[2024-01-24 13:12:36,707] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:36,709] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:36,709] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f84b060-94b6-4e0f-b6d4-92000af1b532/dqc_reference
[2024-01-24 13:12:37,938] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:37,939] [INFO] Task started: Prodigal
[2024-01-24 13:12:37,940] [INFO] Running command: gunzip -c /var/lib/cwl/stgc879578a-2b35-4cd5-a197-a12f2065b9de/GCF_003403095.1_ASM340309v1_genomic.fna.gz | prodigal -d GCF_003403095.1_ASM340309v1_genomic.fna/cds.fna -a GCF_003403095.1_ASM340309v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:53,806] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:53,807] [INFO] Task started: HMMsearch
[2024-01-24 13:12:53,807] [INFO] Running command: hmmsearch --tblout GCF_003403095.1_ASM340309v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f84b060-94b6-4e0f-b6d4-92000af1b532/dqc_reference/reference_markers.hmm GCF_003403095.1_ASM340309v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:54,216] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:54,217] [INFO] Found 6/6 markers.
[2024-01-24 13:12:54,267] [INFO] Query marker FASTA was written to GCF_003403095.1_ASM340309v1_genomic.fna/markers.fasta
[2024-01-24 13:12:54,267] [INFO] Task started: Blastn
[2024-01-24 13:12:54,268] [INFO] Running command: blastn -query GCF_003403095.1_ASM340309v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f84b060-94b6-4e0f-b6d4-92000af1b532/dqc_reference/reference_markers.fasta -out GCF_003403095.1_ASM340309v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:55,103] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:55,106] [INFO] Selected 11 target genomes.
[2024-01-24 13:12:55,106] [INFO] Target genome list was writen to GCF_003403095.1_ASM340309v1_genomic.fna/target_genomes.txt
[2024-01-24 13:12:55,114] [INFO] Task started: fastANI
[2024-01-24 13:12:55,115] [INFO] Running command: fastANI --query /var/lib/cwl/stgc879578a-2b35-4cd5-a197-a12f2065b9de/GCF_003403095.1_ASM340309v1_genomic.fna.gz --refList GCF_003403095.1_ASM340309v1_genomic.fna/target_genomes.txt --output GCF_003403095.1_ASM340309v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:05,088] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:05,089] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f84b060-94b6-4e0f-b6d4-92000af1b532/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:05,089] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f84b060-94b6-4e0f-b6d4-92000af1b532/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:05,100] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:05,100] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:05,101] [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
Thalassospira indica	strain=PB8BT	GCA_003403095.1	1891279	1891279	type	True	100.0	1564	1567	95	conclusive
Thalassospira tepidiphila	strain=DSM 18888	GCA_011927685.1	393657	393657	type	True	94.5923	1351	1567	95	below_threshold
Thalassospira tepidiphila	strain=MCCC 1A03514	GCA_001662875.1	393657	393657	type	True	94.5887	1339	1567	95	below_threshold
Thalassospira profundimaris	strain=WP0211	GCA_000300275.1	502049	502049	suspected-type	True	94.462	1304	1567	95	below_threshold
Thalassospira australica	strain=NP 3b2	GCA_000763295.1	1528106	1528106	type	True	84.8219	1068	1567	95	below_threshold
Thalassospira povalilytica	strain=Zumi 95	GCA_002844235.1	732237	732237	type	True	83.8905	1097	1567	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:05,103] [INFO] DFAST Taxonomy check result was written to GCF_003403095.1_ASM340309v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:05,103] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:05,104] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:05,104] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f84b060-94b6-4e0f-b6d4-92000af1b532/dqc_reference/checkm_data
[2024-01-24 13:13:05,106] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:05,154] [INFO] Task started: CheckM
[2024-01-24 13:13:05,154] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003403095.1_ASM340309v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003403095.1_ASM340309v1_genomic.fna/checkm_input GCF_003403095.1_ASM340309v1_genomic.fna/checkm_result
[2024-01-24 13:13:54,552] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:54,553] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:54,574] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:54,575] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:54,575] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003403095.1_ASM340309v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:54,576] [INFO] Task started: Blastn
[2024-01-24 13:13:54,576] [INFO] Running command: blastn -query GCF_003403095.1_ASM340309v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f84b060-94b6-4e0f-b6d4-92000af1b532/dqc_reference/reference_markers_gtdb.fasta -out GCF_003403095.1_ASM340309v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:56,000] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:56,003] [INFO] Selected 7 target genomes.
[2024-01-24 13:13:56,003] [INFO] Target genome list was writen to GCF_003403095.1_ASM340309v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:56,013] [INFO] Task started: fastANI
[2024-01-24 13:13:56,014] [INFO] Running command: fastANI --query /var/lib/cwl/stgc879578a-2b35-4cd5-a197-a12f2065b9de/GCF_003403095.1_ASM340309v1_genomic.fna.gz --refList GCF_003403095.1_ASM340309v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003403095.1_ASM340309v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:03,745] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:03,758] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:03,759] [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_003403095.1	s__Thalassospira indica	100.0	1565	1567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_017922435.1	s__Thalassospira sp017922435	94.5938	1342	1567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.2246	N/A	N/A	N/A	N/A	1	-
GCF_001662875.1	s__Thalassospira tepidiphila	94.5887	1339	1567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.4963	96.58	95.57	0.94	0.88	15	-
GCF_000300275.1	s__Thalassospira profundimaris	94.4635	1304	1567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.4963	N/A	N/A	N/A	N/A	1	-
GCF_011806525.1	s__Thalassospira sp011806525	87.9708	1225	1567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000948415.1	s__Thalassospira sp000948415	87.9645	1207	1567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709775.1	s__Thalassospira sp002709775	87.7948	1137	1567	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:03,763] [INFO] GTDB search result was written to GCF_003403095.1_ASM340309v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:03,764] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:03,767] [INFO] DFAST_QC result json was written to GCF_003403095.1_ASM340309v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:03,767] [INFO] DFAST_QC completed!
[2024-01-24 13:14:03,767] [INFO] Total running time: 0h1m27s