[2023-06-28 18:01:52,305] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:01:52,308] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:01:52,308] [INFO] DQC Reference Directory: /var/lib/cwl/stgb18a6f53-ac2e-4d40-8494-5f67a59f15e7/dqc_reference
[2023-06-28 18:01:53,567] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:01:53,568] [INFO] Task started: Prodigal
[2023-06-28 18:01:53,568] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d37e162-b7be-4403-804e-43e01cf1aed6/GCA_005789645.1_ASM578964v1_genomic.fna.gz | prodigal -d GCA_005789645.1_ASM578964v1_genomic.fna/cds.fna -a GCA_005789645.1_ASM578964v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:02:04,008] [INFO] Task succeeded: Prodigal
[2023-06-28 18:02:04,009] [INFO] Task started: HMMsearch
[2023-06-28 18:02:04,009] [INFO] Running command: hmmsearch --tblout GCA_005789645.1_ASM578964v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb18a6f53-ac2e-4d40-8494-5f67a59f15e7/dqc_reference/reference_markers.hmm GCA_005789645.1_ASM578964v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:02:04,267] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:02:04,268] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2d37e162-b7be-4403-804e-43e01cf1aed6/GCA_005789645.1_ASM578964v1_genomic.fna.gz]
[2023-06-28 18:02:04,300] [INFO] Query marker FASTA was written to GCA_005789645.1_ASM578964v1_genomic.fna/markers.fasta
[2023-06-28 18:02:04,301] [INFO] Task started: Blastn
[2023-06-28 18:02:04,301] [INFO] Running command: blastn -query GCA_005789645.1_ASM578964v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb18a6f53-ac2e-4d40-8494-5f67a59f15e7/dqc_reference/reference_markers.fasta -out GCA_005789645.1_ASM578964v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:02:04,929] [INFO] Task succeeded: Blastn
[2023-06-28 18:02:04,934] [INFO] Selected 20 target genomes.
[2023-06-28 18:02:04,934] [INFO] Target genome list was writen to GCA_005789645.1_ASM578964v1_genomic.fna/target_genomes.txt
[2023-06-28 18:02:04,939] [INFO] Task started: fastANI
[2023-06-28 18:02:04,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d37e162-b7be-4403-804e-43e01cf1aed6/GCA_005789645.1_ASM578964v1_genomic.fna.gz --refList GCA_005789645.1_ASM578964v1_genomic.fna/target_genomes.txt --output GCA_005789645.1_ASM578964v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:02:24,456] [INFO] Task succeeded: fastANI
[2023-06-28 18:02:24,457] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb18a6f53-ac2e-4d40-8494-5f67a59f15e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:02:24,457] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb18a6f53-ac2e-4d40-8494-5f67a59f15e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:02:24,474] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:02:24,474] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 18:02:24,474] [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
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	74.8043	81	1043	95	below_threshold
Corallococcus praedator	strain=CA031B	GCA_003612125.1	2316724	2316724	type	True	74.7669	96	1043	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	74.7477	83	1043	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	74.7156	90	1043	95	below_threshold
Corallococcus terminator	strain=CA054A	GCA_003611635.1	2316733	2316733	type	True	74.682	85	1043	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	74.6694	83	1043	95	below_threshold
Micromonospora marina	strain=DSM 45555	GCA_900091565.1	307120	307120	type	True	74.6405	85	1043	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	74.6392	141	1043	95	below_threshold
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	74.6248	51	1043	95	below_threshold
Paucibacter toxinivorans	strain=DSM 16998	GCA_004362525.1	270368	270368	type	True	74.6183	63	1043	95	below_threshold
Frankia asymbiotica	strain=NRRL B-16386	GCA_001983105.1	1834516	1834516	type	True	74.6103	95	1043	95	below_threshold
Corallococcus exercitus	strain=AB043A	GCA_003611585.1	2316736	2316736	type	True	74.6014	114	1043	95	below_threshold
Microbacterium halophytorum	strain=YJYP 303	GCA_002970975.1	2067568	2067568	type	True	74.5766	73	1043	95	below_threshold
Microbacterium hatanonis	strain=JCM14558	GCA_008017415.1	404366	404366	type	True	74.5069	52	1043	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 18:02:24,477] [INFO] DFAST Taxonomy check result was written to GCA_005789645.1_ASM578964v1_genomic.fna/tc_result.tsv
[2023-06-28 18:02:24,477] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:02:24,478] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:02:24,478] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb18a6f53-ac2e-4d40-8494-5f67a59f15e7/dqc_reference/checkm_data
[2023-06-28 18:02:24,479] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:02:24,520] [INFO] Task started: CheckM
[2023-06-28 18:02:24,520] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_005789645.1_ASM578964v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_005789645.1_ASM578964v1_genomic.fna/checkm_input GCA_005789645.1_ASM578964v1_genomic.fna/checkm_result
[2023-06-28 18:03:04,157] [INFO] Task succeeded: CheckM
[2023-06-28 18:03:04,159] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.03%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:03:04,184] [INFO] ===== Completeness check finished =====
[2023-06-28 18:03:04,184] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:03:04,185] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_005789645.1_ASM578964v1_genomic.fna/markers.fasta)
[2023-06-28 18:03:04,185] [INFO] Task started: Blastn
[2023-06-28 18:03:04,185] [INFO] Running command: blastn -query GCA_005789645.1_ASM578964v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb18a6f53-ac2e-4d40-8494-5f67a59f15e7/dqc_reference/reference_markers_gtdb.fasta -out GCA_005789645.1_ASM578964v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:03:05,085] [INFO] Task succeeded: Blastn
[2023-06-28 18:03:05,090] [INFO] Selected 17 target genomes.
[2023-06-28 18:03:05,091] [INFO] Target genome list was writen to GCA_005789645.1_ASM578964v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:03:05,103] [INFO] Task started: fastANI
[2023-06-28 18:03:05,103] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d37e162-b7be-4403-804e-43e01cf1aed6/GCA_005789645.1_ASM578964v1_genomic.fna.gz --refList GCA_005789645.1_ASM578964v1_genomic.fna/target_genomes_gtdb.txt --output GCA_005789645.1_ASM578964v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:03:17,649] [INFO] Task succeeded: fastANI
[2023-06-28 18:03:17,664] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 18:03:17,665] [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_005789645.1	s__SXXH01 sp005789645	100.0	1024	1043	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__SXXH01	95.0	99.62	99.60	0.89	0.88	4	conclusive
GCA_903829565.1	s__SXXH01 sp903829565	79.0087	332	1043	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__SXXH01	95.0	98.11	97.95	0.77	0.75	5	-
GCA_005799545.1	s__SYGM01 sp005799545	77.2277	191	1043	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__SYGM01	95.0	99.85	99.85	0.93	0.92	3	-
GCA_016709875.1	s__JADJLZ01 sp016709875	77.0516	294	1043	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJLZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795205.1	s__JAEUHZ01 sp016795205	76.995	348	1043	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JAEUHZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795245.1	s__JAEUIA01 sp016795245	76.7819	231	1043	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JAEUIA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903892045.1	s__F1-120-MAGs118 sp903892045	76.5676	255	1043	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__F1-120-MAGs118	95.0	99.41	99.41	0.87	0.87	3	-
GCA_016714045.1	s__JADJNY01 sp016714045	76.3522	359	1043	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJNY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005778045.1	s__F1-120-MAGs118 sp005778045	76.3473	195	1043	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__F1-120-MAGs118	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872715.1	s__F1-120-MAGs118 sp016872715	76.2703	250	1043	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__F1-120-MAGs118	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525785.1	s__WYBT01 sp011525785	76.187	305	1043	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__WYBT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691855.1	s__JABFRZ01 sp009691855	75.9818	208	1043	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JABFRZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296785.1	s__GW928-bin9 sp004296785	75.7887	218	1043	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GW928-bin9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826945.1	s__RBC036 sp902826945	75.7663	285	1043	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__RBC036	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:03:17,667] [INFO] GTDB search result was written to GCA_005789645.1_ASM578964v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:03:17,667] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:03:17,673] [INFO] DFAST_QC result json was written to GCA_005789645.1_ASM578964v1_genomic.fna/dqc_result.json
[2023-06-28 18:03:17,673] [INFO] DFAST_QC completed!
[2023-06-28 18:03:17,673] [INFO] Total running time: 0h1m25s