM305635v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003056355.1_ASM305635v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:21,690] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:21,704] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:21,704] [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_003056355.1	s__Devosia naphthalenivorans	100.0	1468	1472	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_003056345.1	s__Devosia submarina	82.0424	795	1472	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	81.5601	725	1472	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	81.4426	757	1472	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	81.3758	783	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.99	99.98	0.99	0.98	4	-
GCF_001427605.1	s__Devosia sp001427605	81.3301	722	1472	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	81.2405	716	1472	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	81.1969	697	1472	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	80.9765	686	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000735585.1	s__Devosia sp000735585	80.9737	722	1472	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	80.8218	673	1472	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:21,706] [INFO] GTDB search result was written to GCF_003056355.1_ASM305635v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:21,707] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:21,710] [INFO] DFAST_QC result json was written to GCF_003056355.1_ASM305635v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:21,710] [INFO] DFAST_QC completed!
[2024-01-24 13:59:21,710] [INFO] Total running time: 0h1m26s