[2024-01-24 13:18:59,766] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:59,768] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:59,769] [INFO] DQC Reference Directory: /var/lib/cwl/stgedd07010-1226-4cae-8b82-76b456448eac/dqc_reference
[2024-01-24 13:19:01,072] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:01,073] [INFO] Task started: Prodigal
[2024-01-24 13:19:01,073] [INFO] Running command: gunzip -c /var/lib/cwl/stg0cb76855-6a00-4900-980e-c5f335e9f5b8/GCF_000152825.2_ASM15282v2_genomic.fna.gz | prodigal -d GCF_000152825.2_ASM15282v2_genomic.fna/cds.fna -a GCF_000152825.2_ASM15282v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:10,127] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:10,127] [INFO] Task started: HMMsearch
[2024-01-24 13:19:10,127] [INFO] Running command: hmmsearch --tblout GCF_000152825.2_ASM15282v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgedd07010-1226-4cae-8b82-76b456448eac/dqc_reference/reference_markers.hmm GCF_000152825.2_ASM15282v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:10,441] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:10,443] [INFO] Found 6/6 markers.
[2024-01-24 13:19:10,471] [INFO] Query marker FASTA was written to GCF_000152825.2_ASM15282v2_genomic.fna/markers.fasta
[2024-01-24 13:19:10,471] [INFO] Task started: Blastn
[2024-01-24 13:19:10,472] [INFO] Running command: blastn -query GCF_000152825.2_ASM15282v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgedd07010-1226-4cae-8b82-76b456448eac/dqc_reference/reference_markers.fasta -out GCF_000152825.2_ASM15282v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:11,311] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:11,314] [INFO] Selected 19 target genomes.
[2024-01-24 13:19:11,315] [INFO] Target genome list was writen to GCF_000152825.2_ASM15282v2_genomic.fna/target_genomes.txt
[2024-01-24 13:19:11,323] [INFO] Task started: fastANI
[2024-01-24 13:19:11,323] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cb76855-6a00-4900-980e-c5f335e9f5b8/GCF_000152825.2_ASM15282v2_genomic.fna.gz --refList GCF_000152825.2_ASM15282v2_genomic.fna/target_genomes.txt --output GCF_000152825.2_ASM15282v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:25,786] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:25,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgedd07010-1226-4cae-8b82-76b456448eac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:25,787] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgedd07010-1226-4cae-8b82-76b456448eac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:25,793] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:25,794] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:25,794] [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
Parvularcula bermudensis	strain=HTCC2503	GCA_000152825.2	208216	208216	type	True	100.0	967	967	95	conclusive
Parvularcula oceani	strain=JLT2013	GCA_000733125.1	1247963	1247963	type	True	78.2699	124	967	95	below_threshold
Marinicaulis flavus	strain=SY-3-19	GCA_002943565.1	2058213	2058213	type	True	77.1177	82	967	95	below_threshold
Parvularcula marina	strain=SM1705	GCA_003399445.1	2292771	2292771	type	True	77.0106	123	967	95	below_threshold
Parvularcula dongshanensis	strain=DSM 102850	GCA_014199615.1	1173995	1173995	type	True	76.6031	69	967	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:25,796] [INFO] DFAST Taxonomy check result was written to GCF_000152825.2_ASM15282v2_genomic.fna/tc_result.tsv
[2024-01-24 13:19:25,796] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:25,797] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:25,797] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgedd07010-1226-4cae-8b82-76b456448eac/dqc_reference/checkm_data
[2024-01-24 13:19:25,798] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:25,846] [INFO] Task started: CheckM
[2024-01-24 13:19:25,846] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000152825.2_ASM15282v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000152825.2_ASM15282v2_genomic.fna/checkm_input GCF_000152825.2_ASM15282v2_genomic.fna/checkm_result
[2024-01-24 13:19:58,125] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:58,126] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:58,141] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:58,141] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:58,142] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000152825.2_ASM15282v2_genomic.fna/markers.fasta)
[2024-01-24 13:19:58,142] [INFO] Task started: Blastn
[2024-01-24 13:19:58,142] [INFO] Running command: blastn -query GCF_000152825.2_ASM15282v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgedd07010-1226-4cae-8b82-76b456448eac/dqc_reference/reference_markers_gtdb.fasta -out GCF_000152825.2_ASM15282v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:59,369] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:59,373] [INFO] Selected 23 target genomes.
[2024-01-24 13:19:59,373] [INFO] Target genome list was writen to GCF_000152825.2_ASM15282v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:59,430] [INFO] Task started: fastANI
[2024-01-24 13:19:59,430] [INFO] Running command: fastANI --query /var/lib/cwl/stg0cb76855-6a00-4900-980e-c5f335e9f5b8/GCF_000152825.2_ASM15282v2_genomic.fna.gz --refList GCF_000152825.2_ASM15282v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000152825.2_ASM15282v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:14,699] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:14,709] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:14,709] [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_000152825.2	s__Parvularcula bermudensis	100.0	967	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000733125.1	s__Parvularcula oceani	78.2699	124	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002943565.1	s__Marinicaulis flavus	77.1527	80	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003399445.1	s__Parvularcula sp003399445	77.0106	123	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199615.1	s__Parvularcula dongshanensis	76.6031	69	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002704915.1	s__Marinicaulis sp002704915	75.8328	52	967	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:14,711] [INFO] GTDB search result was written to GCF_000152825.2_ASM15282v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:14,711] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:14,714] [INFO] DFAST_QC result json was written to GCF_000152825.2_ASM15282v2_genomic.fna/dqc_result.json
[2024-01-24 13:20:14,714] [INFO] DFAST_QC completed!
[2024-01-24 13:20:14,714] [INFO] Total running time: 0h1m15s