[2024-01-24 12:00:36,711] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:00:36,713] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:00:36,713] [INFO] DQC Reference Directory: /var/lib/cwl/stga6385e97-2e84-477f-b270-a98c2946931e/dqc_reference
[2024-01-24 12:00:39,380] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:00:39,381] [INFO] Task started: Prodigal
[2024-01-24 12:00:39,381] [INFO] Running command: gunzip -c /var/lib/cwl/stg55329a8e-8150-4c31-941b-7a85909e331f/GCF_003987135.1_ASM398713v1_genomic.fna.gz | prodigal -d GCF_003987135.1_ASM398713v1_genomic.fna/cds.fna -a GCF_003987135.1_ASM398713v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:00:46,074] [INFO] Task succeeded: Prodigal
[2024-01-24 12:00:46,075] [INFO] Task started: HMMsearch
[2024-01-24 12:00:46,075] [INFO] Running command: hmmsearch --tblout GCF_003987135.1_ASM398713v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6385e97-2e84-477f-b270-a98c2946931e/dqc_reference/reference_markers.hmm GCF_003987135.1_ASM398713v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:00:46,333] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:00:46,334] [INFO] Found 6/6 markers.
[2024-01-24 12:00:46,362] [INFO] Query marker FASTA was written to GCF_003987135.1_ASM398713v1_genomic.fna/markers.fasta
[2024-01-24 12:00:46,363] [INFO] Task started: Blastn
[2024-01-24 12:00:46,363] [INFO] Running command: blastn -query GCF_003987135.1_ASM398713v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6385e97-2e84-477f-b270-a98c2946931e/dqc_reference/reference_markers.fasta -out GCF_003987135.1_ASM398713v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:47,068] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:47,073] [INFO] Selected 21 target genomes.
[2024-01-24 12:00:47,073] [INFO] Target genome list was writen to GCF_003987135.1_ASM398713v1_genomic.fna/target_genomes.txt
[2024-01-24 12:00:47,103] [INFO] Task started: fastANI
[2024-01-24 12:00:47,103] [INFO] Running command: fastANI --query /var/lib/cwl/stg55329a8e-8150-4c31-941b-7a85909e331f/GCF_003987135.1_ASM398713v1_genomic.fna.gz --refList GCF_003987135.1_ASM398713v1_genomic.fna/target_genomes.txt --output GCF_003987135.1_ASM398713v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:58,958] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:58,959] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6385e97-2e84-477f-b270-a98c2946931e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:58,960] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6385e97-2e84-477f-b270-a98c2946931e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:58,972] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:00:58,972] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:00:58,972] [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
Aliidiomarina iranensis	strain=GBPy7	GCA_003987135.1	1434071	1434071	type	True	100.0	864	866	95	conclusive
Aliidiomarina shirensis	strain=AIS	GCA_003987345.1	1048642	1048642	type	True	81.4614	527	866	95	below_threshold
Aliidiomarina haloalkalitolerans	strain=AK5	GCA_003987315.1	859059	859059	type	True	78.4423	140	866	95	below_threshold
Aliidiomarina indica	strain=SW123	GCA_015354615.1	2749147	2749147	type	True	78.1755	153	866	95	below_threshold
Aliidiomarina halalkaliphila	strain=IM 1326	GCA_007096385.1	2593535	2593535	type	True	78.1481	134	866	95	below_threshold
Pseudidiomarina tainanensis	strain=PIN1	GCA_004214835.1	502365	502365	type	True	77.9071	59	866	95	below_threshold
Pseudidiomarina marina	strain=PIM1	GCA_003987045.1	502366	502366	type	True	77.3719	64	866	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:58,974] [INFO] DFAST Taxonomy check result was written to GCF_003987135.1_ASM398713v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:58,974] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:58,975] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:58,975] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6385e97-2e84-477f-b270-a98c2946931e/dqc_reference/checkm_data
[2024-01-24 12:00:58,976] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:59,007] [INFO] Task started: CheckM
[2024-01-24 12:00:59,007] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003987135.1_ASM398713v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003987135.1_ASM398713v1_genomic.fna/checkm_input GCF_003987135.1_ASM398713v1_genomic.fna/checkm_result
[2024-01-24 12:01:24,457] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:24,459] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:24,481] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:24,481] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:24,482] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003987135.1_ASM398713v1_genomic.fna/markers.fasta)
[2024-01-24 12:01:24,482] [INFO] Task started: Blastn
[2024-01-24 12:01:24,483] [INFO] Running command: blastn -query GCF_003987135.1_ASM398713v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6385e97-2e84-477f-b270-a98c2946931e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003987135.1_ASM398713v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:25,564] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:25,567] [INFO] Selected 15 target genomes.
[2024-01-24 12:01:25,567] [INFO] Target genome list was writen to GCF_003987135.1_ASM398713v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:25,579] [INFO] Task started: fastANI
[2024-01-24 12:01:25,580] [INFO] Running command: fastANI --query /var/lib/cwl/stg55329a8e-8150-4c31-941b-7a85909e331f/GCF_003987135.1_ASM398713v1_genomic.fna.gz --refList GCF_003987135.1_ASM398713v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003987135.1_ASM398713v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:01:33,549] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:33,561] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:01:33,561] [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_003987135.1	s__Aliidiomarina iranensis	100.0	864	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003987345.1	s__Aliidiomarina shirensis	81.4776	525	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	99.30	99.30	0.95	0.95	2	-
GCF_000218785.1	s__Aliidiomarina sp000218785	81.1529	485	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015354615.1	s__Aliidiomarina sp015354615	78.1643	152	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007096385.1	s__Aliidiomarina sp007096385	78.1481	134	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004214835.1	s__Pseudidiomarina tainanensis	77.9071	59	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	97.72	97.72	0.94	0.94	2	-
GCA_018222985.1	s__Pseudidiomarina sp018222985	77.9061	61	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003987215.1	s__Pseudidiomarina halophila	77.8534	54	866	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudidiomarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:01:33,563] [INFO] GTDB search result was written to GCF_003987135.1_ASM398713v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:01:33,564] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:01:33,566] [INFO] DFAST_QC result json was written to GCF_003987135.1_ASM398713v1_genomic.fna/dqc_result.json
[2024-01-24 12:01:33,566] [INFO] DFAST_QC completed!
[2024-01-24 12:01:33,567] [INFO] Total running time: 0h0m57s