[2024-01-24 13:36:45,624] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,626] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,627] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c15db2b-d4c6-4c00-a24a-b5d9595f95c7/dqc_reference
[2024-01-24 13:36:46,983] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:46,984] [INFO] Task started: Prodigal
[2024-01-24 13:36:46,984] [INFO] Running command: gunzip -c /var/lib/cwl/stg38e1292b-f36f-4e48-bb88-c2f3a19b98b8/GCF_008831545.1_ASM883154v1_genomic.fna.gz | prodigal -d GCF_008831545.1_ASM883154v1_genomic.fna/cds.fna -a GCF_008831545.1_ASM883154v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:10,099] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:10,099] [INFO] Task started: HMMsearch
[2024-01-24 13:37:10,099] [INFO] Running command: hmmsearch --tblout GCF_008831545.1_ASM883154v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c15db2b-d4c6-4c00-a24a-b5d9595f95c7/dqc_reference/reference_markers.hmm GCF_008831545.1_ASM883154v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:10,408] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:10,410] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg38e1292b-f36f-4e48-bb88-c2f3a19b98b8/GCF_008831545.1_ASM883154v1_genomic.fna.gz]
[2024-01-24 13:37:10,450] [INFO] Query marker FASTA was written to GCF_008831545.1_ASM883154v1_genomic.fna/markers.fasta
[2024-01-24 13:37:10,450] [INFO] Task started: Blastn
[2024-01-24 13:37:10,450] [INFO] Running command: blastn -query GCF_008831545.1_ASM883154v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c15db2b-d4c6-4c00-a24a-b5d9595f95c7/dqc_reference/reference_markers.fasta -out GCF_008831545.1_ASM883154v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:11,017] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:11,020] [INFO] Selected 7 target genomes.
[2024-01-24 13:37:11,021] [INFO] Target genome list was writen to GCF_008831545.1_ASM883154v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:11,030] [INFO] Task started: fastANI
[2024-01-24 13:37:11,031] [INFO] Running command: fastANI --query /var/lib/cwl/stg38e1292b-f36f-4e48-bb88-c2f3a19b98b8/GCF_008831545.1_ASM883154v1_genomic.fna.gz --refList GCF_008831545.1_ASM883154v1_genomic.fna/target_genomes.txt --output GCF_008831545.1_ASM883154v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:18,515] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:18,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c15db2b-d4c6-4c00-a24a-b5d9595f95c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:18,515] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c15db2b-d4c6-4c00-a24a-b5d9595f95c7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:18,523] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:18,523] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:18,523] [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 halophilus	strain=ZS-3	GCA_008831545.1	2650975	2650975	type	True	100.0	1481	1483	95	conclusive
Halorussus salinus	strain=YJ-37-H	GCA_004765815.2	1364935	1364935	type	True	80.5177	805	1483	95	below_threshold
Halorussus pelagicus	strain=RC-68	GCA_004087835.1	2505977	2505977	type	True	80.4831	685	1483	95	below_threshold
Halorussus ruber	strain=YC25	GCA_004765785.1	1126238	1126238	type	True	80.3799	784	1483	95	below_threshold
Halorussus amylolyticus	strain=YC93	GCA_004143485.2	1126242	1126242	type	True	80.2882	702	1483	95	below_threshold
Halorussus rarus	strain=TBN4	GCA_003369835.1	660515	660515	type	True	79.3416	690	1483	95	below_threshold
Halorussus marinus	strain=LYG-36	GCA_004765795.1	2505976	2505976	type	True	78.9926	583	1483	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:18,525] [INFO] DFAST Taxonomy check result was written to GCF_008831545.1_ASM883154v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:18,526] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:18,526] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:18,526] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c15db2b-d4c6-4c00-a24a-b5d9595f95c7/dqc_reference/checkm_data
[2024-01-24 13:37:18,527] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:18,572] [INFO] Task started: CheckM
[2024-01-24 13:37:18,572] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008831545.1_ASM883154v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008831545.1_ASM883154v1_genomic.fna/checkm_input GCF_008831545.1_ASM883154v1_genomic.fna/checkm_result
[2024-01-24 13:38:22,393] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:22,394] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:22,417] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:22,418] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:22,418] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008831545.1_ASM883154v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:22,418] [INFO] Task started: Blastn
[2024-01-24 13:38:22,419] [INFO] Running command: blastn -query GCF_008831545.1_ASM883154v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c15db2b-d4c6-4c00-a24a-b5d9595f95c7/dqc_reference/reference_markers_gtdb.fasta -out GCF_008831545.1_ASM883154v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:22,920] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:22,923] [INFO] Selected 9 target genomes.
[2024-01-24 13:38:22,924] [INFO] Target genome list was writen to GCF_008831545.1_ASM883154v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:22,944] [INFO] Task started: fastANI
[2024-01-24 13:38:22,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg38e1292b-f36f-4e48-bb88-c2f3a19b98b8/GCF_008831545.1_ASM883154v1_genomic.fna.gz --refList GCF_008831545.1_ASM883154v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008831545.1_ASM883154v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:31,840] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:31,848] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:31,848] [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_008831545.1	s__Halorussus sp008831545	100.0	1481	1483	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004765815.2	s__Halorussus salinus	80.5338	802	1483	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	80.4395	690	1483	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	80.3901	782	1483	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	80.3817	751	1483	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	80.282	798	1483	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004143485.2	s__Halorussus amylolyticus	80.2652	706	1483	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	79.341	690	1483	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004765795.1	s__Halorussus sp004765795	78.9709	585	1483	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	98.88	98.88	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:31,850] [INFO] GTDB search result was written to GCF_008831545.1_ASM883154v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:31,850] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:31,853] [INFO] DFAST_QC result json was written to GCF_008831545.1_ASM883154v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:31,853] [INFO] DFAST_QC completed!
[2024-01-24 13:38:31,853] [INFO] Total running time: 0h1m46s