[2024-01-25 20:03:20,451] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:03:20,452] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:03:20,452] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d433a9b-08eb-49a7-9890-77d23d1820a0/dqc_reference
[2024-01-25 20:03:21,584] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:03:21,585] [INFO] Task started: Prodigal
[2024-01-25 20:03:21,585] [INFO] Running command: gunzip -c /var/lib/cwl/stg82a40f47-00e2-4c49-b5f3-8f526b496747/GCF_016698645.1_ASM1669864v1_genomic.fna.gz | prodigal -d GCF_016698645.1_ASM1669864v1_genomic.fna/cds.fna -a GCF_016698645.1_ASM1669864v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:03:31,537] [INFO] Task succeeded: Prodigal
[2024-01-25 20:03:31,537] [INFO] Task started: HMMsearch
[2024-01-25 20:03:31,537] [INFO] Running command: hmmsearch --tblout GCF_016698645.1_ASM1669864v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d433a9b-08eb-49a7-9890-77d23d1820a0/dqc_reference/reference_markers.hmm GCF_016698645.1_ASM1669864v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:03:31,762] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:03:31,763] [INFO] Found 6/6 markers.
[2024-01-25 20:03:31,790] [INFO] Query marker FASTA was written to GCF_016698645.1_ASM1669864v1_genomic.fna/markers.fasta
[2024-01-25 20:03:31,790] [INFO] Task started: Blastn
[2024-01-25 20:03:31,790] [INFO] Running command: blastn -query GCF_016698645.1_ASM1669864v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d433a9b-08eb-49a7-9890-77d23d1820a0/dqc_reference/reference_markers.fasta -out GCF_016698645.1_ASM1669864v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:32,698] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:32,701] [INFO] Selected 14 target genomes.
[2024-01-25 20:03:32,702] [INFO] Target genome list was writen to GCF_016698645.1_ASM1669864v1_genomic.fna/target_genomes.txt
[2024-01-25 20:03:32,717] [INFO] Task started: fastANI
[2024-01-25 20:03:32,717] [INFO] Running command: fastANI --query /var/lib/cwl/stg82a40f47-00e2-4c49-b5f3-8f526b496747/GCF_016698645.1_ASM1669864v1_genomic.fna.gz --refList GCF_016698645.1_ASM1669864v1_genomic.fna/target_genomes.txt --output GCF_016698645.1_ASM1669864v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:03:44,330] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:44,331] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d433a9b-08eb-49a7-9890-77d23d1820a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:03:44,331] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d433a9b-08eb-49a7-9890-77d23d1820a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:03:44,341] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:03:44,341] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:03:44,341] [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 oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	100.0	1165	1165	95	conclusive
Devosia ginsengisoli	strain=Gsoil 520	GCA_007859655.1	400770	400770	type	True	83.6398	877	1165	95	below_threshold
Devosia psychrophila	strain=CGMCC 1.10210	GCA_900112505.1	728005	728005	type	True	81.6776	767	1165	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	81.6702	780	1165	95	below_threshold
Devosia psychrophila	strain=Cr7-05	GCA_000971275.1	728005	728005	type	True	81.6582	752	1165	95	below_threshold
Devosia naphthalenivorans	strain=CM5-1	GCA_003056355.1	2082392	2082392	type	True	80.9278	651	1165	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	80.6764	652	1165	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	80.6378	692	1165	95	below_threshold
Devosia epidermidihirudinis	strain=E84	GCA_000971295.1	1293439	1293439	type	True	80.5959	650	1165	95	below_threshold
Devosia equisanguinis	strain=CIP 111628	GCA_900631955.1	2490941	2490941	type	True	80.246	626	1165	95	below_threshold
Devosia submarina	strain=JCM 18935	GCA_003056345.1	1173082	1173082	type	True	80.0206	572	1165	95	below_threshold
Devosia indica	strain=IO390501	GCA_003056405.1	2079253	2079253	type	True	79.8137	607	1165	95	below_threshold
Devosia rhizoryzae	strain=LEGU1	GCA_016698665.1	2774137	2774137	type	True	79.7422	575	1165	95	below_threshold
Pelagibacterium sediminicola	strain=IMCC34151	GCA_003390885.1	2248761	2248761	type	True	77.7539	260	1165	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:03:44,342] [INFO] DFAST Taxonomy check result was written to GCF_016698645.1_ASM1669864v1_genomic.fna/tc_result.tsv
[2024-01-25 20:03:44,343] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:03:44,343] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:03:44,343] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d433a9b-08eb-49a7-9890-77d23d1820a0/dqc_reference/checkm_data
[2024-01-25 20:03:44,344] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:03:44,379] [INFO] Task started: CheckM
[2024-01-25 20:03:44,379] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016698645.1_ASM1669864v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016698645.1_ASM1669864v1_genomic.fna/checkm_input GCF_016698645.1_ASM1669864v1_genomic.fna/checkm_result
[2024-01-25 20:04:15,039] [INFO] Task succeeded: CheckM
[2024-01-25 20:04:15,040] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:04:15,058] [INFO] ===== Completeness check finished =====
[2024-01-25 20:04:15,058] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:04:15,059] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016698645.1_ASM1669864v1_genomic.fna/markers.fasta)
[2024-01-25 20:04:15,059] [INFO] Task started: Blastn
[2024-01-25 20:04:15,060] [INFO] Running command: blastn -query GCF_016698645.1_ASM1669864v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d433a9b-08eb-49a7-9890-77d23d1820a0/dqc_reference/reference_markers_gtdb.fasta -out GCF_016698645.1_ASM1669864v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:16,872] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:16,875] [INFO] Selected 8 target genomes.
[2024-01-25 20:04:16,875] [INFO] Target genome list was writen to GCF_016698645.1_ASM1669864v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:04:16,886] [INFO] Task started: fastANI
[2024-01-25 20:04:16,886] [INFO] Running command: fastANI --query /var/lib/cwl/stg82a40f47-00e2-4c49-b5f3-8f526b496747/GCF_016698645.1_ASM1669864v1_genomic.fna.gz --refList GCF_016698645.1_ASM1669864v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016698645.1_ASM1669864v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:04:25,192] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:25,198] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:04:25,198] [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_016698645.1	s__Devosia sp016698645	100.0	1165	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014860165.1	s__Devosia sp014860165	85.2982	920	1165	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	84.0926	828	1165	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	84.0816	864	1165	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	83.6144	879	1165	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	83.4274	846	1165	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.99	99.98	0.99	0.98	4	-
GCF_900110945.1	s__Devosia sp900110945	82.6004	795	1165	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	81.3475	724	1165	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 20:04:25,200] [INFO] GTDB search result was written to GCF_016698645.1_ASM1669864v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:04:25,200] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:04:25,203] [INFO] DFAST_QC result json was written to GCF_016698645.1_ASM1669864v1_genomic.fna/dqc_result.json
[2024-01-25 20:04:25,203] [INFO] DFAST_QC completed!
[2024-01-25 20:04:25,203] [INFO] Total running time: 0h1m5s