[2023-06-08 16:16:11,681] [INFO] DFAST_QC pipeline started.
[2023-06-08 16:16:11,683] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 16:16:11,684] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b82eaf1-09d1-4013-baf6-e30120d9556f/dqc_reference
[2023-06-08 16:16:12,897] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 16:16:12,898] [INFO] Task started: Prodigal
[2023-06-08 16:16:12,899] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd3ca5f9-23ba-43ca-bdbf-05ee4ae907b6/GCA_945861025.1_LH-02apr19-314_genomic.fna.gz | prodigal -d GCA_945861025.1_LH-02apr19-314_genomic.fna/cds.fna -a GCA_945861025.1_LH-02apr19-314_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 16:16:22,799] [INFO] Task succeeded: Prodigal
[2023-06-08 16:16:22,799] [INFO] Task started: HMMsearch
[2023-06-08 16:16:22,800] [INFO] Running command: hmmsearch --tblout GCA_945861025.1_LH-02apr19-314_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b82eaf1-09d1-4013-baf6-e30120d9556f/dqc_reference/reference_markers.hmm GCA_945861025.1_LH-02apr19-314_genomic.fna/protein.faa > /dev/null
[2023-06-08 16:16:23,024] [INFO] Task succeeded: HMMsearch
[2023-06-08 16:16:23,026] [INFO] Found 6/6 markers.
[2023-06-08 16:16:23,056] [INFO] Query marker FASTA was written to GCA_945861025.1_LH-02apr19-314_genomic.fna/markers.fasta
[2023-06-08 16:16:23,057] [INFO] Task started: Blastn
[2023-06-08 16:16:23,057] [INFO] Running command: blastn -query GCA_945861025.1_LH-02apr19-314_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b82eaf1-09d1-4013-baf6-e30120d9556f/dqc_reference/reference_markers.fasta -out GCA_945861025.1_LH-02apr19-314_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 16:16:23,724] [INFO] Task succeeded: Blastn
[2023-06-08 16:16:23,729] [INFO] Selected 20 target genomes.
[2023-06-08 16:16:23,729] [INFO] Target genome list was writen to GCA_945861025.1_LH-02apr19-314_genomic.fna/target_genomes.txt
[2023-06-08 16:16:23,733] [INFO] Task started: fastANI
[2023-06-08 16:16:23,733] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd3ca5f9-23ba-43ca-bdbf-05ee4ae907b6/GCA_945861025.1_LH-02apr19-314_genomic.fna.gz --refList GCA_945861025.1_LH-02apr19-314_genomic.fna/target_genomes.txt --output GCA_945861025.1_LH-02apr19-314_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 16:16:36,179] [INFO] Task succeeded: fastANI
[2023-06-08 16:16:36,180] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b82eaf1-09d1-4013-baf6-e30120d9556f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 16:16:36,180] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b82eaf1-09d1-4013-baf6-e30120d9556f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 16:16:36,192] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 16:16:36,192] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 16:16:36,193] [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
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.7792	121	905	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.7416	54	905	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.691	111	905	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	76.5543	122	905	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	76.4637	88	905	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.2515	76	905	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 16:16:36,195] [INFO] DFAST Taxonomy check result was written to GCA_945861025.1_LH-02apr19-314_genomic.fna/tc_result.tsv
[2023-06-08 16:16:36,195] [INFO] ===== Taxonomy check completed =====
[2023-06-08 16:16:36,195] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 16:16:36,196] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b82eaf1-09d1-4013-baf6-e30120d9556f/dqc_reference/checkm_data
[2023-06-08 16:16:36,197] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 16:16:36,229] [INFO] Task started: CheckM
[2023-06-08 16:16:36,229] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945861025.1_LH-02apr19-314_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945861025.1_LH-02apr19-314_genomic.fna/checkm_input GCA_945861025.1_LH-02apr19-314_genomic.fna/checkm_result
[2023-06-08 16:17:09,682] [INFO] Task succeeded: CheckM
[2023-06-08 16:17:09,683] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 16:17:09,705] [INFO] ===== Completeness check finished =====
[2023-06-08 16:17:09,705] [INFO] ===== Start GTDB Search =====
[2023-06-08 16:17:09,705] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945861025.1_LH-02apr19-314_genomic.fna/markers.fasta)
[2023-06-08 16:17:09,706] [INFO] Task started: Blastn
[2023-06-08 16:17:09,706] [INFO] Running command: blastn -query GCA_945861025.1_LH-02apr19-314_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b82eaf1-09d1-4013-baf6-e30120d9556f/dqc_reference/reference_markers_gtdb.fasta -out GCA_945861025.1_LH-02apr19-314_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 16:17:10,678] [INFO] Task succeeded: Blastn
[2023-06-08 16:17:10,683] [INFO] Selected 20 target genomes.
[2023-06-08 16:17:10,683] [INFO] Target genome list was writen to GCA_945861025.1_LH-02apr19-314_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 16:17:10,695] [INFO] Task started: fastANI
[2023-06-08 16:17:10,696] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd3ca5f9-23ba-43ca-bdbf-05ee4ae907b6/GCA_945861025.1_LH-02apr19-314_genomic.fna.gz --refList GCA_945861025.1_LH-02apr19-314_genomic.fna/target_genomes_gtdb.txt --output GCA_945861025.1_LH-02apr19-314_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 16:17:19,962] [INFO] Task succeeded: fastANI
[2023-06-08 16:17:19,977] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 16:17:19,977] [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_009726095.1	s__WLMZ01 sp009726095	79.1291	435	905	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__WLMZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903919215.1	s__UBA668 sp903919215	77.3226	131	905	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016722025.1	s__UBA668 sp002299395	77.2948	211	905	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA668	95.0	99.06	98.90	0.95	0.90	7	-
GCA_009702045.1	s__UBA668 sp009702045	77.2019	166	905	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA668	95.0	99.96	99.94	0.98	0.97	6	-
GCA_006515795.1	s__VFMC01 sp006515795	77.0347	142	905	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__VFMC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213625.1	s__UBA668 sp016213625	77.0014	217	905	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__UBA668	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871395.1	s__Casp-actino8 sp016871395	76.8901	88	905	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009704425.1	s__Casp-actino8 sp009704425	76.8447	101	905	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009704985.1	s__VFMC01 sp009704985	76.7972	176	905	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__VFMC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213745.1	s__JABSQH01 sp013213745	76.3715	89	905	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JABSQH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007122945.1	s__SKSP01 sp007122945	76.3526	101	905	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	99.05	99.05	0.83	0.83	2	-
GCA_005787025.1	s__Casp-actino8 sp005787025	76.286	54	905	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002175.1	s__Ilumatobacter_A sp013002175	75.998	81	905	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 16:17:19,979] [INFO] GTDB search result was written to GCA_945861025.1_LH-02apr19-314_genomic.fna/result_gtdb.tsv
[2023-06-08 16:17:19,980] [INFO] ===== GTDB Search completed =====
[2023-06-08 16:17:19,983] [INFO] DFAST_QC result json was written to GCA_945861025.1_LH-02apr19-314_genomic.fna/dqc_result.json
[2023-06-08 16:17:19,983] [INFO] DFAST_QC completed!
[2023-06-08 16:17:19,983] [INFO] Total running time: 0h1m8s