[2024-01-24 13:49:40,843] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:40,845] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:40,845] [INFO] DQC Reference Directory: /var/lib/cwl/stge3e17957-81e0-454e-a103-78dc74be1a35/dqc_reference
[2024-01-24 13:49:42,110] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:42,111] [INFO] Task started: Prodigal
[2024-01-24 13:49:42,111] [INFO] Running command: gunzip -c /var/lib/cwl/stg432bbb4b-5259-44cf-935d-5e15e41de1b5/GCF_013336795.1_ASM1333679v1_genomic.fna.gz | prodigal -d GCF_013336795.1_ASM1333679v1_genomic.fna/cds.fna -a GCF_013336795.1_ASM1333679v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:51,251] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:51,252] [INFO] Task started: HMMsearch
[2024-01-24 13:49:51,252] [INFO] Running command: hmmsearch --tblout GCF_013336795.1_ASM1333679v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3e17957-81e0-454e-a103-78dc74be1a35/dqc_reference/reference_markers.hmm GCF_013336795.1_ASM1333679v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:51,530] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:51,532] [INFO] Found 6/6 markers.
[2024-01-24 13:49:51,570] [INFO] Query marker FASTA was written to GCF_013336795.1_ASM1333679v1_genomic.fna/markers.fasta
[2024-01-24 13:49:51,570] [INFO] Task started: Blastn
[2024-01-24 13:49:51,571] [INFO] Running command: blastn -query GCF_013336795.1_ASM1333679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3e17957-81e0-454e-a103-78dc74be1a35/dqc_reference/reference_markers.fasta -out GCF_013336795.1_ASM1333679v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:52,402] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:52,406] [INFO] Selected 28 target genomes.
[2024-01-24 13:49:52,406] [INFO] Target genome list was writen to GCF_013336795.1_ASM1333679v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:52,441] [INFO] Task started: fastANI
[2024-01-24 13:49:52,443] [INFO] Running command: fastANI --query /var/lib/cwl/stg432bbb4b-5259-44cf-935d-5e15e41de1b5/GCF_013336795.1_ASM1333679v1_genomic.fna.gz --refList GCF_013336795.1_ASM1333679v1_genomic.fna/target_genomes.txt --output GCF_013336795.1_ASM1333679v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:08,421] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:08,422] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3e17957-81e0-454e-a103-78dc74be1a35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:08,422] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3e17957-81e0-454e-a103-78dc74be1a35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:08,442] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:50:08,442] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:50:08,442] [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 pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	78.4296	313	933	95	below_threshold
Allopontixanthobacter sediminis	strain=KCTC 42453	GCA_009828115.1	1689985	1689985	type	True	78.1711	285	933	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	78.0999	239	933	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	78.088	256	933	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	78.0873	292	933	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	78.0839	343	933	95	below_threshold
Qipengyuania aurantiaca	strain=1NDH13	GCA_019711375.1	2867233	2867233	type	True	78.0394	299	933	95	below_threshold
Alteriqipengyuania lutimaris	strain=S-5	GCA_003363135.1	1538146	1538146	type	True	77.9913	274	933	95	below_threshold
Qipengyuania seohaensis	strain=SW-135	GCA_002795865.1	266951	266951	type	True	77.9867	265	933	95	below_threshold
Croceicoccus hydrothermalis	strain=JLT1	GCA_022378335.1	2867964	2867964	type	True	77.977	246	933	95	below_threshold
Pelagerythrobacter marensis	strain=DSM 21428	GCA_001461885.1	543877	543877	type	True	77.9738	271	933	95	below_threshold
Alteriqipengyuania lutimaris	strain=CECT 8624	GCA_014191645.1	1538146	1538146	type	True	77.9683	275	933	95	below_threshold
Qipengyuania algicida	strain=KEMB 9005-328	GCA_009828025.1	1836209	1836209	type	True	77.957	238	933	95	below_threshold
Pelagerythrobacter marensis	strain=KCTC 22370	GCA_001028625.1	543877	543877	type	True	77.9285	272	933	95	below_threshold
Qipengyuania vesicularis	strain=1NDH10	GCA_019711415.1	2867232	2867232	type	True	77.8914	263	933	95	below_threshold
Tsuneonella amylolytica	strain=NS1	GCA_003626915.1	2338327	2338327	type	True	77.8779	293	933	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	77.8237	293	933	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	77.7829	277	933	95	below_threshold
Allopontixanthobacter confluentis	strain=KCTC 52259	GCA_009827615.1	1849021	1849021	type	True	77.7729	271	933	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	77.772	307	933	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	77.754	257	933	95	below_threshold
Croceicoccus bisphenolivorans	strain=H4	GCA_001634625.1	1783232	1783232	type	True	77.742	237	933	95	below_threshold
Croceibacterium mercuriale	strain=Coronado	GCA_000802385.1	1572751	1572751	type	True	77.7262	250	933	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	77.6506	320	933	95	below_threshold
Pontixanthobacter luteolus	strain=SW-109	GCA_009828095.1	295089	295089	type	True	77.5603	255	933	95	below_threshold
Croceicoccus sediminis	strain=S2-4-2	GCA_007570835.1	2571150	2571150	type	True	77.5277	221	933	95	below_threshold
Novosphingobium marinum	strain=CGMCC 1.12918	GCA_014640055.1	1514948	1514948	type	True	77.2492	235	933	95	below_threshold
Novosphingobium decolorationis	strain=502str22	GCA_018417475.1	2698673	2698673	type	True	77.0954	195	933	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:08,444] [INFO] DFAST Taxonomy check result was written to GCF_013336795.1_ASM1333679v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:08,445] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:08,445] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:08,446] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3e17957-81e0-454e-a103-78dc74be1a35/dqc_reference/checkm_data
[2024-01-24 13:50:08,447] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:08,481] [INFO] Task started: CheckM
[2024-01-24 13:50:08,481] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013336795.1_ASM1333679v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013336795.1_ASM1333679v1_genomic.fna/checkm_input GCF_013336795.1_ASM1333679v1_genomic.fna/checkm_result
[2024-01-24 13:50:37,235] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:37,237] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:37,254] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:37,254] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:37,255] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013336795.1_ASM1333679v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:37,255] [INFO] Task started: Blastn
[2024-01-24 13:50:37,255] [INFO] Running command: blastn -query GCF_013336795.1_ASM1333679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3e17957-81e0-454e-a103-78dc74be1a35/dqc_reference/reference_markers_gtdb.fasta -out GCF_013336795.1_ASM1333679v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:38,395] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:38,399] [INFO] Selected 22 target genomes.
[2024-01-24 13:50:38,399] [INFO] Target genome list was writen to GCF_013336795.1_ASM1333679v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:38,435] [INFO] Task started: fastANI
[2024-01-24 13:50:38,435] [INFO] Running command: fastANI --query /var/lib/cwl/stg432bbb4b-5259-44cf-935d-5e15e41de1b5/GCF_013336795.1_ASM1333679v1_genomic.fna.gz --refList GCF_013336795.1_ASM1333679v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013336795.1_ASM1333679v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:50,941] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:50,962] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:50,963] [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_013336795.1	s__Pseudopontixanthobacter muriae	100.0	932	933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012979275.1	s__Pseudopontixanthobacter vadosimaris	85.1248	648	933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pseudopontixanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018636735.1	s__Alteriqipengyuania sp018636735	78.4182	285	933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004114695.1	s__Parerythrobacter sp004114695	78.3237	319	933	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	78.1565	288	933	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	78.1332	315	933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCF_015999305.1	s__Alteriqipengyuania sp015999305	78.1117	296	933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827515.1	s__Pelagerythrobacter marinus	78.0607	346	933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678665.1	s__Qipengyuania sp001678665	78.0315	330	933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186705.1	s__Alteriqipengyuania sp000186705	78.0092	287	933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013005.1	s__Altererythrobacter_D litoralis_A	77.9324	295	933	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_005884405.1	s__Qipengyuania marisflavi	77.9296	269	933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	77.8958	301	933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827615.1	s__Pseudopontixanthobacter_A confluentis	77.7729	271	933	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_015529805.1	s__Qipengyuania soli	77.7646	257	933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729695.1	s__Alteriqipengyuania sp002729695	77.6305	255	933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.53	99.11	0.93	0.90	4	-
GCA_017302615.1	s__Novosphingobium sp017302615	77.597	223	933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007570835.1	s__Croceicoccus sediminis	77.5258	222	933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002556635.1	s__Novosphingobium sp002556635	77.3821	249	933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004211435.1	s__Novosphingobium sp004211435	77.2074	203	933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018417475.1	s__Novosphingobium sp000813185	77.0954	195	933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	97.53	97.53	0.86	0.86	2	-
GCA_004282995.1	s__Altererythrobacter_D sp004282995	77.0769	154	933	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Altererythrobacter_D	95.0	99.06	99.06	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:50,964] [INFO] GTDB search result was written to GCF_013336795.1_ASM1333679v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:50,965] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:50,970] [INFO] DFAST_QC result json was written to GCF_013336795.1_ASM1333679v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:50,970] [INFO] DFAST_QC completed!
[2024-01-24 13:50:50,970] [INFO] Total running time: 0h1m10s