[2024-01-24 14:30:44,919] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:44,921] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:44,922] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d7b71af-77b6-4766-a9cf-86270e7c7cc7/dqc_reference
[2024-01-24 14:30:46,257] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:46,266] [INFO] Task started: Prodigal
[2024-01-24 14:30:46,266] [INFO] Running command: gunzip -c /var/lib/cwl/stgad0e0af7-4736-4434-994b-3322ef78b16e/GCF_004765795.1_ASM476579v1_genomic.fna.gz | prodigal -d GCF_004765795.1_ASM476579v1_genomic.fna/cds.fna -a GCF_004765795.1_ASM476579v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:04,521] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:04,521] [INFO] Task started: HMMsearch
[2024-01-24 14:31:04,521] [INFO] Running command: hmmsearch --tblout GCF_004765795.1_ASM476579v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d7b71af-77b6-4766-a9cf-86270e7c7cc7/dqc_reference/reference_markers.hmm GCF_004765795.1_ASM476579v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:04,805] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:04,806] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgad0e0af7-4736-4434-994b-3322ef78b16e/GCF_004765795.1_ASM476579v1_genomic.fna.gz]
[2024-01-24 14:31:04,842] [INFO] Query marker FASTA was written to GCF_004765795.1_ASM476579v1_genomic.fna/markers.fasta
[2024-01-24 14:31:04,842] [INFO] Task started: Blastn
[2024-01-24 14:31:04,842] [INFO] Running command: blastn -query GCF_004765795.1_ASM476579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d7b71af-77b6-4766-a9cf-86270e7c7cc7/dqc_reference/reference_markers.fasta -out GCF_004765795.1_ASM476579v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:05,402] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:05,406] [INFO] Selected 8 target genomes.
[2024-01-24 14:31:05,406] [INFO] Target genome list was writen to GCF_004765795.1_ASM476579v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:05,415] [INFO] Task started: fastANI
[2024-01-24 14:31:05,415] [INFO] Running command: fastANI --query /var/lib/cwl/stgad0e0af7-4736-4434-994b-3322ef78b16e/GCF_004765795.1_ASM476579v1_genomic.fna.gz --refList GCF_004765795.1_ASM476579v1_genomic.fna/target_genomes.txt --output GCF_004765795.1_ASM476579v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:15,172] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:15,173] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d7b71af-77b6-4766-a9cf-86270e7c7cc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:15,173] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d7b71af-77b6-4766-a9cf-86270e7c7cc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:15,181] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:15,182] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:15,182] [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
Halorussus marinus	strain=LYG-36	GCA_004765795.1	2505976	2505976	type	True	100.0	1238	1238	95	conclusive
Halorussus halobius	strain=HD8-83	GCA_004765805.1	1710537	1710537	type	True	83.3352	763	1238	95	below_threshold
Halorussus rarus	strain=TBN4	GCA_003369835.1	660515	660515	type	True	82.7464	804	1238	95	below_threshold
Halorussus litoreus	strain=HD8-51	GCA_003382685.1	1710536	1710536	type	True	82.0078	735	1238	95	below_threshold
Halorussus salinus	strain=YJ-37-H	GCA_004765815.2	1364935	1364935	type	True	81.4054	763	1238	95	below_threshold
Halorussus ruber	strain=YC25	GCA_004765785.1	1126238	1126238	type	True	81.2255	727	1238	95	below_threshold
Halorussus pelagicus	strain=RC-68	GCA_004087835.1	2505977	2505977	type	True	81.0488	695	1238	95	below_threshold
Halostella limicola	strain=LT12	GCA_003675875.1	2448456	2448456	type	True	79.0951	549	1238	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:15,184] [INFO] DFAST Taxonomy check result was written to GCF_004765795.1_ASM476579v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:15,184] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:15,184] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:15,185] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d7b71af-77b6-4766-a9cf-86270e7c7cc7/dqc_reference/checkm_data
[2024-01-24 14:31:15,186] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:15,228] [INFO] Task started: CheckM
[2024-01-24 14:31:15,229] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004765795.1_ASM476579v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004765795.1_ASM476579v1_genomic.fna/checkm_input GCF_004765795.1_ASM476579v1_genomic.fna/checkm_result
[2024-01-24 14:32:04,611] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:04,613] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:04,636] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:04,636] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:04,637] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004765795.1_ASM476579v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:04,637] [INFO] Task started: Blastn
[2024-01-24 14:32:04,637] [INFO] Running command: blastn -query GCF_004765795.1_ASM476579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d7b71af-77b6-4766-a9cf-86270e7c7cc7/dqc_reference/reference_markers_gtdb.fasta -out GCF_004765795.1_ASM476579v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:05,187] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:05,191] [INFO] Selected 11 target genomes.
[2024-01-24 14:32:05,191] [INFO] Target genome list was writen to GCF_004765795.1_ASM476579v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:05,215] [INFO] Task started: fastANI
[2024-01-24 14:32:05,215] [INFO] Running command: fastANI --query /var/lib/cwl/stgad0e0af7-4736-4434-994b-3322ef78b16e/GCF_004765795.1_ASM476579v1_genomic.fna.gz --refList GCF_004765795.1_ASM476579v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004765795.1_ASM476579v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:17,056] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:17,070] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:17,070] [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_004765795.1	s__Halorussus sp004765795	100.0	1238	1238	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	98.88	98.88	0.88	0.88	2	conclusive
GCF_004765805.1	s__Halorussus sp004765805	83.289	767	1238	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003369835.1	s__Halorussus rarus	82.7274	807	1238	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003382685.1	s__Halorussus litoreus	82.0155	734	1238	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004765815.2	s__Halorussus salinus	81.4292	760	1238	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005239435.1	s__Halorussus sp005239435	81.2511	754	1238	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004765785.1	s__Halorussus ruber	81.2204	728	1238	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003023465.1	s__Halorussus sp003023465	81.1714	477	1238	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010747475.1	s__Halorussus sp010747475	81.1336	720	1238	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004087835.1	s__Halorussus sp004087835	81.035	696	1238	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003023565.1	s__Halostella sp003023565	78.5582	453	1238	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:17,072] [INFO] GTDB search result was written to GCF_004765795.1_ASM476579v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:17,073] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:17,076] [INFO] DFAST_QC result json was written to GCF_004765795.1_ASM476579v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:17,077] [INFO] DFAST_QC completed!
[2024-01-24 14:32:17,077] [INFO] Total running time: 0h1m32s