[2024-01-24 11:35:23,600] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:23,606] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:23,606] [INFO] DQC Reference Directory: /var/lib/cwl/stg645071d1-8050-4243-b194-0d58a07d73f8/dqc_reference
[2024-01-24 11:35:26,245] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:26,246] [INFO] Task started: Prodigal
[2024-01-24 11:35:26,246] [INFO] Running command: gunzip -c /var/lib/cwl/stgff7cf0f2-b384-45d8-9be8-0464e498606b/GCF_001281485.1_ASM128148v1_genomic.fna.gz | prodigal -d GCF_001281485.1_ASM128148v1_genomic.fna/cds.fna -a GCF_001281485.1_ASM128148v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:34,871] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:34,871] [INFO] Task started: HMMsearch
[2024-01-24 11:35:34,872] [INFO] Running command: hmmsearch --tblout GCF_001281485.1_ASM128148v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg645071d1-8050-4243-b194-0d58a07d73f8/dqc_reference/reference_markers.hmm GCF_001281485.1_ASM128148v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:35,182] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:35,184] [INFO] Found 6/6 markers.
[2024-01-24 11:35:35,213] [INFO] Query marker FASTA was written to GCF_001281485.1_ASM128148v1_genomic.fna/markers.fasta
[2024-01-24 11:35:35,214] [INFO] Task started: Blastn
[2024-01-24 11:35:35,214] [INFO] Running command: blastn -query GCF_001281485.1_ASM128148v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg645071d1-8050-4243-b194-0d58a07d73f8/dqc_reference/reference_markers.fasta -out GCF_001281485.1_ASM128148v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:36,116] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:36,119] [INFO] Selected 22 target genomes.
[2024-01-24 11:35:36,119] [INFO] Target genome list was writen to GCF_001281485.1_ASM128148v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:36,128] [INFO] Task started: fastANI
[2024-01-24 11:35:36,128] [INFO] Running command: fastANI --query /var/lib/cwl/stgff7cf0f2-b384-45d8-9be8-0464e498606b/GCF_001281485.1_ASM128148v1_genomic.fna.gz --refList GCF_001281485.1_ASM128148v1_genomic.fna/target_genomes.txt --output GCF_001281485.1_ASM128148v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:48,129] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:48,130] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg645071d1-8050-4243-b194-0d58a07d73f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:48,131] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg645071d1-8050-4243-b194-0d58a07d73f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:48,151] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:35:48,152] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:35:48,152] [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
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	80.4367	457	928	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	80.3428	452	928	95	below_threshold
Qipengyuania gaetbuli	strain=DSM 16225	GCA_009827315.1	266952	266952	type	True	79.9877	452	928	95	below_threshold
Qipengyuania xiamenensis	strain=1XM1-15A	GCA_019711495.1	2867237	2867237	type	True	79.9491	433	928	95	below_threshold
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	79.8293	418	928	95	below_threshold
Qipengyuania intermedia	strain=GH38	GCA_019711615.1	2867244	2867244	type	True	79.785	404	928	95	below_threshold
Qipengyuania seohaensis	strain=SW-135	GCA_002795865.1	266951	266951	type	True	79.7747	398	928	95	below_threshold
Qipengyuania xiapuensis	strain=1NDW9	GCA_019711395.1	2867236	2867236	type	True	79.6583	448	928	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	79.5926	439	928	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	79.5083	387	928	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	79.1379	380	928	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	79.0939	389	928	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	79.067	320	928	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	78.9391	403	928	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	78.886	409	928	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	78.8645	378	928	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.8265	379	928	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	78.8236	416	928	95	below_threshold
Alteriqipengyuania lutimaris	strain=S-5	GCA_003363135.1	1538146	1538146	type	True	78.7197	374	928	95	below_threshold
Alteriqipengyuania lutimaris	strain=CECT 8624	GCA_014191645.1	1538146	1538146	type	True	78.6851	366	928	95	below_threshold
Erythrobacter ramosus	strain=JCM 10282	GCA_009828055.1	35811	35811	type	True	78.3251	371	928	95	below_threshold
Erythrobacter ramosus	strain=DSM 8510	GCA_014195675.1	35811	35811	type	True	78.3232	376	928	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:48,153] [INFO] DFAST Taxonomy check result was written to GCF_001281485.1_ASM128148v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:48,154] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:48,154] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:48,155] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg645071d1-8050-4243-b194-0d58a07d73f8/dqc_reference/checkm_data
[2024-01-24 11:35:48,156] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:48,183] [INFO] Task started: CheckM
[2024-01-24 11:35:48,183] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001281485.1_ASM128148v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001281485.1_ASM128148v1_genomic.fna/checkm_input GCF_001281485.1_ASM128148v1_genomic.fna/checkm_result
[2024-01-24 11:36:18,123] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:18,124] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:18,145] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:18,145] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:18,146] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001281485.1_ASM128148v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:18,146] [INFO] Task started: Blastn
[2024-01-24 11:36:18,146] [INFO] Running command: blastn -query GCF_001281485.1_ASM128148v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg645071d1-8050-4243-b194-0d58a07d73f8/dqc_reference/reference_markers_gtdb.fasta -out GCF_001281485.1_ASM128148v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:19,780] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:19,784] [INFO] Selected 21 target genomes.
[2024-01-24 11:36:19,784] [INFO] Target genome list was writen to GCF_001281485.1_ASM128148v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:19,801] [INFO] Task started: fastANI
[2024-01-24 11:36:19,802] [INFO] Running command: fastANI --query /var/lib/cwl/stgff7cf0f2-b384-45d8-9be8-0464e498606b/GCF_001281485.1_ASM128148v1_genomic.fna.gz --refList GCF_001281485.1_ASM128148v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001281485.1_ASM128148v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:31,287] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:31,310] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:31,310] [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_001281485.1	s__Erythrobacter epoxidivorans	100.0	928	928	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900177715.1	s__Erythrobacter xiamenensis	80.1172	522	928	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827315.1	s__Qipengyuania gaetbuli	79.9942	451	928	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	79.9293	425	928	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	97.07	97.03	0.89	0.88	4	-
GCF_000181515.1	s__Qipengyuania sp000181515	79.8942	430	928	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002795865.1	s__Qipengyuania seohaensis	79.7879	397	928	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011047315.1	s__Erythrobacter sp011047315	79.5739	452	928	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827535.1	s__Altererythrobacter_F oceanensis	79.3876	444	928	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altererythrobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018205975.1	s__Erythrobacter sp018205975	79.3868	431	928	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000714765.1	s__Erythrobacter sp000714765	79.1738	404	928	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248395.1	s__Qipengyuania sp003248395	79.1632	310	928	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827295.1	s__Qipengyuania pelagi	79.0939	389	928	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009993605.1	s__Qipengyuania sp009993605	79.0202	355	928	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001165.1	s__Qipengyuania sp013001165	79.0081	356	928	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155685.1	s__Erythrobacter colymbi	78.9279	404	928	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176355.1	s__Alteriqipengyuania bathyomarina	78.8253	378	928	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	98.10	96.53	0.93	0.90	11	-
GCA_011054555.1	s__Erythrobacter sp011054555	78.8112	299	928	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001516125.1	s__Erythrobacter sp001516125	78.7607	292	928	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903934325.1	s__Erythrobacter sp903934325	78.7357	384	928	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_014983025.1	s__Erythrobacter sp014983025	78.4331	307	928	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822125.1	s__Erythrobacter sp013822125	78.357	329	928	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:31,312] [INFO] GTDB search result was written to GCF_001281485.1_ASM128148v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:31,313] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:31,317] [INFO] DFAST_QC result json was written to GCF_001281485.1_ASM128148v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:31,317] [INFO] DFAST_QC completed!
[2024-01-24 11:36:31,317] [INFO] Total running time: 0h1m8s