[2024-01-24 13:40:30,226] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:30,235] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:30,235] [INFO] DQC Reference Directory: /var/lib/cwl/stg22a97521-4b30-4eb0-9ac4-2fd34d744578/dqc_reference
[2024-01-24 13:40:31,611] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:31,612] [INFO] Task started: Prodigal
[2024-01-24 13:40:31,612] [INFO] Running command: gunzip -c /var/lib/cwl/stg73fd0f45-49a8-45d2-9903-9a1843ccded1/GCF_009828115.1_ASM982811v1_genomic.fna.gz | prodigal -d GCF_009828115.1_ASM982811v1_genomic.fna/cds.fna -a GCF_009828115.1_ASM982811v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:41,481] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:41,481] [INFO] Task started: HMMsearch
[2024-01-24 13:40:41,481] [INFO] Running command: hmmsearch --tblout GCF_009828115.1_ASM982811v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22a97521-4b30-4eb0-9ac4-2fd34d744578/dqc_reference/reference_markers.hmm GCF_009828115.1_ASM982811v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:41,753] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:41,754] [INFO] Found 6/6 markers.
[2024-01-24 13:40:41,782] [INFO] Query marker FASTA was written to GCF_009828115.1_ASM982811v1_genomic.fna/markers.fasta
[2024-01-24 13:40:41,782] [INFO] Task started: Blastn
[2024-01-24 13:40:41,782] [INFO] Running command: blastn -query GCF_009828115.1_ASM982811v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22a97521-4b30-4eb0-9ac4-2fd34d744578/dqc_reference/reference_markers.fasta -out GCF_009828115.1_ASM982811v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:42,644] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:42,648] [INFO] Selected 22 target genomes.
[2024-01-24 13:40:42,649] [INFO] Target genome list was writen to GCF_009828115.1_ASM982811v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:42,659] [INFO] Task started: fastANI
[2024-01-24 13:40:42,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg73fd0f45-49a8-45d2-9903-9a1843ccded1/GCF_009828115.1_ASM982811v1_genomic.fna.gz --refList GCF_009828115.1_ASM982811v1_genomic.fna/target_genomes.txt --output GCF_009828115.1_ASM982811v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:55,001] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:55,002] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22a97521-4b30-4eb0-9ac4-2fd34d744578/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:55,002] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22a97521-4b30-4eb0-9ac4-2fd34d744578/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:55,020] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:40:55,021] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:55,021] [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
Allopontixanthobacter sediminis	strain=KCTC 42453	GCA_009828115.1	1689985	1689985	type	True	100.0	1050	1050	95	conclusive
Allopontixanthobacter confluentis	strain=KCTC 52259	GCA_009827615.1	1849021	1849021	type	True	78.7715	412	1050	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	78.5693	353	1050	95	below_threshold
Pontixanthobacter luteolus	strain=SW-109	GCA_009828095.1	295089	295089	type	True	78.4505	334	1050	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	78.4388	349	1050	95	below_threshold
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	78.4026	349	1050	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	78.3187	344	1050	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	78.2943	324	1050	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	78.2757	362	1050	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	78.2602	388	1050	95	below_threshold
Tsuneonella rigui	strain=KCTC 42620	GCA_003958625.1	1708790	1708790	type	True	78.2005	314	1050	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	78.1286	321	1050	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.0652	341	1050	95	below_threshold
Tsuneonella amylolytica	strain=NS1	GCA_003626915.1	2338327	2338327	type	True	78.0071	315	1050	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	77.9715	257	1050	95	below_threshold
Pontixanthobacter aquaemixtae	strain=KCTC 52763	GCA_009827395.1	1958940	1958940	type	True	77.9558	287	1050	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	77.9532	299	1050	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	77.9338	291	1050	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	77.8506	326	1050	95	below_threshold
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	77.8283	285	1050	95	below_threshold
Croceibacterium atlanticum	strain=DSM 100738	GCA_014199315.1	1267766	1267766	type	True	77.8017	283	1050	95	below_threshold
Pontixanthobacter aestiaquae	strain=KCTC 42006	GCA_009827455.1	1509367	1509367	type	True	77.6151	256	1050	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:55,023] [INFO] DFAST Taxonomy check result was written to GCF_009828115.1_ASM982811v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:55,023] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:55,024] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:55,024] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22a97521-4b30-4eb0-9ac4-2fd34d744578/dqc_reference/checkm_data
[2024-01-24 13:40:55,025] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:55,060] [INFO] Task started: CheckM
[2024-01-24 13:40:55,060] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009828115.1_ASM982811v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009828115.1_ASM982811v1_genomic.fna/checkm_input GCF_009828115.1_ASM982811v1_genomic.fna/checkm_result
[2024-01-24 13:41:28,580] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:28,582] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:28,620] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:28,620] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:28,621] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009828115.1_ASM982811v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:28,621] [INFO] Task started: Blastn
[2024-01-24 13:41:28,621] [INFO] Running command: blastn -query GCF_009828115.1_ASM982811v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22a97521-4b30-4eb0-9ac4-2fd34d744578/dqc_reference/reference_markers_gtdb.fasta -out GCF_009828115.1_ASM982811v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:30,227] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:30,230] [INFO] Selected 23 target genomes.
[2024-01-24 13:41:30,230] [INFO] Target genome list was writen to GCF_009828115.1_ASM982811v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:30,266] [INFO] Task started: fastANI
[2024-01-24 13:41:30,266] [INFO] Running command: fastANI --query /var/lib/cwl/stg73fd0f45-49a8-45d2-9903-9a1843ccded1/GCF_009828115.1_ASM982811v1_genomic.fna.gz --refList GCF_009828115.1_ASM982811v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009828115.1_ASM982811v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:43,476] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:43,500] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:43,500] [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_009828115.1	s__Pseudopontixanthobacter_A sediminis	100.0	1050	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009827615.1	s__Pseudopontixanthobacter_A confluentis	78.7823	412	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763545.1	s__JACXVD01 sp014763545	78.5964	378	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCF_009828095.1	s__Pontixanthobacter luteolus	78.4519	335	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005884405.1	s__Qipengyuania marisflavi	78.3619	308	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827315.1	s__Qipengyuania gaetbuli	78.3374	344	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827515.1	s__Pelagerythrobacter marinus	78.2696	387	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016461955.1	s__QFOP01 sp003248785	78.2325	323	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__QFOP01	95.0	98.23	98.19	0.91	0.89	3	-
GCF_002269345.1	s__Tsuneonella mangrovi	78.2034	313	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	78.2009	356	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012979275.1	s__Pseudopontixanthobacter vadosimaris	78.2003	318	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003958625.1	s__Tsuneonella rigui	78.1698	316	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177715.1	s__Erythrobacter xiamenensis	78.141	318	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011047315.1	s__Erythrobacter sp011047315	78.0737	358	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013005.1	s__Altererythrobacter_D litoralis_A	78.067	339	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altererythrobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005434975.1	s__Parerythrobacter lutipelagi	78.0602	318	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626915.1	s__Tsuneonella amylolytica	78.0071	315	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687545.1	s__Paraurantiacibacter namhicola	78.0032	296	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Paraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744735.1	s__Caenibius sp017744735	77.9082	301	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	99.56	99.56	0.78	0.78	2	-
GCF_001008165.2	s__Croceibacterium atlanticum	77.8505	283	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002279825.1	s__Croceibacterium sp002279825	77.7368	272	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	99.89	99.89	0.97	0.97	2	-
GCF_002870965.1	s__Tsuneonella flava	77.6141	280	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	99.01	98.03	0.92	0.87	3	-
GCF_009827455.1	s__Pontixanthobacter aestiaquae	77.6077	258	1050	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:43,502] [INFO] GTDB search result was written to GCF_009828115.1_ASM982811v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:43,502] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:43,507] [INFO] DFAST_QC result json was written to GCF_009828115.1_ASM982811v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:43,507] [INFO] DFAST_QC completed!
[2024-01-24 13:41:43,507] [INFO] Total running time: 0h1m13s