[2024-01-24 12:36:24,814] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:24,816] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:24,816] [INFO] DQC Reference Directory: /var/lib/cwl/stg11f0319a-89e3-486b-b9c2-65ce26e2f715/dqc_reference
[2024-01-24 12:36:26,188] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:26,189] [INFO] Task started: Prodigal
[2024-01-24 12:36:26,189] [INFO] Running command: gunzip -c /var/lib/cwl/stge00056bb-6d24-4d8f-a1d7-8724c16763d8/GCF_028617075.1_ASM2861707v1_genomic.fna.gz | prodigal -d GCF_028617075.1_ASM2861707v1_genomic.fna/cds.fna -a GCF_028617075.1_ASM2861707v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:33,968] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:33,968] [INFO] Task started: HMMsearch
[2024-01-24 12:36:33,968] [INFO] Running command: hmmsearch --tblout GCF_028617075.1_ASM2861707v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11f0319a-89e3-486b-b9c2-65ce26e2f715/dqc_reference/reference_markers.hmm GCF_028617075.1_ASM2861707v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:34,206] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:34,208] [INFO] Found 6/6 markers.
[2024-01-24 12:36:34,246] [INFO] Query marker FASTA was written to GCF_028617075.1_ASM2861707v1_genomic.fna/markers.fasta
[2024-01-24 12:36:34,247] [INFO] Task started: Blastn
[2024-01-24 12:36:34,247] [INFO] Running command: blastn -query GCF_028617075.1_ASM2861707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11f0319a-89e3-486b-b9c2-65ce26e2f715/dqc_reference/reference_markers.fasta -out GCF_028617075.1_ASM2861707v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:34,861] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:34,865] [INFO] Selected 13 target genomes.
[2024-01-24 12:36:34,865] [INFO] Target genome list was writen to GCF_028617075.1_ASM2861707v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:34,871] [INFO] Task started: fastANI
[2024-01-24 12:36:34,871] [INFO] Running command: fastANI --query /var/lib/cwl/stge00056bb-6d24-4d8f-a1d7-8724c16763d8/GCF_028617075.1_ASM2861707v1_genomic.fna.gz --refList GCF_028617075.1_ASM2861707v1_genomic.fna/target_genomes.txt --output GCF_028617075.1_ASM2861707v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:36:43,412] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:43,413] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11f0319a-89e3-486b-b9c2-65ce26e2f715/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:36:43,414] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11f0319a-89e3-486b-b9c2-65ce26e2f715/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:36:43,425] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:36:43,426] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:36:43,426] [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
Rubrobacter marinus	strain=SCSIO 52915	GCA_011492965.1	2653852	2653852	type	True	77.6864	326	1006	95	below_threshold
Rubrobacter tropicus	strain=SCSIO 52909	GCA_011492945.1	2653851	2653851	type	True	77.6012	290	1006	95	below_threshold
Rubrobacter radiotolerans	strain=DSM 5868	GCA_900175965.1	42256	42256	type	True	77.5592	254	1006	95	below_threshold
Rubrobacter aplysinae	strain=RV113	GCA_001029505.1	909625	909625	type	True	77.3965	221	1006	95	below_threshold
Rubrobacter indicoceani	strain=SCSIO 08198	GCA_003568865.1	2051957	2051957	type	True	76.7361	176	1006	95	below_threshold
Kineococcus radiotolerans	strain=SRS30216	GCA_000017305.1	131568	131568	type	True	75.0847	76	1006	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	75.0685	92	1006	95	below_threshold
Streptomyces filipinensis	strain=JCM 4369	GCA_014649495.1	66887	66887	type	True	74.8753	81	1006	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:36:43,428] [INFO] DFAST Taxonomy check result was written to GCF_028617075.1_ASM2861707v1_genomic.fna/tc_result.tsv
[2024-01-24 12:36:43,429] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:36:43,429] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:36:43,429] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11f0319a-89e3-486b-b9c2-65ce26e2f715/dqc_reference/checkm_data
[2024-01-24 12:36:43,431] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:36:43,463] [INFO] Task started: CheckM
[2024-01-24 12:36:43,463] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028617075.1_ASM2861707v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028617075.1_ASM2861707v1_genomic.fna/checkm_input GCF_028617075.1_ASM2861707v1_genomic.fna/checkm_result
[2024-01-24 12:37:10,602] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:10,604] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:10,628] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:10,628] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:10,629] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028617075.1_ASM2861707v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:10,629] [INFO] Task started: Blastn
[2024-01-24 12:37:10,629] [INFO] Running command: blastn -query GCF_028617075.1_ASM2861707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11f0319a-89e3-486b-b9c2-65ce26e2f715/dqc_reference/reference_markers_gtdb.fasta -out GCF_028617075.1_ASM2861707v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:11,569] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:11,574] [INFO] Selected 14 target genomes.
[2024-01-24 12:37:11,574] [INFO] Target genome list was writen to GCF_028617075.1_ASM2861707v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:11,590] [INFO] Task started: fastANI
[2024-01-24 12:37:11,590] [INFO] Running command: fastANI --query /var/lib/cwl/stge00056bb-6d24-4d8f-a1d7-8724c16763d8/GCF_028617075.1_ASM2861707v1_genomic.fna.gz --refList GCF_028617075.1_ASM2861707v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028617075.1_ASM2861707v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:19,262] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:19,278] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:37:19,278] [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_007164525.1	s__Rubrobacter_B xylanophilus_A	81.144	472	1006	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014185.1	s__Rubrobacter_B xylanophilus	79.7975	482	1006	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902810695.1	s__CADDYV01 sp902810695	78.8989	412	1006	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__CADDYV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004337705.1	s__Rubrobacter_C taiwanensis	78.8562	316	1006	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004563715.1	s__SIRX01 sp004563715	78.0964	297	1006	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SIRX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016781725.1	s__SCSIO-52909 sp016781725	77.9361	227	1006	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	98.84	98.84	0.72	0.72	2	-
GCF_011492965.1	s__SCSIO-52915 sp011492965	77.706	324	1006	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902812425.1	s__SCSIO-52909 sp902812425	77.6005	243	1006	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52909	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900175965.1	s__Rubrobacter radiotolerans	77.5592	254	1006	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter	95.0	99.98	99.98	1.00	1.00	2	-
GCA_016781705.1	s__SCSIO-52915 sp016781705	77.4938	202	1006	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013812245.1	s__JACDGB01 sp013812245	77.4444	166	1006	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__JACDGB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013695915.1	s__Rubrobacter_A sp013695915	77.4266	210	1006	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__Rubrobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016781885.1	s__SCSIO-52915 sp016781885	77.3574	129	1006	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__SCSIO-52915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013817025.1	s__JACDDK01 sp013817025	76.7553	72	1006	d__Bacteria;p__Actinobacteriota;c__Rubrobacteria;o__Rubrobacterales;f__Rubrobacteraceae;g__JACDDK01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:37:19,279] [INFO] GTDB search result was written to GCF_028617075.1_ASM2861707v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:19,280] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:19,284] [INFO] DFAST_QC result json was written to GCF_028617075.1_ASM2861707v1_genomic.fna/dqc_result.json
[2024-01-24 12:37:19,284] [INFO] DFAST_QC completed!
[2024-01-24 12:37:19,284] [INFO] Total running time: 0h0m54s