[2024-01-24 14:55:08,347] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:08,348] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:08,349] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c0f8144-12dd-4fd6-9fb1-cb536ab8244b/dqc_reference
[2024-01-24 14:55:10,008] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:10,009] [INFO] Task started: Prodigal
[2024-01-24 14:55:10,009] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf62dd87-343e-4a5e-86b7-411ca1e3c173/GCF_002993335.1_ASM299333v1_genomic.fna.gz | prodigal -d GCF_002993335.1_ASM299333v1_genomic.fna/cds.fna -a GCF_002993335.1_ASM299333v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:18,470] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:18,471] [INFO] Task started: HMMsearch
[2024-01-24 14:55:18,471] [INFO] Running command: hmmsearch --tblout GCF_002993335.1_ASM299333v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c0f8144-12dd-4fd6-9fb1-cb536ab8244b/dqc_reference/reference_markers.hmm GCF_002993335.1_ASM299333v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:18,729] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:18,731] [INFO] Found 6/6 markers.
[2024-01-24 14:55:18,766] [INFO] Query marker FASTA was written to GCF_002993335.1_ASM299333v1_genomic.fna/markers.fasta
[2024-01-24 14:55:18,767] [INFO] Task started: Blastn
[2024-01-24 14:55:18,767] [INFO] Running command: blastn -query GCF_002993335.1_ASM299333v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c0f8144-12dd-4fd6-9fb1-cb536ab8244b/dqc_reference/reference_markers.fasta -out GCF_002993335.1_ASM299333v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:19,382] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:19,386] [INFO] Selected 18 target genomes.
[2024-01-24 14:55:19,386] [INFO] Target genome list was writen to GCF_002993335.1_ASM299333v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:19,395] [INFO] Task started: fastANI
[2024-01-24 14:55:19,396] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf62dd87-343e-4a5e-86b7-411ca1e3c173/GCF_002993335.1_ASM299333v1_genomic.fna.gz --refList GCF_002993335.1_ASM299333v1_genomic.fna/target_genomes.txt --output GCF_002993335.1_ASM299333v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:30,921] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:30,922] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c0f8144-12dd-4fd6-9fb1-cb536ab8244b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:30,922] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c0f8144-12dd-4fd6-9fb1-cb536ab8244b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:30,933] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:30,933] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:30,933] [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
Alkalicoccus urumqiensis	strain=BZ-SZ-XJ18	GCA_002993335.1	1548213	1548213	type	True	100.0	1080	1083	95	conclusive
Alkalicoccus saliphilus	strain=6AG	GCA_003044065.1	200989	200989	type	True	77.6036	162	1083	95	below_threshold
Alteribacter natronophilus	strain=M30	GCA_006007885.1	2583810	2583810	type	True	77.386	60	1083	95	below_threshold
Alkalicoccus chagannorensis	strain=DSM 18086	GCA_000429725.1	427072	427072	type	True	77.3824	187	1083	95	below_threshold
Alkalicoccus halolimnae	strain=BZ-SZ-XJ29	GCA_008014775.1	1667239	1667239	type	True	77.3378	130	1083	95	below_threshold
Salisediminibacterium selenitireducens	strain=MLS10	GCA_000093085.1	85683	85683	type	True	77.1556	84	1083	95	below_threshold
Alkalicoccus daliensis	strain=CGMCC 1.10369	GCA_900103955.1	745820	745820	type	True	76.9437	118	1083	95	below_threshold
Alteribacter lacisalsi	strain=YSP-3	GCA_003226345.1	2045244	2045244	type	True	76.9193	70	1083	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:30,935] [INFO] DFAST Taxonomy check result was written to GCF_002993335.1_ASM299333v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:30,936] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:30,936] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:30,936] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c0f8144-12dd-4fd6-9fb1-cb536ab8244b/dqc_reference/checkm_data
[2024-01-24 14:55:30,938] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:30,971] [INFO] Task started: CheckM
[2024-01-24 14:55:30,972] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002993335.1_ASM299333v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002993335.1_ASM299333v1_genomic.fna/checkm_input GCF_002993335.1_ASM299333v1_genomic.fna/checkm_result
[2024-01-24 14:56:02,668] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:02,669] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:02,692] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:02,692] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:02,693] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002993335.1_ASM299333v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:02,693] [INFO] Task started: Blastn
[2024-01-24 14:56:02,693] [INFO] Running command: blastn -query GCF_002993335.1_ASM299333v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c0f8144-12dd-4fd6-9fb1-cb536ab8244b/dqc_reference/reference_markers_gtdb.fasta -out GCF_002993335.1_ASM299333v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:03,523] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:03,527] [INFO] Selected 16 target genomes.
[2024-01-24 14:56:03,527] [INFO] Target genome list was writen to GCF_002993335.1_ASM299333v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:03,542] [INFO] Task started: fastANI
[2024-01-24 14:56:03,542] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf62dd87-343e-4a5e-86b7-411ca1e3c173/GCF_002993335.1_ASM299333v1_genomic.fna.gz --refList GCF_002993335.1_ASM299333v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002993335.1_ASM299333v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:13,424] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:13,437] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:13,437] [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_002993335.1	s__Alkalicoccus urumqiensis	100.0	1080	1083	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_007692495.1	s__Alkalicoccus sp007692495	77.9536	114	1083	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003560495.1	s__Alkalicoccus sp003560495	77.6618	121	1083	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	99.31	99.31	0.92	0.92	2	-
GCF_012034335.1	s__Alkalicoccus luteus	77.6556	169	1083	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003044065.1	s__Alkalicoccus saliphilus	77.585	163	1083	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429725.1	s__Alkalicoccus chagannorensis	77.3782	187	1083	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008014775.1	s__Alkalicoccus halolimnae	77.3378	130	1083	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000093085.1	s__Salisediminibacterium selenitireducens	77.1556	84	1083	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Salisediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:13,442] [INFO] GTDB search result was written to GCF_002993335.1_ASM299333v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:13,443] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:13,446] [INFO] DFAST_QC result json was written to GCF_002993335.1_ASM299333v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:13,447] [INFO] DFAST_QC completed!
[2024-01-24 14:56:13,447] [INFO] Total running time: 0h1m5s