[2024-01-24 15:09:55,827] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:09:55,831] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:09:55,831] [INFO] DQC Reference Directory: /var/lib/cwl/stg036b1656-bc81-4c75-b231-aa4b5e2ca6f4/dqc_reference
[2024-01-24 15:09:58,159] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:09:58,160] [INFO] Task started: Prodigal
[2024-01-24 15:09:58,160] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f8fbeea-a894-4b8f-9b61-3ba04a4f0c06/GCF_003660445.1_ASM366044v1_genomic.fna.gz | prodigal -d GCF_003660445.1_ASM366044v1_genomic.fna/cds.fna -a GCF_003660445.1_ASM366044v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:09,820] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:09,821] [INFO] Task started: HMMsearch
[2024-01-24 15:10:09,821] [INFO] Running command: hmmsearch --tblout GCF_003660445.1_ASM366044v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg036b1656-bc81-4c75-b231-aa4b5e2ca6f4/dqc_reference/reference_markers.hmm GCF_003660445.1_ASM366044v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:10,157] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:10,158] [INFO] Found 6/6 markers.
[2024-01-24 15:10:10,209] [INFO] Query marker FASTA was written to GCF_003660445.1_ASM366044v1_genomic.fna/markers.fasta
[2024-01-24 15:10:10,210] [INFO] Task started: Blastn
[2024-01-24 15:10:10,210] [INFO] Running command: blastn -query GCF_003660445.1_ASM366044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg036b1656-bc81-4c75-b231-aa4b5e2ca6f4/dqc_reference/reference_markers.fasta -out GCF_003660445.1_ASM366044v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:11,229] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:11,233] [INFO] Selected 22 target genomes.
[2024-01-24 15:10:11,233] [INFO] Target genome list was writen to GCF_003660445.1_ASM366044v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:11,257] [INFO] Task started: fastANI
[2024-01-24 15:10:11,257] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f8fbeea-a894-4b8f-9b61-3ba04a4f0c06/GCF_003660445.1_ASM366044v1_genomic.fna.gz --refList GCF_003660445.1_ASM366044v1_genomic.fna/target_genomes.txt --output GCF_003660445.1_ASM366044v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:26,839] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:26,840] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg036b1656-bc81-4c75-b231-aa4b5e2ca6f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:26,840] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg036b1656-bc81-4c75-b231-aa4b5e2ca6f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:26,857] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:10:26,858] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:26,858] [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
Croceibacterium ferulae	strain=SX2RGS8	GCA_003660445.1	1854641	1854641	type	True	100.0	1183	1184	95	conclusive
Croceibacterium mercuriale	strain=Coronado	GCA_000802385.1	1572751	1572751	type	True	87.5216	861	1184	95	below_threshold
Croceicoccus marinus	strain=E4A9	GCA_001661675.2	450378	450378	type	True	78.8997	402	1184	95	below_threshold
Alteraurantiacibacter aestuarii	strain=JCM 16339	GCA_009827405.1	650004	650004	type	True	78.8316	252	1184	95	below_threshold
Croceibacterium xixiisoli	strain=S36	GCA_009827305.1	1476466	1476466	type	True	78.6308	402	1184	95	below_threshold
Aurantiacibacter luteus	strain=KA37	GCA_001010945.1	1581420	1581420	type	True	78.5217	377	1184	95	below_threshold
Aurantiacibacter odishensis	strain=KCTC 23981	GCA_003605195.1	1155476	1155476	type	True	78.4989	338	1184	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	78.4914	378	1184	95	below_threshold
Croceibacterium atlanticum	strain=26DY36	GCA_001008165.2	1267766	1267766	type	True	78.4349	360	1184	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	78.4168	327	1184	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	78.3701	304	1184	95	below_threshold
Croceibacterium atlanticum	strain=DSM 100738	GCA_014199315.1	1267766	1267766	type	True	78.3656	366	1184	95	below_threshold
Alteriqipengyuania abyssalis	strain=NZ-12B	GCA_019857185.1	2860200	2860200	type	True	78.2671	334	1184	95	below_threshold
Aurantiacibacter suaedae	strain=GH3-15	GCA_005434915.1	2545755	2545755	type	True	78.0841	329	1184	95	below_threshold
Qipengyuania huizhouensis	strain=YG19	GCA_019711635.1	2867245	2867245	type	True	78.0759	211	1184	95	below_threshold
Croceicoccus mobilis	strain=CGMCC 1.15360	GCA_014642595.1	1703339	1703339	type	True	78.0662	336	1184	95	below_threshold
Croceicoccus mobilis	strain=Ery22	GCA_001661965.1	1703339	1703339	type	True	78.0571	341	1184	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	77.988	249	1184	95	below_threshold
Novosphingobium endophyticum	strain=CGMCC 1.15095	GCA_014640675.1	1955250	1955250	type	True	77.9521	296	1184	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	77.7382	279	1184	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	77.266	294	1184	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	77.2073	293	1184	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:26,859] [INFO] DFAST Taxonomy check result was written to GCF_003660445.1_ASM366044v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:26,860] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:26,860] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:26,861] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg036b1656-bc81-4c75-b231-aa4b5e2ca6f4/dqc_reference/checkm_data
[2024-01-24 15:10:26,862] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:26,900] [INFO] Task started: CheckM
[2024-01-24 15:10:26,901] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003660445.1_ASM366044v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003660445.1_ASM366044v1_genomic.fna/checkm_input GCF_003660445.1_ASM366044v1_genomic.fna/checkm_result
[2024-01-24 15:11:04,813] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:04,814] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:04,844] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:04,844] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:04,845] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003660445.1_ASM366044v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:04,845] [INFO] Task started: Blastn
[2024-01-24 15:11:04,845] [INFO] Running command: blastn -query GCF_003660445.1_ASM366044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg036b1656-bc81-4c75-b231-aa4b5e2ca6f4/dqc_reference/reference_markers_gtdb.fasta -out GCF_003660445.1_ASM366044v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:06,743] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:06,746] [INFO] Selected 20 target genomes.
[2024-01-24 15:11:06,747] [INFO] Target genome list was writen to GCF_003660445.1_ASM366044v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:06,761] [INFO] Task started: fastANI
[2024-01-24 15:11:06,761] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f8fbeea-a894-4b8f-9b61-3ba04a4f0c06/GCF_003660445.1_ASM366044v1_genomic.fna.gz --refList GCF_003660445.1_ASM366044v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003660445.1_ASM366044v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:20,390] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:20,406] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:20,407] [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_003660445.1	s__Croceibacterium ferulae	100.0	1183	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000802385.1	s__Croceibacterium mercuriale	87.5243	861	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359685.1	s__Croceibacterium sp014359685	80.6198	319	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569745.1	s__Croceibacterium sp003569745	79.8282	448	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001683845.1	s__Croceibacterium sp001683845	79.62	419	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827655.1	s__Alteraurantiacibacter buctensis	79.0739	422	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001661675.2	s__Croceicoccus marinus	78.9218	400	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceicoccus	95.0	96.65	96.65	0.86	0.86	2	-
GCF_009827305.1	s__Croceibacterium xixiisoli	78.6301	402	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Croceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001010945.1	s__Alteraurantiacibacter luteus	78.5255	376	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	78.4456	350	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744735.1	s__Caenibius sp017744735	78.4351	346	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Caenibius	95.0	99.56	99.56	0.78	0.78	2	-
GCF_003815535.1	s__Alteraurantiacibacter spongiae	78.3975	358	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135625.1	s__Pelagerythrobacter rhizovicinus	78.3889	330	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015999305.1	s__Alteriqipengyuania sp015999305	78.3537	335	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176355.1	s__Alteriqipengyuania bathyomarina	78.1357	326	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	98.10	96.53	0.93	0.90	11	-
GCF_001557325.1	s__Erythrobacter donghaensis_B	78.0365	327	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Erythrobacter	95.0	99.70	99.64	0.86	0.85	7	-
GCA_002712945.1	s__Alteriqipengyuania sp002712945	77.877	163	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteriqipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002341345.1	s__Alteraurantiacibacter sp002341345	77.8746	261	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Alteraurantiacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341505.2	s__Sphingomonas sp004341505	77.7627	307	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.45	95.45	0.78	0.78	2	-
GCF_001421765.1	s__Sphingomonas sp001421765	77.3195	302	1184	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:20,413] [INFO] GTDB search result was written to GCF_003660445.1_ASM366044v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:20,414] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:20,418] [INFO] DFAST_QC result json was written to GCF_003660445.1_ASM366044v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:20,418] [INFO] DFAST_QC completed!
[2024-01-24 15:11:20,418] [INFO] Total running time: 0h1m25s