[2024-01-24 13:58:55,817] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:55,819] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:55,819] [INFO] DQC Reference Directory: /var/lib/cwl/stg262cd0ee-0054-48b9-a77b-0c5852a97473/dqc_reference
[2024-01-24 13:58:57,210] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:57,211] [INFO] Task started: Prodigal
[2024-01-24 13:58:57,211] [INFO] Running command: gunzip -c /var/lib/cwl/stg458cb323-2e61-46b8-805c-3a291c23ec8a/GCF_030409775.1_ASM3040977v1_genomic.fna.gz | prodigal -d GCF_030409775.1_ASM3040977v1_genomic.fna/cds.fna -a GCF_030409775.1_ASM3040977v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:59:06,957] [INFO] Task succeeded: Prodigal
[2024-01-24 13:59:06,957] [INFO] Task started: HMMsearch
[2024-01-24 13:59:06,957] [INFO] Running command: hmmsearch --tblout GCF_030409775.1_ASM3040977v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg262cd0ee-0054-48b9-a77b-0c5852a97473/dqc_reference/reference_markers.hmm GCF_030409775.1_ASM3040977v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:59:07,202] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:59:07,203] [INFO] Found 6/6 markers.
[2024-01-24 13:59:07,232] [INFO] Query marker FASTA was written to GCF_030409775.1_ASM3040977v1_genomic.fna/markers.fasta
[2024-01-24 13:59:07,233] [INFO] Task started: Blastn
[2024-01-24 13:59:07,233] [INFO] Running command: blastn -query GCF_030409775.1_ASM3040977v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg262cd0ee-0054-48b9-a77b-0c5852a97473/dqc_reference/reference_markers.fasta -out GCF_030409775.1_ASM3040977v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:08,079] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:08,082] [INFO] Selected 21 target genomes.
[2024-01-24 13:59:08,082] [INFO] Target genome list was writen to GCF_030409775.1_ASM3040977v1_genomic.fna/target_genomes.txt
[2024-01-24 13:59:08,095] [INFO] Task started: fastANI
[2024-01-24 13:59:08,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg458cb323-2e61-46b8-805c-3a291c23ec8a/GCF_030409775.1_ASM3040977v1_genomic.fna.gz --refList GCF_030409775.1_ASM3040977v1_genomic.fna/target_genomes.txt --output GCF_030409775.1_ASM3040977v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:19,225] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:19,225] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg262cd0ee-0054-48b9-a77b-0c5852a97473/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:19,226] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg262cd0ee-0054-48b9-a77b-0c5852a97473/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:19,244] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:59:19,244] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:19,244] [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
Pontixanthobacter aestiaquae	strain=KCTC 42006	GCA_009827455.1	1509367	1509367	type	True	99.9964	955	955	95	conclusive
Pontixanthobacter aquaemixtae	strain=KCTC 52763	GCA_009827395.1	1958940	1958940	type	True	80.0578	538	955	95	below_threshold
Pontixanthobacter rizhaonensis	strain=RZ02	GCA_012972675.1	2730337	2730337	type	True	78.3553	296	955	95	below_threshold
Pontixanthobacter gangjinensis	strain=JCM 17802	GCA_009827545.1	1028742	1028742	type	True	78.1963	342	955	95	below_threshold
Pontixanthobacter luteolus	strain=SW-109	GCA_009828095.1	295089	295089	type	True	78.1727	372	955	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	77.6837	222	955	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	77.4832	212	955	95	below_threshold
Allopontixanthobacter sediminis	strain=KCTC 42453	GCA_009828115.1	1689985	1689985	type	True	77.4726	259	955	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	77.3893	204	955	95	below_threshold
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	77.3863	174	955	95	below_threshold
Altererythrobacter lutimaris	strain=JGD-16	GCA_013371495.1	2743979	2743979	type	True	77.2758	192	955	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	77.2255	207	955	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	77.2246	216	955	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	77.2071	189	955	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	77.1897	193	955	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	77.1893	205	955	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	77.1583	224	955	95	below_threshold
Alteriqipengyuania lutimaris	strain=S-5	GCA_003363135.1	1538146	1538146	type	True	77.0964	195	955	95	below_threshold
Alteriqipengyuania lutimaris	strain=CECT 8624	GCA_014191645.1	1538146	1538146	type	True	77.0964	195	955	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_000714795.1	39960	39960	type	True	77.0777	201	955	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	77.0387	198	955	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:19,246] [INFO] DFAST Taxonomy check result was written to GCF_030409775.1_ASM3040977v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:19,247] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:19,247] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:19,247] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg262cd0ee-0054-48b9-a77b-0c5852a97473/dqc_reference/checkm_data
[2024-01-24 13:59:19,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:19,281] [INFO] Task started: CheckM
[2024-01-24 13:59:19,281] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409775.1_ASM3040977v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409775.1_ASM3040977v1_genomic.fna/checkm_input GCF_030409775.1_ASM3040977v1_genomic.fna/checkm_result
[2024-01-24 13:59:49,720] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:49,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:49,752] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:49,753] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:49,753] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409775.1_ASM3040977v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:49,754] [INFO] Task started: Blastn
[2024-01-24 13:59:49,754] [INFO] Running command: blastn -query GCF_030409775.1_ASM3040977v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg262cd0ee-0054-48b9-a77b-0c5852a97473/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409775.1_ASM3040977v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:51,091] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:51,096] [INFO] Selected 16 target genomes.
[2024-01-24 13:59:51,096] [INFO] Target genome list was writen to GCF_030409775.1_ASM3040977v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:51,121] [INFO] Task started: fastANI
[2024-01-24 13:59:51,121] [INFO] Running command: fastANI --query /var/lib/cwl/stg458cb323-2e61-46b8-805c-3a291c23ec8a/GCF_030409775.1_ASM3040977v1_genomic.fna.gz --refList GCF_030409775.1_ASM3040977v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409775.1_ASM3040977v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:59,726] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:59,741] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:59,742] [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_009827455.1	s__Pontixanthobacter aestiaquae	99.9964	955	955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017812015.1	s__Pontixanthobacter sp017812015	83.1018	757	955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827395.1	s__Pontixanthobacter aquaemixtae	80.0583	538	955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012972675.1	s__Pontixanthobacter rizhaonensis	78.3496	297	955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827545.1	s__Pontixanthobacter gangjinensis	78.1963	342	955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828095.1	s__Pontixanthobacter luteolus	78.1727	372	955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114695.1	s__Parerythrobacter sp004114695	77.5	296	955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828115.1	s__Pseudopontixanthobacter_A sediminis	77.4615	260	955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001281485.1	s__Erythrobacter epoxidivorans	77.4585	203	955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001008165.2	s__Croceibacterium atlanticum	77.3617	174	955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009827295.1	s__Qipengyuania pelagi	77.2171	215	955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001719165.1	s__Erythrobacter litoralis	77.1903	192	955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003581645.1	s__Pelagerythrobacter aerophilus	77.1893	205	955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248395.1	s__Qipengyuania sp003248395	77.0813	163	955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015529805.1	s__Qipengyuania soli	77.0387	198	955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340475.1	s__Alteripontixanthobacter maritimus	76.8468	207	955	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteripontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:59,743] [INFO] GTDB search result was written to GCF_030409775.1_ASM3040977v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:59,744] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:59,748] [INFO] DFAST_QC result json was written to GCF_030409775.1_ASM3040977v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:59,748] [INFO] DFAST_QC completed!
[2024-01-24 13:59:59,748] [INFO] Total running time: 0h1m4s