[2023-06-29 07:09:27,701] [INFO] DFAST_QC pipeline started.
[2023-06-29 07:09:27,704] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 07:09:27,704] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b3c02ab-ebd6-463d-847c-e430cd526739/dqc_reference
[2023-06-29 07:09:28,926] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 07:09:28,927] [INFO] Task started: Prodigal
[2023-06-29 07:09:28,927] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9e3f459-43a2-48ca-b464-468ba586f185/GCA_005791925.1_ASM579192v1_genomic.fna.gz | prodigal -d GCA_005791925.1_ASM579192v1_genomic.fna/cds.fna -a GCA_005791925.1_ASM579192v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 07:09:34,977] [INFO] Task succeeded: Prodigal
[2023-06-29 07:09:34,978] [INFO] Task started: HMMsearch
[2023-06-29 07:09:34,978] [INFO] Running command: hmmsearch --tblout GCA_005791925.1_ASM579192v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b3c02ab-ebd6-463d-847c-e430cd526739/dqc_reference/reference_markers.hmm GCA_005791925.1_ASM579192v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 07:09:35,165] [INFO] Task succeeded: HMMsearch
[2023-06-29 07:09:35,167] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgb9e3f459-43a2-48ca-b464-468ba586f185/GCA_005791925.1_ASM579192v1_genomic.fna.gz]
[2023-06-29 07:09:35,198] [INFO] Query marker FASTA was written to GCA_005791925.1_ASM579192v1_genomic.fna/markers.fasta
[2023-06-29 07:09:35,199] [INFO] Task started: Blastn
[2023-06-29 07:09:35,199] [INFO] Running command: blastn -query GCA_005791925.1_ASM579192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b3c02ab-ebd6-463d-847c-e430cd526739/dqc_reference/reference_markers.fasta -out GCA_005791925.1_ASM579192v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 07:09:35,684] [INFO] Task succeeded: Blastn
[2023-06-29 07:09:35,703] [INFO] Selected 5 target genomes.
[2023-06-29 07:09:35,703] [INFO] Target genome list was writen to GCA_005791925.1_ASM579192v1_genomic.fna/target_genomes.txt
[2023-06-29 07:09:35,707] [INFO] Task started: fastANI
[2023-06-29 07:09:35,707] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9e3f459-43a2-48ca-b464-468ba586f185/GCA_005791925.1_ASM579192v1_genomic.fna.gz --refList GCA_005791925.1_ASM579192v1_genomic.fna/target_genomes.txt --output GCA_005791925.1_ASM579192v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 07:09:38,918] [INFO] Task succeeded: fastANI
[2023-06-29 07:09:38,919] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b3c02ab-ebd6-463d-847c-e430cd526739/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 07:09:38,919] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b3c02ab-ebd6-463d-847c-e430cd526739/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 07:09:38,929] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 07:09:38,929] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 07:09:38,929] [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
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	78.1234	247	602	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	77.6461	218	602	95	below_threshold
Sphingomonas horti	strain=MAH-20	GCA_009753715.1	2682842	2682842	type	True	76.9993	185	602	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	76.7151	169	602	95	below_threshold
Sphingomonas vulcanisoli	strain=CECT 8804	GCA_011761305.1	1658060	1658060	type	True	76.24	111	602	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 07:09:38,932] [INFO] DFAST Taxonomy check result was written to GCA_005791925.1_ASM579192v1_genomic.fna/tc_result.tsv
[2023-06-29 07:09:38,933] [INFO] ===== Taxonomy check completed =====
[2023-06-29 07:09:38,933] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 07:09:38,933] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b3c02ab-ebd6-463d-847c-e430cd526739/dqc_reference/checkm_data
[2023-06-29 07:09:38,934] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 07:09:38,978] [INFO] Task started: CheckM
[2023-06-29 07:09:38,979] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_005791925.1_ASM579192v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_005791925.1_ASM579192v1_genomic.fna/checkm_input GCA_005791925.1_ASM579192v1_genomic.fna/checkm_result
[2023-06-29 07:10:01,574] [INFO] Task succeeded: CheckM
[2023-06-29 07:10:01,576] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 31.60%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 07:10:01,597] [INFO] ===== Completeness check finished =====
[2023-06-29 07:10:01,597] [INFO] ===== Start GTDB Search =====
[2023-06-29 07:10:01,598] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_005791925.1_ASM579192v1_genomic.fna/markers.fasta)
[2023-06-29 07:10:01,598] [INFO] Task started: Blastn
[2023-06-29 07:10:01,598] [INFO] Running command: blastn -query GCA_005791925.1_ASM579192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b3c02ab-ebd6-463d-847c-e430cd526739/dqc_reference/reference_markers_gtdb.fasta -out GCA_005791925.1_ASM579192v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 07:10:02,056] [INFO] Task succeeded: Blastn
[2023-06-29 07:10:02,060] [INFO] Selected 5 target genomes.
[2023-06-29 07:10:02,060] [INFO] Target genome list was writen to GCA_005791925.1_ASM579192v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 07:10:02,067] [INFO] Task started: fastANI
[2023-06-29 07:10:02,067] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9e3f459-43a2-48ca-b464-468ba586f185/GCA_005791925.1_ASM579192v1_genomic.fna.gz --refList GCA_005791925.1_ASM579192v1_genomic.fna/target_genomes_gtdb.txt --output GCA_005791925.1_ASM579192v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 07:10:06,159] [INFO] Task succeeded: fastANI
[2023-06-29 07:10:06,167] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 07:10:06,167] [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_004564275.1	s__Allosphingosinicella parva	78.1379	246	602	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239785.1	s__Allosphingosinicella sp019239785	77.5083	213	602	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135585.1	s__Allosphingosinicella sp004135585	77.3525	255	602	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009753715.1	s__Sphingomonas_B horti	76.9978	186	602	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004796535.1	s__Sphingomonas_L sp004796535	76.703	170	602	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_L	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 07:10:06,169] [INFO] GTDB search result was written to GCA_005791925.1_ASM579192v1_genomic.fna/result_gtdb.tsv
[2023-06-29 07:10:06,170] [INFO] ===== GTDB Search completed =====
[2023-06-29 07:10:06,174] [INFO] DFAST_QC result json was written to GCA_005791925.1_ASM579192v1_genomic.fna/dqc_result.json
[2023-06-29 07:10:06,174] [INFO] DFAST_QC completed!
[2023-06-29 07:10:06,174] [INFO] Total running time: 0h0m38s