[2023-06-18 18:10:14,996] [INFO] DFAST_QC pipeline started.
[2023-06-18 18:10:15,000] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 18:10:15,000] [INFO] DQC Reference Directory: /var/lib/cwl/stg266d28e9-ae29-43f4-9062-9c05203dd1ba/dqc_reference
[2023-06-18 18:10:16,726] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 18:10:16,727] [INFO] Task started: Prodigal
[2023-06-18 18:10:16,727] [INFO] Running command: gunzip -c /var/lib/cwl/stgd5bc37a8-9dc2-489d-a2a1-1e9e7beebffe/GCA_018820005.1_ASM1882000v1_genomic.fna.gz | prodigal -d GCA_018820005.1_ASM1882000v1_genomic.fna/cds.fna -a GCA_018820005.1_ASM1882000v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 18:10:26,309] [INFO] Task succeeded: Prodigal
[2023-06-18 18:10:26,309] [INFO] Task started: HMMsearch
[2023-06-18 18:10:26,310] [INFO] Running command: hmmsearch --tblout GCA_018820005.1_ASM1882000v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg266d28e9-ae29-43f4-9062-9c05203dd1ba/dqc_reference/reference_markers.hmm GCA_018820005.1_ASM1882000v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 18:10:26,561] [INFO] Task succeeded: HMMsearch
[2023-06-18 18:10:26,562] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgd5bc37a8-9dc2-489d-a2a1-1e9e7beebffe/GCA_018820005.1_ASM1882000v1_genomic.fna.gz]
[2023-06-18 18:10:26,604] [INFO] Query marker FASTA was written to GCA_018820005.1_ASM1882000v1_genomic.fna/markers.fasta
[2023-06-18 18:10:26,605] [INFO] Task started: Blastn
[2023-06-18 18:10:26,605] [INFO] Running command: blastn -query GCA_018820005.1_ASM1882000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg266d28e9-ae29-43f4-9062-9c05203dd1ba/dqc_reference/reference_markers.fasta -out GCA_018820005.1_ASM1882000v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:10:27,255] [INFO] Task succeeded: Blastn
[2023-06-18 18:10:27,259] [INFO] Selected 10 target genomes.
[2023-06-18 18:10:27,260] [INFO] Target genome list was writen to GCA_018820005.1_ASM1882000v1_genomic.fna/target_genomes.txt
[2023-06-18 18:10:27,263] [INFO] Task started: fastANI
[2023-06-18 18:10:27,263] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5bc37a8-9dc2-489d-a2a1-1e9e7beebffe/GCA_018820005.1_ASM1882000v1_genomic.fna.gz --refList GCA_018820005.1_ASM1882000v1_genomic.fna/target_genomes.txt --output GCA_018820005.1_ASM1882000v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 18:10:34,928] [INFO] Task succeeded: fastANI
[2023-06-18 18:10:34,929] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg266d28e9-ae29-43f4-9062-9c05203dd1ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 18:10:34,929] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg266d28e9-ae29-43f4-9062-9c05203dd1ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 18:10:34,943] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 18:10:34,943] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 18:10:34,944] [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	81.9324	508	820	95	below_threshold
Devosia ginsengisoli	strain=Gsoil 520	GCA_007859655.1	400770	400770	type	True	80.7978	447	820	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	80.4315	426	820	95	below_threshold
Devosia psychrophila	strain=CGMCC 1.10210	GCA_900112505.1	728005	728005	type	True	79.8982	423	820	95	below_threshold
Devosia limi	strain=DSM 17137	GCA_900128975.1	288995	288995	type	True	79.8145	392	820	95	below_threshold
Devosia epidermidihirudinis	strain=E84	GCA_000971295.1	1293439	1293439	type	True	79.7619	369	820	95	below_threshold
Devosia limi	strain=DSM 17137	GCA_000970435.1	288995	288995	type	True	79.7571	393	820	95	below_threshold
Devosia naphthalenivorans	strain=CM5-1	GCA_003056355.1	2082392	2082392	type	True	79.6105	379	820	95	below_threshold
Devosia submarina	strain=JCM 18935	GCA_003056345.1	1173082	1173082	type	True	78.6942	330	820	95	below_threshold
Devosia riboflavina	strain=IFO13584	GCA_000743575.1	46914	46914	type	True	78.6519	343	820	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 18:10:34,947] [INFO] DFAST Taxonomy check result was written to GCA_018820005.1_ASM1882000v1_genomic.fna/tc_result.tsv
[2023-06-18 18:10:34,948] [INFO] ===== Taxonomy check completed =====
[2023-06-18 18:10:34,948] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 18:10:34,948] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg266d28e9-ae29-43f4-9062-9c05203dd1ba/dqc_reference/checkm_data
[2023-06-18 18:10:34,950] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 18:10:34,998] [INFO] Task started: CheckM
[2023-06-18 18:10:34,998] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018820005.1_ASM1882000v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018820005.1_ASM1882000v1_genomic.fna/checkm_input GCA_018820005.1_ASM1882000v1_genomic.fna/checkm_result
[2023-06-18 18:11:07,354] [INFO] Task succeeded: CheckM
[2023-06-18 18:11:07,356] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 43.75%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-18 18:11:07,388] [INFO] ===== Completeness check finished =====
[2023-06-18 18:11:07,389] [INFO] ===== Start GTDB Search =====
[2023-06-18 18:11:07,389] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018820005.1_ASM1882000v1_genomic.fna/markers.fasta)
[2023-06-18 18:11:07,390] [INFO] Task started: Blastn
[2023-06-18 18:11:07,390] [INFO] Running command: blastn -query GCA_018820005.1_ASM1882000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg266d28e9-ae29-43f4-9062-9c05203dd1ba/dqc_reference/reference_markers_gtdb.fasta -out GCA_018820005.1_ASM1882000v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:11:08,186] [INFO] Task succeeded: Blastn
[2023-06-18 18:11:08,192] [INFO] Selected 9 target genomes.
[2023-06-18 18:11:08,192] [INFO] Target genome list was writen to GCA_018820005.1_ASM1882000v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 18:11:08,196] [INFO] Task started: fastANI
[2023-06-18 18:11:08,197] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5bc37a8-9dc2-489d-a2a1-1e9e7beebffe/GCA_018820005.1_ASM1882000v1_genomic.fna.gz --refList GCA_018820005.1_ASM1882000v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018820005.1_ASM1882000v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 18:11:15,070] [INFO] Task succeeded: fastANI
[2023-06-18 18:11:15,083] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 18:11:15,083] [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_018820005.1	s__Devosia sp018820005	100.0	807	820	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_005222805.1	s__Devosia sp005222805	85.9738	592	820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014926585.1	s__Devosia sp014926585	81.9375	508	820	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	81.1657	475	820	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	80.9858	449	820	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	80.8152	445	820	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	80.7239	439	820	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	80.5007	448	820	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	79.8145	392	820	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.98	99.98	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-18 18:11:15,085] [INFO] GTDB search result was written to GCA_018820005.1_ASM1882000v1_genomic.fna/result_gtdb.tsv
[2023-06-18 18:11:15,088] [INFO] ===== GTDB Search completed =====
[2023-06-18 18:11:15,092] [INFO] DFAST_QC result json was written to GCA_018820005.1_ASM1882000v1_genomic.fna/dqc_result.json
[2023-06-18 18:11:15,092] [INFO] DFAST_QC completed!
[2023-06-18 18:11:15,092] [INFO] Total running time: 0h1m0s