[2023-06-17 14:33:06,887] [INFO] DFAST_QC pipeline started.
[2023-06-17 14:33:06,890] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 14:33:06,890] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9448190-65cb-4989-906d-d0c13b866828/dqc_reference
[2023-06-17 14:33:08,104] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 14:33:08,105] [INFO] Task started: Prodigal
[2023-06-17 14:33:08,105] [INFO] Running command: gunzip -c /var/lib/cwl/stg10df5af5-4268-48c5-8bec-403d36f6119e/GCA_905480065.1_3_20180319_Bin_20180319_Bin_175_1_genomic.fna.gz | prodigal -d GCA_905480065.1_3_20180319_Bin_20180319_Bin_175_1_genomic.fna/cds.fna -a GCA_905480065.1_3_20180319_Bin_20180319_Bin_175_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 14:33:13,859] [INFO] Task succeeded: Prodigal
[2023-06-17 14:33:13,859] [INFO] Task started: HMMsearch
[2023-06-17 14:33:13,860] [INFO] Running command: hmmsearch --tblout GCA_905480065.1_3_20180319_Bin_20180319_Bin_175_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9448190-65cb-4989-906d-d0c13b866828/dqc_reference/reference_markers.hmm GCA_905480065.1_3_20180319_Bin_20180319_Bin_175_1_genomic.fna/protein.faa > /dev/null
[2023-06-17 14:33:14,057] [INFO] Task succeeded: HMMsearch
[2023-06-17 14:33:14,058] [INFO] Found 6/6 markers.
[2023-06-17 14:33:14,085] [INFO] Query marker FASTA was written to GCA_905480065.1_3_20180319_Bin_20180319_Bin_175_1_genomic.fna/markers.fasta
[2023-06-17 14:33:14,086] [INFO] Task started: Blastn
[2023-06-17 14:33:14,086] [INFO] Running command: blastn -query GCA_905480065.1_3_20180319_Bin_20180319_Bin_175_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9448190-65cb-4989-906d-d0c13b866828/dqc_reference/reference_markers.fasta -out GCA_905480065.1_3_20180319_Bin_20180319_Bin_175_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:33:14,913] [INFO] Task succeeded: Blastn
[2023-06-17 14:33:14,919] [INFO] Selected 36 target genomes.
[2023-06-17 14:33:14,919] [INFO] Target genome list was writen to GCA_905480065.1_3_20180319_Bin_20180319_Bin_175_1_genomic.fna/target_genomes.txt
[2023-06-17 14:33:14,924] [INFO] Task started: fastANI
[2023-06-17 14:33:14,924] [INFO] Running command: fastANI --query /var/lib/cwl/stg10df5af5-4268-48c5-8bec-403d36f6119e/GCA_905480065.1_3_20180319_Bin_20180319_Bin_175_1_genomic.fna.gz --refList GCA_905480065.1_3_20180319_Bin_20180319_Bin_175_1_genomic.fna/target_genomes.txt --output GCA_905480065.1_3_20180319_Bin_20180319_Bin_175_1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 14:33:34,420] [INFO] Task succeeded: fastANI
[2023-06-17 14:33:34,421] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9448190-65cb-4989-906d-d0c13b866828/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 14:33:34,422] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9448190-65cb-4989-906d-d0c13b866828/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 14:33:34,435] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 14:33:34,435] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 14:33:34,435] [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
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.8427	115	606	95	below_threshold
Acidihalobacter prosperus	strain=DSM 5130	GCA_000754095.2	160660	160660	type	True	76.6582	54	606	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.6196	91	606	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	76.3272	81	606	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	76.2633	58	606	95	below_threshold
Thiogranum longum	strain=DSM 19610	GCA_004339085.1	1537524	1537524	type	True	76.2255	69	606	95	below_threshold
Thioalkalivibrio thiocyanoxidans	strain=ARh2	GCA_000385215.1	152475	152475	type	True	75.9879	51	606	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	75.8292	56	606	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	75.7992	60	606	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	75.6387	51	606	95	below_threshold
Plasticicumulans acidivorans	strain=DSM 23606	GCA_003182095.1	886464	886464	type	True	75.45	54	606	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 14:33:34,437] [INFO] DFAST Taxonomy check result was written to GCA_905480065.1_3_20180319_Bin_20180319_Bin_175_1_genomic.fna/tc_result.tsv
[2023-06-17 14:33:34,438] [INFO] ===== Taxonomy check completed =====
[2023-06-17 14:33:34,438] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 14:33:34,438] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9448190-65cb-4989-906d-d0c13b866828/dqc_reference/checkm_data
[2023-06-17 14:33:34,439] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 14:33:34,462] [INFO] Task started: CheckM
[2023-06-17 14:33:34,462] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905480065.1_3_20180319_Bin_20180319_Bin_175_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905480065.1_3_20180319_Bin_20180319_Bin_175_1_genomic.fna/checkm_input GCA_905480065.1_3_20180319_Bin_20180319_Bin_175_1_genomic.fna/checkm_result
[2023-06-17 14:33:57,699] [INFO] Task succeeded: CheckM
[2023-06-17 14:33:57,701] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 14:33:57,722] [INFO] ===== Completeness check finished =====
[2023-06-17 14:33:57,723] [INFO] ===== Start GTDB Search =====
[2023-06-17 14:33:57,723] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905480065.1_3_20180319_Bin_20180319_Bin_175_1_genomic.fna/markers.fasta)
[2023-06-17 14:33:57,723] [INFO] Task started: Blastn
[2023-06-17 14:33:57,724] [INFO] Running command: blastn -query GCA_905480065.1_3_20180319_Bin_20180319_Bin_175_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9448190-65cb-4989-906d-d0c13b866828/dqc_reference/reference_markers_gtdb.fasta -out GCA_905480065.1_3_20180319_Bin_20180319_Bin_175_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 14:33:59,122] [INFO] Task succeeded: Blastn
[2023-06-17 14:33:59,127] [INFO] Selected 23 target genomes.
[2023-06-17 14:33:59,128] [INFO] Target genome list was writen to GCA_905480065.1_3_20180319_Bin_20180319_Bin_175_1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 14:33:59,137] [INFO] Task started: fastANI
[2023-06-17 14:33:59,138] [INFO] Running command: fastANI --query /var/lib/cwl/stg10df5af5-4268-48c5-8bec-403d36f6119e/GCA_905480065.1_3_20180319_Bin_20180319_Bin_175_1_genomic.fna.gz --refList GCA_905480065.1_3_20180319_Bin_20180319_Bin_175_1_genomic.fna/target_genomes_gtdb.txt --output GCA_905480065.1_3_20180319_Bin_20180319_Bin_175_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 14:34:10,387] [INFO] Task succeeded: fastANI
[2023-06-17 14:34:10,401] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 14:34:10,401] [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
GCA_905480065.1	s__UBA9214 sp905480065	100.0	595	606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA9214;f__UBA9214;g__UBA9214	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013041945.1	s__UBA9214 sp013041945	77.9444	172	606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA9214;f__UBA9214;g__UBA9214	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479705.1	s__UBA9214 sp905479705	77.7138	154	606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA9214;f__UBA9214;g__UBA9214	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003230545.1	s__SZUA-186 sp003230545	77.0423	132	606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA9214;f__UBA9214;g__SZUA-186	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011321775.1	s__Thiogranum sp011321775	76.9966	103	606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494295.1	s__Thiogranum sp015494295	76.9865	123	606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	99.47	99.47	0.86	0.86	2	-
GCF_003932505.1	s__Thiohalobacter thiocyanaticus	76.8852	113	606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002356355.1	s__Thiohalobacter thiocyanaticus_A	76.8006	124	606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	98.53	98.53	0.93	0.93	2	-
GCA_016214925.1	s__JAHJQQ01 sp016214925	76.7074	70	606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JAHJQQ01;f__JAHJQQ01;g__JAHJQQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000754095.2	s__Acidihalobacter prosperus	76.6582	54	606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Acidihalobacteraceae;g__Acidihalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762505.1	s__SpSt-1174 sp014762505	76.6337	83	606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003454335.1	s__UBA9214 sp003454335	76.3521	90	606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA9214;f__UBA9214;g__UBA9214	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218375.1	s__JAHJQQ01 sp016218375	76.264	82	606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JAHJQQ01;f__JAHJQQ01;g__JAHJQQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011371455.1	s__DRQN01 sp011371455	76.2423	50	606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SZUA-152;f__SZUA-152;g__DRQN01	95.0	97.38	97.35	0.90	0.88	5	-
GCF_004339085.1	s__Thiogranum longum	76.2255	69	606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-19610;f__DSM-19610;g__Thiogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005240065.1	s__Ga0077554 sp005240065	76.196	57	606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ga0077554;f__Ga007554;g__Ga0077554	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125505.1	s__RI-92 sp016125505	75.8686	50	606	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__UBA6429;f__UBA6429;g__RI-92	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 14:34:10,404] [INFO] GTDB search result was written to GCA_905480065.1_3_20180319_Bin_20180319_Bin_175_1_genomic.fna/result_gtdb.tsv
[2023-06-17 14:34:10,404] [INFO] ===== GTDB Search completed =====
[2023-06-17 14:34:10,408] [INFO] DFAST_QC result json was written to GCA_905480065.1_3_20180319_Bin_20180319_Bin_175_1_genomic.fna/dqc_result.json
[2023-06-17 14:34:10,408] [INFO] DFAST_QC completed!
[2023-06-17 14:34:10,408] [INFO] Total running time: 0h1m4s