[2024-01-24 12:47:48,959] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:48,961] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:48,961] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2f16fc7-623b-4954-8643-45060a2ddeaf/dqc_reference
[2024-01-24 12:47:50,374] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:50,376] [INFO] Task started: Prodigal
[2024-01-24 12:47:50,376] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1cfc973-fb4e-414a-9170-04d315a9b8cf/GCF_004143485.2_ASM414348v2_genomic.fna.gz | prodigal -d GCF_004143485.2_ASM414348v2_genomic.fna/cds.fna -a GCF_004143485.2_ASM414348v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:48:09,415] [INFO] Task succeeded: Prodigal
[2024-01-24 12:48:09,415] [INFO] Task started: HMMsearch
[2024-01-24 12:48:09,415] [INFO] Running command: hmmsearch --tblout GCF_004143485.2_ASM414348v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2f16fc7-623b-4954-8643-45060a2ddeaf/dqc_reference/reference_markers.hmm GCF_004143485.2_ASM414348v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:48:09,663] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:48:09,665] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf1cfc973-fb4e-414a-9170-04d315a9b8cf/GCF_004143485.2_ASM414348v2_genomic.fna.gz]
[2024-01-24 12:48:09,699] [INFO] Query marker FASTA was written to GCF_004143485.2_ASM414348v2_genomic.fna/markers.fasta
[2024-01-24 12:48:09,699] [INFO] Task started: Blastn
[2024-01-24 12:48:09,700] [INFO] Running command: blastn -query GCF_004143485.2_ASM414348v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2f16fc7-623b-4954-8643-45060a2ddeaf/dqc_reference/reference_markers.fasta -out GCF_004143485.2_ASM414348v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:10,281] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:10,286] [INFO] Selected 7 target genomes.
[2024-01-24 12:48:10,286] [INFO] Target genome list was writen to GCF_004143485.2_ASM414348v2_genomic.fna/target_genomes.txt
[2024-01-24 12:48:10,291] [INFO] Task started: fastANI
[2024-01-24 12:48:10,291] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1cfc973-fb4e-414a-9170-04d315a9b8cf/GCF_004143485.2_ASM414348v2_genomic.fna.gz --refList GCF_004143485.2_ASM414348v2_genomic.fna/target_genomes.txt --output GCF_004143485.2_ASM414348v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:17,962] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:17,962] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2f16fc7-623b-4954-8643-45060a2ddeaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:17,963] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2f16fc7-623b-4954-8643-45060a2ddeaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:17,970] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:48:17,971] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:48:17,971] [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 amylolyticus	strain=YC93	GCA_004143485.2	1126242	1126242	type	True	100.0	1243	1248	95	conclusive
Halorussus salinus	strain=YJ-37-H	GCA_004765815.2	1364935	1364935	type	True	82.1925	843	1248	95	below_threshold
Halorussus pelagicus	strain=RC-68	GCA_004087835.1	2505977	2505977	type	True	82.076	739	1248	95	below_threshold
Halorussus ruber	strain=YC25	GCA_004765785.1	1126238	1126238	type	True	81.9717	795	1248	95	below_threshold
Halorussus litoreus	strain=HD8-51	GCA_003382685.1	1710536	1710536	type	True	81.6582	741	1248	95	below_threshold
Halorussus rarus	strain=TBN4	GCA_003369835.1	660515	660515	type	True	81.464	779	1248	95	below_threshold
Halorussus halobius	strain=HD8-83	GCA_004765805.1	1710537	1710537	type	True	81.402	750	1248	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:48:17,973] [INFO] DFAST Taxonomy check result was written to GCF_004143485.2_ASM414348v2_genomic.fna/tc_result.tsv
[2024-01-24 12:48:17,973] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:17,973] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:17,973] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2f16fc7-623b-4954-8643-45060a2ddeaf/dqc_reference/checkm_data
[2024-01-24 12:48:17,975] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:18,016] [INFO] Task started: CheckM
[2024-01-24 12:48:18,017] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004143485.2_ASM414348v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004143485.2_ASM414348v2_genomic.fna/checkm_input GCF_004143485.2_ASM414348v2_genomic.fna/checkm_result
[2024-01-24 12:49:09,241] [INFO] Task succeeded: CheckM
[2024-01-24 12:49:09,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:49:09,269] [INFO] ===== Completeness check finished =====
[2024-01-24 12:49:09,270] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:49:09,270] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004143485.2_ASM414348v2_genomic.fna/markers.fasta)
[2024-01-24 12:49:09,271] [INFO] Task started: Blastn
[2024-01-24 12:49:09,271] [INFO] Running command: blastn -query GCF_004143485.2_ASM414348v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2f16fc7-623b-4954-8643-45060a2ddeaf/dqc_reference/reference_markers_gtdb.fasta -out GCF_004143485.2_ASM414348v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:49:09,765] [INFO] Task succeeded: Blastn
[2024-01-24 12:49:09,770] [INFO] Selected 9 target genomes.
[2024-01-24 12:49:09,770] [INFO] Target genome list was writen to GCF_004143485.2_ASM414348v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:49:09,777] [INFO] Task started: fastANI
[2024-01-24 12:49:09,778] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1cfc973-fb4e-414a-9170-04d315a9b8cf/GCF_004143485.2_ASM414348v2_genomic.fna.gz --refList GCF_004143485.2_ASM414348v2_genomic.fna/target_genomes_gtdb.txt --output GCF_004143485.2_ASM414348v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:19,472] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:19,489] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:49:19,489] [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_004143485.2	s__Halorussus amylolyticus	100.0	1239	1248	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	82.1694	847	1248	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	82.1173	821	1248	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	82.1061	795	1248	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	82.0614	740	1248	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	82.0197	790	1248	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003382685.1	s__Halorussus litoreus	81.7019	736	1248	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	81.4784	776	1248	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004765805.1	s__Halorussus sp004765805	81.458	741	1248	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:49:19,492] [INFO] GTDB search result was written to GCF_004143485.2_ASM414348v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:19,492] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:19,497] [INFO] DFAST_QC result json was written to GCF_004143485.2_ASM414348v2_genomic.fna/dqc_result.json
[2024-01-24 12:49:19,497] [INFO] DFAST_QC completed!
[2024-01-24 12:49:19,498] [INFO] Total running time: 0h1m31s