[2024-01-25 17:53:50,648] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:53:50,649] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:53:50,649] [INFO] DQC Reference Directory: /var/lib/cwl/stg55f24096-e35a-41f5-8aaa-4df18c995011/dqc_reference
[2024-01-25 17:53:51,813] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:53:51,814] [INFO] Task started: Prodigal
[2024-01-25 17:53:51,815] [INFO] Running command: gunzip -c /var/lib/cwl/stge1284e42-d502-4d89-8aa5-8405e20e5c48/GCF_030814695.1_ASM3081469v1_genomic.fna.gz | prodigal -d GCF_030814695.1_ASM3081469v1_genomic.fna/cds.fna -a GCF_030814695.1_ASM3081469v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:54:19,808] [INFO] Task succeeded: Prodigal
[2024-01-25 17:54:19,809] [INFO] Task started: HMMsearch
[2024-01-25 17:54:19,809] [INFO] Running command: hmmsearch --tblout GCF_030814695.1_ASM3081469v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55f24096-e35a-41f5-8aaa-4df18c995011/dqc_reference/reference_markers.hmm GCF_030814695.1_ASM3081469v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:54:20,073] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:54:20,074] [INFO] Found 6/6 markers.
[2024-01-25 17:54:20,117] [INFO] Query marker FASTA was written to GCF_030814695.1_ASM3081469v1_genomic.fna/markers.fasta
[2024-01-25 17:54:20,118] [INFO] Task started: Blastn
[2024-01-25 17:54:20,118] [INFO] Running command: blastn -query GCF_030814695.1_ASM3081469v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55f24096-e35a-41f5-8aaa-4df18c995011/dqc_reference/reference_markers.fasta -out GCF_030814695.1_ASM3081469v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:20,688] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:20,690] [INFO] Selected 25 target genomes.
[2024-01-25 17:54:20,691] [INFO] Target genome list was writen to GCF_030814695.1_ASM3081469v1_genomic.fna/target_genomes.txt
[2024-01-25 17:54:20,712] [INFO] Task started: fastANI
[2024-01-25 17:54:20,712] [INFO] Running command: fastANI --query /var/lib/cwl/stge1284e42-d502-4d89-8aa5-8405e20e5c48/GCF_030814695.1_ASM3081469v1_genomic.fna.gz --refList GCF_030814695.1_ASM3081469v1_genomic.fna/target_genomes.txt --output GCF_030814695.1_ASM3081469v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:54:39,315] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:39,315] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55f24096-e35a-41f5-8aaa-4df18c995011/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:54:39,316] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55f24096-e35a-41f5-8aaa-4df18c995011/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:54:39,322] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:54:39,322] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:54:39,322] [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
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	75.1911	51	1909	95	below_threshold
Sphaerisporangium siamense	strain=DSM 45784	GCA_014205275.1	795645	795645	type	True	74.9113	66	1909	95	below_threshold
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	74.8205	100	1909	95	below_threshold
Sphaerisporangium krabiense	strain=DSM 45790	GCA_014200435.1	763782	763782	type	True	74.7825	64	1909	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	74.7131	56	1909	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	74.7123	56	1909	95	below_threshold
Sphaerisporangium krabiense	strain=NBRC 107571	GCA_016863355.1	763782	763782	type	True	74.6571	62	1909	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:54:39,324] [INFO] DFAST Taxonomy check result was written to GCF_030814695.1_ASM3081469v1_genomic.fna/tc_result.tsv
[2024-01-25 17:54:39,324] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:54:39,324] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:54:39,324] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55f24096-e35a-41f5-8aaa-4df18c995011/dqc_reference/checkm_data
[2024-01-25 17:54:39,325] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:54:39,380] [INFO] Task started: CheckM
[2024-01-25 17:54:39,380] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030814695.1_ASM3081469v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030814695.1_ASM3081469v1_genomic.fna/checkm_input GCF_030814695.1_ASM3081469v1_genomic.fna/checkm_result
[2024-01-25 17:55:58,286] [INFO] Task succeeded: CheckM
[2024-01-25 17:55:58,288] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:55:58,304] [INFO] ===== Completeness check finished =====
[2024-01-25 17:55:58,304] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:55:58,305] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030814695.1_ASM3081469v1_genomic.fna/markers.fasta)
[2024-01-25 17:55:58,305] [INFO] Task started: Blastn
[2024-01-25 17:55:58,305] [INFO] Running command: blastn -query GCF_030814695.1_ASM3081469v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55f24096-e35a-41f5-8aaa-4df18c995011/dqc_reference/reference_markers_gtdb.fasta -out GCF_030814695.1_ASM3081469v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:55:59,312] [INFO] Task succeeded: Blastn
[2024-01-25 17:55:59,316] [INFO] Selected 17 target genomes.
[2024-01-25 17:55:59,316] [INFO] Target genome list was writen to GCF_030814695.1_ASM3081469v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:55:59,335] [INFO] Task started: fastANI
[2024-01-25 17:55:59,335] [INFO] Running command: fastANI --query /var/lib/cwl/stge1284e42-d502-4d89-8aa5-8405e20e5c48/GCF_030814695.1_ASM3081469v1_genomic.fna.gz --refList GCF_030814695.1_ASM3081469v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030814695.1_ASM3081469v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:56:12,474] [INFO] Task succeeded: fastANI
[2024-01-25 17:56:12,484] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:56:12,484] [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_012799755.1	s__JAAZKQ01 sp012799755	83.524	790	1909	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__UBA1407;g__JAAZKQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002070945.1	s__JAAZKI01 sp002070945	77.343	250	1909	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__UBA1407;g__JAAZKI01	95.0	99.22	99.02	0.93	0.92	3	-
GCA_012799905.1	s__JAAZKI01 sp012799905	77.0006	188	1909	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__UBA1407;g__JAAZKI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001603055.1	s__Lenti-02 sp001603055	76.6692	155	1909	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__Lenti-02;g__Lenti-02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012515455.1	s__JAAZIZ01 sp012515455	76.6335	75	1909	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__UBA1407;g__JAAZIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016288215.1	s__Tb-RUG-64 sp016288215	76.579	115	1909	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__UBA1407;g__Tb-RUG-64	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900769285.1	s__CAAGGB01 sp900769285	76.5041	169	1909	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__UBA1407;g__CAAGGB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902776645.1	s__UBA1407 sp902776645	76.0107	129	1909	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__UBA1407;g__UBA1407	95.0	97.32	96.58	0.88	0.85	5	-
GCA_017458805.1	s__RGIG3456 sp017458805	75.9876	84	1909	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__UBA1407;g__RGIG3456	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017431185.1	s__RGIG2581 sp017431185	75.963	59	1909	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__UBA1407;g__RGIG2581	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017554445.1	s__UBA1407 sp017554445	75.9006	85	1909	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__UBA1407;g__UBA1407	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903896595.1	s__CAITYL01 sp903896595	75.71	91	1909	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__CAITYL01;g__CAITYL01	95.0	99.89	99.89	0.95	0.95	2	-
GCA_902783355.1	s__CACZQQ01 sp902783355	75.707	50	1909	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__UBA1407;g__CACZQQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017617415.1	s__RGIG1601 sp017617415	75.6726	53	1909	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__UBA1407;g__RGIG1601	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903921725.1	s__CAIXRA01 sp903921725	75.5453	70	1909	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__CAITYL01;g__CAIXRA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:56:12,486] [INFO] GTDB search result was written to GCF_030814695.1_ASM3081469v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:56:12,486] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:56:12,489] [INFO] DFAST_QC result json was written to GCF_030814695.1_ASM3081469v1_genomic.fna/dqc_result.json
[2024-01-25 17:56:12,489] [INFO] DFAST_QC completed!
[2024-01-25 17:56:12,489] [INFO] Total running time: 0h2m22s