[2024-01-24 15:18:50,156] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:50,165] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:50,166] [INFO] DQC Reference Directory: /var/lib/cwl/stg08b6026d-10bd-450d-b665-4759a4291669/dqc_reference
[2024-01-24 15:18:51,473] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:51,474] [INFO] Task started: Prodigal
[2024-01-24 15:18:51,475] [INFO] Running command: gunzip -c /var/lib/cwl/stg029a33f9-37f5-4db7-813e-ae63224249a2/GCF_004358425.1_ASM435842v1_genomic.fna.gz | prodigal -d GCF_004358425.1_ASM435842v1_genomic.fna/cds.fna -a GCF_004358425.1_ASM435842v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:58,708] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:58,708] [INFO] Task started: HMMsearch
[2024-01-24 15:18:58,708] [INFO] Running command: hmmsearch --tblout GCF_004358425.1_ASM435842v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08b6026d-10bd-450d-b665-4759a4291669/dqc_reference/reference_markers.hmm GCF_004358425.1_ASM435842v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:58,936] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:58,937] [INFO] Found 6/6 markers.
[2024-01-24 15:18:58,965] [INFO] Query marker FASTA was written to GCF_004358425.1_ASM435842v1_genomic.fna/markers.fasta
[2024-01-24 15:18:58,965] [INFO] Task started: Blastn
[2024-01-24 15:18:58,965] [INFO] Running command: blastn -query GCF_004358425.1_ASM435842v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08b6026d-10bd-450d-b665-4759a4291669/dqc_reference/reference_markers.fasta -out GCF_004358425.1_ASM435842v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:59,967] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:59,978] [INFO] Selected 22 target genomes.
[2024-01-24 15:18:59,979] [INFO] Target genome list was writen to GCF_004358425.1_ASM435842v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:59,987] [INFO] Task started: fastANI
[2024-01-24 15:18:59,988] [INFO] Running command: fastANI --query /var/lib/cwl/stg029a33f9-37f5-4db7-813e-ae63224249a2/GCF_004358425.1_ASM435842v1_genomic.fna.gz --refList GCF_004358425.1_ASM435842v1_genomic.fna/target_genomes.txt --output GCF_004358425.1_ASM435842v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:12,839] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:12,840] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08b6026d-10bd-450d-b665-4759a4291669/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:12,840] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08b6026d-10bd-450d-b665-4759a4291669/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:12,857] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:19:12,858] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:19:12,858] [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
Tsuneonella rigui	strain=KCTC 42620	GCA_003958625.1	1708790	1708790	type	True	79.3908	382	805	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	79.2115	386	805	95	below_threshold
Tsuneonella amylolytica	strain=NS1	GCA_003626915.1	2338327	2338327	type	True	79.1719	397	805	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	79.1062	372	805	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	79.077	368	805	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	78.9702	406	805	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	78.8778	401	805	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	78.8159	358	805	95	below_threshold
Erythrobacter cryptus	strain=DSM 12079	GCA_000422985.1	196588	196588	type	True	78.7964	370	805	95	below_threshold
Alteriqipengyuania lutimaris	strain=S-5	GCA_003363135.1	1538146	1538146	type	True	78.7489	355	805	95	below_threshold
Qipengyuania soli	strain=6D36	GCA_015529805.1	2782568	2782568	type	True	78.7163	345	805	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	78.6844	357	805	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	78.6744	336	805	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	78.6666	419	805	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_001719165.1	39960	39960	type	True	78.6607	337	805	95	below_threshold
Erythrobacter litoralis	strain=DSM 8509	GCA_000714795.1	39960	39960	type	True	78.6589	341	805	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	78.5125	284	805	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	78.4972	324	805	95	below_threshold
Qipengyuania flava	strain=DSM 16421	GCA_011762005.1	192812	192812	type	True	78.4418	365	805	95	below_threshold
Erythrobacter sanguineus	strain=JCM 20691	GCA_002155655.1	198312	198312	type	True	78.2535	315	805	95	below_threshold
Novosphingobium arvoryzae	strain=KCTC 32422	GCA_014652615.1	1256514	1256514	type	True	77.8906	259	805	95	below_threshold
Aurantiacibacter zhengii	strain=V18	GCA_003584125.1	2307003	2307003	type	True	77.7356	241	805	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:12,860] [INFO] DFAST Taxonomy check result was written to GCF_004358425.1_ASM435842v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:12,861] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:12,861] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:12,862] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08b6026d-10bd-450d-b665-4759a4291669/dqc_reference/checkm_data
[2024-01-24 15:19:12,864] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:12,897] [INFO] Task started: CheckM
[2024-01-24 15:19:12,898] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004358425.1_ASM435842v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004358425.1_ASM435842v1_genomic.fna/checkm_input GCF_004358425.1_ASM435842v1_genomic.fna/checkm_result
[2024-01-24 15:19:38,976] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:38,977] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:38,999] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:39,000] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:39,000] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004358425.1_ASM435842v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:39,001] [INFO] Task started: Blastn
[2024-01-24 15:19:39,001] [INFO] Running command: blastn -query GCF_004358425.1_ASM435842v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08b6026d-10bd-450d-b665-4759a4291669/dqc_reference/reference_markers_gtdb.fasta -out GCF_004358425.1_ASM435842v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:40,737] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:40,740] [INFO] Selected 20 target genomes.
[2024-01-24 15:19:40,740] [INFO] Target genome list was writen to GCF_004358425.1_ASM435842v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:40,763] [INFO] Task started: fastANI
[2024-01-24 15:19:40,764] [INFO] Running command: fastANI --query /var/lib/cwl/stg029a33f9-37f5-4db7-813e-ae63224249a2/GCF_004358425.1_ASM435842v1_genomic.fna.gz --refList GCF_004358425.1_ASM435842v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004358425.1_ASM435842v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:51,660] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:51,680] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:51,680] [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_004358425.1	s__Qipengyuania sediminis	100.0	805	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016793865.1	s__Qipengyuania sp016793865	80.9223	501	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003958625.1	s__Tsuneonella rigui	79.404	381	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018828205.1	s__Qipengyuania sp018828205	79.2671	341	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626915.1	s__Tsuneonella amylolytica	79.1718	397	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678665.1	s__Qipengyuania sp001678665	79.1543	391	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135625.1	s__Pelagerythrobacter rhizovicinus	79.1184	371	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003581645.1	s__Pelagerythrobacter aerophilus	79.077	368	805	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	78.9967	397	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011765465.1	s__Erythrobacter sp011765465	78.8991	368	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827515.1	s__Pelagerythrobacter marinus	78.888	400	805	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	78.8595	365	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__QFOP01	95.0	98.23	98.19	0.91	0.89	3	-
GCA_011054555.1	s__Erythrobacter sp011054555	78.72	307	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015529805.1	s__Qipengyuania soli	78.7039	346	805	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	78.6607	337	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_015999305.1	s__Alteriqipengyuania sp015999305	78.6303	354	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002377695.1	s__Alteriqipengyuania sp002377695	78.5546	303	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	99.97	99.97	1.00	1.00	2	-
GCF_000186705.1	s__Alteriqipengyuania sp000186705	78.5483	311	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018205975.1	s__Erythrobacter sp018205975	78.483	345	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828065.1	s__Croceibacterium soli	78.4412	310	805	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:51,682] [INFO] GTDB search result was written to GCF_004358425.1_ASM435842v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:51,683] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:51,690] [INFO] DFAST_QC result json was written to GCF_004358425.1_ASM435842v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:51,691] [INFO] DFAST_QC completed!
[2024-01-24 15:19:51,691] [INFO] Total running time: 0h1m2s