[2024-01-24 13:41:16,541] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:16,546] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:16,546] [INFO] DQC Reference Directory: /var/lib/cwl/stg1dd7e6c2-f003-4d92-a3a0-33bcf2e87577/dqc_reference
[2024-01-24 13:41:17,743] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:17,744] [INFO] Task started: Prodigal
[2024-01-24 13:41:17,744] [INFO] Running command: gunzip -c /var/lib/cwl/stg96e963fb-2263-437d-a08a-4257e4f1e799/GCF_005434975.1_ASM543497v1_genomic.fna.gz | prodigal -d GCF_005434975.1_ASM543497v1_genomic.fna/cds.fna -a GCF_005434975.1_ASM543497v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:27,859] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:27,860] [INFO] Task started: HMMsearch
[2024-01-24 13:41:27,860] [INFO] Running command: hmmsearch --tblout GCF_005434975.1_ASM543497v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1dd7e6c2-f003-4d92-a3a0-33bcf2e87577/dqc_reference/reference_markers.hmm GCF_005434975.1_ASM543497v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:28,159] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:28,161] [INFO] Found 6/6 markers.
[2024-01-24 13:41:28,196] [INFO] Query marker FASTA was written to GCF_005434975.1_ASM543497v1_genomic.fna/markers.fasta
[2024-01-24 13:41:28,197] [INFO] Task started: Blastn
[2024-01-24 13:41:28,197] [INFO] Running command: blastn -query GCF_005434975.1_ASM543497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dd7e6c2-f003-4d92-a3a0-33bcf2e87577/dqc_reference/reference_markers.fasta -out GCF_005434975.1_ASM543497v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:29,266] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:29,269] [INFO] Selected 22 target genomes.
[2024-01-24 13:41:29,270] [INFO] Target genome list was writen to GCF_005434975.1_ASM543497v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:29,278] [INFO] Task started: fastANI
[2024-01-24 13:41:29,278] [INFO] Running command: fastANI --query /var/lib/cwl/stg96e963fb-2263-437d-a08a-4257e4f1e799/GCF_005434975.1_ASM543497v1_genomic.fna.gz --refList GCF_005434975.1_ASM543497v1_genomic.fna/target_genomes.txt --output GCF_005434975.1_ASM543497v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:43,457] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:43,458] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1dd7e6c2-f003-4d92-a3a0-33bcf2e87577/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:43,458] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1dd7e6c2-f003-4d92-a3a0-33bcf2e87577/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:43,475] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:43,475] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:43,475] [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
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	79.1018	349	1032	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	78.9545	376	1032	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	78.9505	375	1032	95	below_threshold
Pontixanthobacter aquaemixtae	strain=KCTC 52763	GCA_009827395.1	1958940	1958940	type	True	78.9089	362	1032	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	78.8499	415	1032	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	78.8427	376	1032	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	78.8199	335	1032	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	78.8032	374	1032	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	78.6849	359	1032	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	78.6527	337	1032	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	78.577	339	1032	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	78.5704	355	1032	95	below_threshold
Tsuneonella amylolytica	strain=NS1	GCA_003626915.1	2338327	2338327	type	True	78.3326	299	1032	95	below_threshold
Parerythrobacter jejuensis	strain=JCM 16677	GCA_009827995.1	795812	795812	type	True	78.2885	319	1032	95	below_threshold
Pontixanthobacter luteolus	strain=SW-109	GCA_009828095.1	295089	295089	type	True	78.2729	364	1032	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.2708	353	1032	95	below_threshold
Allopontixanthobacter sediminis	strain=KCTC 42453	GCA_009828115.1	1689985	1689985	type	True	78.1109	320	1032	95	below_threshold
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	78.0757	243	1032	95	below_threshold
Croceibacterium atlanticum	strain=DSM 100738	GCA_014199315.1	1267766	1267766	type	True	78.0368	248	1032	95	below_threshold
Aurantiacibacter suaedae	strain=GH3-15	GCA_005434915.1	2545755	2545755	type	True	77.9973	239	1032	95	below_threshold
Pontixanthobacter aestiaquae	strain=KCTC 42006	GCA_009827455.1	1509367	1509367	type	True	77.7056	285	1032	95	below_threshold
Croceicoccus sediminis	strain=S2-4-2	GCA_007570835.1	2571150	2571150	type	True	77.5173	202	1032	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:43,477] [INFO] DFAST Taxonomy check result was written to GCF_005434975.1_ASM543497v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:43,478] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:43,478] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:43,478] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1dd7e6c2-f003-4d92-a3a0-33bcf2e87577/dqc_reference/checkm_data
[2024-01-24 13:41:43,480] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:43,511] [INFO] Task started: CheckM
[2024-01-24 13:41:43,512] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005434975.1_ASM543497v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005434975.1_ASM543497v1_genomic.fna/checkm_input GCF_005434975.1_ASM543497v1_genomic.fna/checkm_result
[2024-01-24 13:42:16,431] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:16,432] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:16,456] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:16,456] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:16,457] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005434975.1_ASM543497v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:16,457] [INFO] Task started: Blastn
[2024-01-24 13:42:16,457] [INFO] Running command: blastn -query GCF_005434975.1_ASM543497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dd7e6c2-f003-4d92-a3a0-33bcf2e87577/dqc_reference/reference_markers_gtdb.fasta -out GCF_005434975.1_ASM543497v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:18,014] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:18,019] [INFO] Selected 22 target genomes.
[2024-01-24 13:42:18,019] [INFO] Target genome list was writen to GCF_005434975.1_ASM543497v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:18,032] [INFO] Task started: fastANI
[2024-01-24 13:42:18,032] [INFO] Running command: fastANI --query /var/lib/cwl/stg96e963fb-2263-437d-a08a-4257e4f1e799/GCF_005434975.1_ASM543497v1_genomic.fna.gz --refList GCF_005434975.1_ASM543497v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005434975.1_ASM543497v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:29,845] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:29,867] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:29,867] [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_005434975.1	s__Parerythrobacter lutipelagi	100.0	1031	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004114695.1	s__Parerythrobacter sp004114695	79.8922	558	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016764075.1	s__Qipengyuania sp016764075	79.2949	322	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001542855.1	s__Qipengyuania sp001542855	79.0761	396	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCF_009827515.1	s__Pelagerythrobacter marinus	78.9551	376	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827395.1	s__Pontixanthobacter aquaemixtae	78.9089	362	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827315.1	s__Qipengyuania gaetbuli	78.8598	374	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018636735.1	s__Alteriqipengyuania sp018636735	78.7408	314	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011765465.1	s__Erythrobacter sp011765465	78.6653	338	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003581645.1	s__Pelagerythrobacter aerophilus	78.5891	338	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	78.3419	343	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763545.1	s__JACXVD01 sp014763545	78.3124	373	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCF_004135625.1	s__Pelagerythrobacter rhizovicinus	78.2772	354	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004965515.1	s__Alteraurantiacibacter aquimixticola	78.2763	265	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828095.1	s__Pontixanthobacter luteolus	78.2626	365	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015999305.1	s__Alteriqipengyuania sp015999305	78.2521	333	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001515985.1	s__Erythrobacter sp001515985	78.2183	258	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687545.1	s__Paraurantiacibacter namhicola	78.158	271	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Paraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828115.1	s__Pseudopontixanthobacter_A sediminis	78.1109	320	1032	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_005434915.1	s__Alteraurantiacibacter suaedae	77.9952	241	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279825.1	s__Croceibacterium sp002279825	77.907	220	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	99.89	99.89	0.97	0.97	2	-
GCF_013370205.1	s__Actirhodobacter atriluteus	77.8844	287	1032	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Actirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:29,871] [INFO] GTDB search result was written to GCF_005434975.1_ASM543497v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:29,872] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:29,876] [INFO] DFAST_QC result json was written to GCF_005434975.1_ASM543497v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:29,877] [INFO] DFAST_QC completed!
[2024-01-24 13:42:29,877] [INFO] Total running time: 0h1m13s