[2024-01-24 12:06:13,888] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:13,891] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:13,892] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b42748a-cd46-447c-9ffb-c51a634c8a8e/dqc_reference
[2024-01-24 12:06:15,251] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:15,252] [INFO] Task started: Prodigal
[2024-01-24 12:06:15,253] [INFO] Running command: gunzip -c /var/lib/cwl/stg21ed639d-dac6-4a59-b641-b25eab32cc21/GCF_024158985.1_ASM2415898v1_genomic.fna.gz | prodigal -d GCF_024158985.1_ASM2415898v1_genomic.fna/cds.fna -a GCF_024158985.1_ASM2415898v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:27,759] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:27,759] [INFO] Task started: HMMsearch
[2024-01-24 12:06:27,759] [INFO] Running command: hmmsearch --tblout GCF_024158985.1_ASM2415898v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b42748a-cd46-447c-9ffb-c51a634c8a8e/dqc_reference/reference_markers.hmm GCF_024158985.1_ASM2415898v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:28,127] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:28,128] [INFO] Found 6/6 markers.
[2024-01-24 12:06:28,178] [INFO] Query marker FASTA was written to GCF_024158985.1_ASM2415898v1_genomic.fna/markers.fasta
[2024-01-24 12:06:28,178] [INFO] Task started: Blastn
[2024-01-24 12:06:28,178] [INFO] Running command: blastn -query GCF_024158985.1_ASM2415898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b42748a-cd46-447c-9ffb-c51a634c8a8e/dqc_reference/reference_markers.fasta -out GCF_024158985.1_ASM2415898v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:29,021] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:29,024] [INFO] Selected 9 target genomes.
[2024-01-24 12:06:29,025] [INFO] Target genome list was writen to GCF_024158985.1_ASM2415898v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:29,029] [INFO] Task started: fastANI
[2024-01-24 12:06:29,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg21ed639d-dac6-4a59-b641-b25eab32cc21/GCF_024158985.1_ASM2415898v1_genomic.fna.gz --refList GCF_024158985.1_ASM2415898v1_genomic.fna/target_genomes.txt --output GCF_024158985.1_ASM2415898v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:37,896] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:37,897] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b42748a-cd46-447c-9ffb-c51a634c8a8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:37,897] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b42748a-cd46-447c-9ffb-c51a634c8a8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:37,906] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:06:37,906] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:37,906] [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 subaequoris	strain=HST3-14	GCA_024158985.1	395930	395930	type	True	100.0	1234	1234	95	conclusive
Devosia subaequoris	strain=DSM 23447	GCA_014197055.1	395930	395930	type	True	99.9882	1230	1234	95	conclusive
Devosia marina	strain=L53-10-65	GCA_009758415.1	2683198	2683198	type	True	89.1965	1018	1234	95	below_threshold
Devosia indica	strain=IO390501	GCA_003056405.1	2079253	2079253	type	True	87.9932	967	1234	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	82.8243	858	1234	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	81.3638	721	1234	95	below_threshold
Devosia rhizoryzae	strain=LEGU1	GCA_016698665.1	2774137	2774137	type	True	79.6061	607	1234	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	79.4754	627	1234	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	79.3861	548	1234	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:37,908] [INFO] DFAST Taxonomy check result was written to GCF_024158985.1_ASM2415898v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:37,908] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:37,908] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:37,909] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b42748a-cd46-447c-9ffb-c51a634c8a8e/dqc_reference/checkm_data
[2024-01-24 12:06:37,910] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:37,955] [INFO] Task started: CheckM
[2024-01-24 12:06:37,955] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024158985.1_ASM2415898v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024158985.1_ASM2415898v1_genomic.fna/checkm_input GCF_024158985.1_ASM2415898v1_genomic.fna/checkm_result
[2024-01-24 12:07:16,753] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:16,754] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:16,772] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:16,772] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:16,773] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024158985.1_ASM2415898v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:16,773] [INFO] Task started: Blastn
[2024-01-24 12:07:16,773] [INFO] Running command: blastn -query GCF_024158985.1_ASM2415898v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b42748a-cd46-447c-9ffb-c51a634c8a8e/dqc_reference/reference_markers_gtdb.fasta -out GCF_024158985.1_ASM2415898v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:18,132] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:18,137] [INFO] Selected 10 target genomes.
[2024-01-24 12:07:18,138] [INFO] Target genome list was writen to GCF_024158985.1_ASM2415898v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:18,149] [INFO] Task started: fastANI
[2024-01-24 12:07:18,150] [INFO] Running command: fastANI --query /var/lib/cwl/stg21ed639d-dac6-4a59-b641-b25eab32cc21/GCF_024158985.1_ASM2415898v1_genomic.fna.gz --refList GCF_024158985.1_ASM2415898v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024158985.1_ASM2415898v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:27,078] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:27,093] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:27,093] [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_014197055.1	s__Devosia subaequoris	99.9882	1230	1234	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_009758415.1	s__Devosia marina	89.2069	1017	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	97.05	97.05	0.85	0.85	2	-
GCF_003056405.1	s__Devosia indica	87.9932	967	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016411825.1	s__Devosia sp016411825	81.6165	768	1234	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	81.3296	725	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015158295.1	s__Devosia sp015158295	80.557	643	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177655.1	s__Devosia lucknowensis	80.5047	672	1234	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	79.8835	640	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.99	99.98	0.99	0.98	4	-
GCF_001427875.1	s__Devosia sp001427875	79.793	625	1234	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016698665.1	s__Devosia sp016698665	79.5984	609	1234	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 12:07:27,095] [INFO] GTDB search result was written to GCF_024158985.1_ASM2415898v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:27,097] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:27,100] [INFO] DFAST_QC result json was written to GCF_024158985.1_ASM2415898v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:27,100] [INFO] DFAST_QC completed!
[2024-01-24 12:07:27,100] [INFO] Total running time: 0h1m13s