[2024-01-24 11:34:43,198] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:43,204] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:43,205] [INFO] DQC Reference Directory: /var/lib/cwl/stge910cdd7-5030-4b81-91e2-d4de08c44563/dqc_reference
[2024-01-24 11:34:44,635] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:44,636] [INFO] Task started: Prodigal
[2024-01-24 11:34:44,636] [INFO] Running command: gunzip -c /var/lib/cwl/stgceed0b8b-642d-40d1-884e-b6d7a76341c3/GCF_000982415.1_ASM98241v1_genomic.fna.gz | prodigal -d GCF_000982415.1_ASM98241v1_genomic.fna/cds.fna -a GCF_000982415.1_ASM98241v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:55,783] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:55,783] [INFO] Task started: HMMsearch
[2024-01-24 11:34:55,783] [INFO] Running command: hmmsearch --tblout GCF_000982415.1_ASM98241v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge910cdd7-5030-4b81-91e2-d4de08c44563/dqc_reference/reference_markers.hmm GCF_000982415.1_ASM98241v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:56,110] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:56,111] [INFO] Found 6/6 markers.
[2024-01-24 11:34:56,147] [INFO] Query marker FASTA was written to GCF_000982415.1_ASM98241v1_genomic.fna/markers.fasta
[2024-01-24 11:34:56,147] [INFO] Task started: Blastn
[2024-01-24 11:34:56,147] [INFO] Running command: blastn -query GCF_000982415.1_ASM98241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge910cdd7-5030-4b81-91e2-d4de08c44563/dqc_reference/reference_markers.fasta -out GCF_000982415.1_ASM98241v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:56,714] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:56,716] [INFO] Selected 16 target genomes.
[2024-01-24 11:34:56,717] [INFO] Target genome list was writen to GCF_000982415.1_ASM98241v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:56,753] [INFO] Task started: fastANI
[2024-01-24 11:34:56,753] [INFO] Running command: fastANI --query /var/lib/cwl/stgceed0b8b-642d-40d1-884e-b6d7a76341c3/GCF_000982415.1_ASM98241v1_genomic.fna.gz --refList GCF_000982415.1_ASM98241v1_genomic.fna/target_genomes.txt --output GCF_000982415.1_ASM98241v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:08,376] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:08,376] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge910cdd7-5030-4b81-91e2-d4de08c44563/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:08,377] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge910cdd7-5030-4b81-91e2-d4de08c44563/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:08,382] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:08,383] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:08,383] [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
Kiloniella litopenaei	strain=P1-1	GCA_000982415.1	1549748	1549748	type	True	100.0	1403	1405	95	conclusive
Kiloniella majae	strain=M56.1	GCA_002118315.1	1938558	1938558	type	True	83.4078	1039	1405	95	below_threshold
Kiloniella spongiae	strain=MEBiC09566	GCA_001026905.1	1489064	1489064	type	True	83.2434	996	1405	95	below_threshold
Kiloniella laminariae	strain=DSM 19542	GCA_000374005.1	454162	454162	type	True	77.4669	260	1405	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:08,384] [INFO] DFAST Taxonomy check result was written to GCF_000982415.1_ASM98241v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:08,385] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:08,385] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:08,385] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge910cdd7-5030-4b81-91e2-d4de08c44563/dqc_reference/checkm_data
[2024-01-24 11:35:08,387] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:08,432] [INFO] Task started: CheckM
[2024-01-24 11:35:08,432] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000982415.1_ASM98241v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000982415.1_ASM98241v1_genomic.fna/checkm_input GCF_000982415.1_ASM98241v1_genomic.fna/checkm_result
[2024-01-24 11:35:46,904] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:46,909] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:46,928] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:46,928] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:46,929] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000982415.1_ASM98241v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:46,929] [INFO] Task started: Blastn
[2024-01-24 11:35:46,929] [INFO] Running command: blastn -query GCF_000982415.1_ASM98241v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge910cdd7-5030-4b81-91e2-d4de08c44563/dqc_reference/reference_markers_gtdb.fasta -out GCF_000982415.1_ASM98241v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:47,739] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:47,741] [INFO] Selected 9 target genomes.
[2024-01-24 11:35:47,742] [INFO] Target genome list was writen to GCF_000982415.1_ASM98241v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:47,773] [INFO] Task started: fastANI
[2024-01-24 11:35:47,774] [INFO] Running command: fastANI --query /var/lib/cwl/stgceed0b8b-642d-40d1-884e-b6d7a76341c3/GCF_000982415.1_ASM98241v1_genomic.fna.gz --refList GCF_000982415.1_ASM98241v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000982415.1_ASM98241v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:54,490] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:54,500] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:35:54,500] [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_000982415.1	s__Kiloniella litopenaei	100.0	1403	1405	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Kiloniella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900313065.1	s__Kiloniella sp900313065	84.1139	978	1405	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Kiloniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002118315.1	s__Kiloniella majae	83.4124	1038	1405	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Kiloniella	95.0	97.24	97.23	0.93	0.92	3	-
GCF_001026905.1	s__Kiloniella spongiae	83.25	995	1405	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Kiloniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162915.1	s__Kiloniella sp002162915	79.4262	173	1405	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Kiloniella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:35:54,502] [INFO] GTDB search result was written to GCF_000982415.1_ASM98241v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:54,503] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:54,505] [INFO] DFAST_QC result json was written to GCF_000982415.1_ASM98241v1_genomic.fna/dqc_result.json
[2024-01-24 11:35:54,505] [INFO] DFAST_QC completed!
[2024-01-24 11:35:54,505] [INFO] Total running time: 0h1m11s