[2023-06-28 14:46:19,495] [INFO] DFAST_QC pipeline started.
[2023-06-28 14:46:19,497] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 14:46:19,497] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f809324-5f54-46e4-bf37-f2734c6d5a4c/dqc_reference
[2023-06-28 14:46:20,606] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 14:46:20,606] [INFO] Task started: Prodigal
[2023-06-28 14:46:20,606] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d3f4630-da25-4182-9321-d4e237a853ab/GCA_017879965.1_ASM1787996v1_genomic.fna.gz | prodigal -d GCA_017879965.1_ASM1787996v1_genomic.fna/cds.fna -a GCA_017879965.1_ASM1787996v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 14:46:27,299] [INFO] Task succeeded: Prodigal
[2023-06-28 14:46:27,299] [INFO] Task started: HMMsearch
[2023-06-28 14:46:27,299] [INFO] Running command: hmmsearch --tblout GCA_017879965.1_ASM1787996v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f809324-5f54-46e4-bf37-f2734c6d5a4c/dqc_reference/reference_markers.hmm GCA_017879965.1_ASM1787996v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 14:46:27,484] [INFO] Task succeeded: HMMsearch
[2023-06-28 14:46:27,486] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3d3f4630-da25-4182-9321-d4e237a853ab/GCA_017879965.1_ASM1787996v1_genomic.fna.gz]
[2023-06-28 14:46:27,512] [INFO] Query marker FASTA was written to GCA_017879965.1_ASM1787996v1_genomic.fna/markers.fasta
[2023-06-28 14:46:27,512] [INFO] Task started: Blastn
[2023-06-28 14:46:27,512] [INFO] Running command: blastn -query GCA_017879965.1_ASM1787996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f809324-5f54-46e4-bf37-f2734c6d5a4c/dqc_reference/reference_markers.fasta -out GCA_017879965.1_ASM1787996v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:46:28,047] [INFO] Task succeeded: Blastn
[2023-06-28 14:46:28,052] [INFO] Selected 13 target genomes.
[2023-06-28 14:46:28,052] [INFO] Target genome list was writen to GCA_017879965.1_ASM1787996v1_genomic.fna/target_genomes.txt
[2023-06-28 14:46:28,054] [INFO] Task started: fastANI
[2023-06-28 14:46:28,054] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d3f4630-da25-4182-9321-d4e237a853ab/GCA_017879965.1_ASM1787996v1_genomic.fna.gz --refList GCA_017879965.1_ASM1787996v1_genomic.fna/target_genomes.txt --output GCA_017879965.1_ASM1787996v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 14:46:37,451] [INFO] Task succeeded: fastANI
[2023-06-28 14:46:37,452] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f809324-5f54-46e4-bf37-f2734c6d5a4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 14:46:37,452] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f809324-5f54-46e4-bf37-f2734c6d5a4c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 14:46:37,459] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 14:46:37,459] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 14:46:37,459] [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
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	76.9092	218	851	95	below_threshold
Capillimicrobium parvum	strain=0166_1	GCA_021172045.1	2884022	2884022	type	True	76.8699	188	851	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	76.5114	203	851	95	below_threshold
Baekduia soli	strain=BR7-21	GCA_007970665.1	496014	496014	type	True	76.4896	187	851	95	below_threshold
Conexibacter woesei	strain=DSM 14684	GCA_000025265.1	191495	191495	type	True	76.2796	205	851	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	76.2355	168	851	95	below_threshold
Patulibacter americanus	strain=DSM 16676	GCA_000420025.1	588672	588672	type	True	75.8022	123	851	95	below_threshold
Patulibacter minatonensis	strain=DSM 18081	GCA_000519325.1	298163	298163	type	True	75.7026	133	851	95	below_threshold
Miltoncostaea oceani	strain=SCSIO 61214	GCA_018141545.1	2843216	2843216	type	True	75.486	89	851	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 14:46:37,461] [INFO] DFAST Taxonomy check result was written to GCA_017879965.1_ASM1787996v1_genomic.fna/tc_result.tsv
[2023-06-28 14:46:37,461] [INFO] ===== Taxonomy check completed =====
[2023-06-28 14:46:37,461] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 14:46:37,461] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f809324-5f54-46e4-bf37-f2734c6d5a4c/dqc_reference/checkm_data
[2023-06-28 14:46:37,462] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 14:46:37,492] [INFO] Task started: CheckM
[2023-06-28 14:46:37,492] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017879965.1_ASM1787996v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017879965.1_ASM1787996v1_genomic.fna/checkm_input GCA_017879965.1_ASM1787996v1_genomic.fna/checkm_result
[2023-06-28 14:47:00,346] [INFO] Task succeeded: CheckM
[2023-06-28 14:47:00,347] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 13.48%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2023-06-28 14:47:00,369] [INFO] ===== Completeness check finished =====
[2023-06-28 14:47:00,369] [INFO] ===== Start GTDB Search =====
[2023-06-28 14:47:00,370] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017879965.1_ASM1787996v1_genomic.fna/markers.fasta)
[2023-06-28 14:47:00,370] [INFO] Task started: Blastn
[2023-06-28 14:47:00,370] [INFO] Running command: blastn -query GCA_017879965.1_ASM1787996v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f809324-5f54-46e4-bf37-f2734c6d5a4c/dqc_reference/reference_markers_gtdb.fasta -out GCA_017879965.1_ASM1787996v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 14:47:01,120] [INFO] Task succeeded: Blastn
[2023-06-28 14:47:01,124] [INFO] Selected 14 target genomes.
[2023-06-28 14:47:01,124] [INFO] Target genome list was writen to GCA_017879965.1_ASM1787996v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 14:47:01,133] [INFO] Task started: fastANI
[2023-06-28 14:47:01,133] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d3f4630-da25-4182-9321-d4e237a853ab/GCA_017879965.1_ASM1787996v1_genomic.fna.gz --refList GCA_017879965.1_ASM1787996v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017879965.1_ASM1787996v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 14:47:10,534] [INFO] Task succeeded: fastANI
[2023-06-28 14:47:10,543] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 14:47:10,543] [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_016781085.1	s__LC5-1 sp016781085	99.4136	567	851	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__LC5-1	95.0	99.49	99.49	0.89	0.89	2	conclusive
GCF_000425945.1	s__Solirubrobacter sp000425945	77.072	231	851	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Solirubrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268595.1	s__Conexibacter sp018268595	77.0363	161	851	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Conexibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813955.1	s__CADCVQ01 sp013813955	76.9595	98	851	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__CADCVQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806175.1	s__CADCVQ01 sp902806175	76.8751	148	851	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__CADCVQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423665.1	s__Solirubrobacter soli	76.8123	226	851	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Solirubrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017084525.1	s__Baekduia sp017084525	76.6859	175	851	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882375.1	s__Palsa-744 sp017882375	76.6722	114	851	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Palsa-744	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199525.1	s__Conexibacter arvalis	76.5118	203	851	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Conexibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005883905.1	s__AC-49 sp005883905	76.2817	107	851	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__AC-49	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000688095.1	s__Baekduia sp000688095	76.2809	191	851	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Baekduia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806205.1	s__SEOHO-28 sp902806205	76.2784	141	851	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__SEOHO-28	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003044185.1	s__SEOHO-28 sp003044185	76.2447	167	851	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__SEOHO-28	95.0	98.17	98.17	0.92	0.92	2	-
GCA_003244035.1	s__Palsa-465 sp003244035	76.1993	93	851	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Solirubrobacterales;f__Solirubrobacteraceae;g__Palsa-465	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 14:47:10,544] [INFO] GTDB search result was written to GCA_017879965.1_ASM1787996v1_genomic.fna/result_gtdb.tsv
[2023-06-28 14:47:10,545] [INFO] ===== GTDB Search completed =====
[2023-06-28 14:47:10,547] [INFO] DFAST_QC result json was written to GCA_017879965.1_ASM1787996v1_genomic.fna/dqc_result.json
[2023-06-28 14:47:10,547] [INFO] DFAST_QC completed!
[2023-06-28 14:47:10,547] [INFO] Total running time: 0h0m51s