[2024-01-24 14:06:06,968] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:06,971] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:06,971] [INFO] DQC Reference Directory: /var/lib/cwl/stg923d648e-d22a-4ae2-8e20-c1fe913baa54/dqc_reference
[2024-01-24 14:06:08,331] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:08,332] [INFO] Task started: Prodigal
[2024-01-24 14:06:08,333] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb97ede5-30ab-4f06-9c5b-5cac02b14733/GCF_000093085.1_ASM9308v1_genomic.fna.gz | prodigal -d GCF_000093085.1_ASM9308v1_genomic.fna/cds.fna -a GCF_000093085.1_ASM9308v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:18,721] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:18,721] [INFO] Task started: HMMsearch
[2024-01-24 14:06:18,721] [INFO] Running command: hmmsearch --tblout GCF_000093085.1_ASM9308v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg923d648e-d22a-4ae2-8e20-c1fe913baa54/dqc_reference/reference_markers.hmm GCF_000093085.1_ASM9308v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:19,023] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:19,025] [INFO] Found 6/6 markers.
[2024-01-24 14:06:19,061] [INFO] Query marker FASTA was written to GCF_000093085.1_ASM9308v1_genomic.fna/markers.fasta
[2024-01-24 14:06:19,062] [INFO] Task started: Blastn
[2024-01-24 14:06:19,062] [INFO] Running command: blastn -query GCF_000093085.1_ASM9308v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg923d648e-d22a-4ae2-8e20-c1fe913baa54/dqc_reference/reference_markers.fasta -out GCF_000093085.1_ASM9308v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:19,703] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:19,706] [INFO] Selected 23 target genomes.
[2024-01-24 14:06:19,707] [INFO] Target genome list was writen to GCF_000093085.1_ASM9308v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:19,717] [INFO] Task started: fastANI
[2024-01-24 14:06:19,717] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb97ede5-30ab-4f06-9c5b-5cac02b14733/GCF_000093085.1_ASM9308v1_genomic.fna.gz --refList GCF_000093085.1_ASM9308v1_genomic.fna/target_genomes.txt --output GCF_000093085.1_ASM9308v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:34,076] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:34,077] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg923d648e-d22a-4ae2-8e20-c1fe913baa54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:34,077] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg923d648e-d22a-4ae2-8e20-c1fe913baa54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:34,086] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:34,086] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:34,086] [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
Salisediminibacterium selenitireducens	strain=MLS10	GCA_000093085.1	85683	85683	type	True	100.0	1196	1197	95	conclusive
Bacillus shivajii	strain=JCM 32183	GCA_020519665.1	1983719	1983719	type	True	81.0129	50	1197	95	below_threshold
Salisediminibacterium beveridgei	strain=MLTeJB	GCA_001721685.1	632773	632773	type	True	79.0247	325	1197	95	below_threshold
Alteribacter lacisalsi	strain=YSP-3	GCA_003226345.1	2045244	2045244	type	True	77.587	64	1197	95	below_threshold
Alkalicoccus urumqiensis	strain=BZ-SZ-XJ18	GCA_002993335.1	1548213	1548213	type	True	77.3618	79	1197	95	below_threshold
Alteribacter natronophilus	strain=M30	GCA_006007885.1	2583810	2583810	type	True	77.2073	64	1197	95	below_threshold
Alkalicoccus chagannorensis	strain=DSM 18086	GCA_000429725.1	427072	427072	type	True	76.8236	75	1197	95	below_threshold
Salisediminibacterium haloalkalitolerans	strain=10nlg	GCA_900111285.1	1464123	1464123	type	True	76.5437	69	1197	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:34,088] [INFO] DFAST Taxonomy check result was written to GCF_000093085.1_ASM9308v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:34,088] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:34,088] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:34,089] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg923d648e-d22a-4ae2-8e20-c1fe913baa54/dqc_reference/checkm_data
[2024-01-24 14:06:34,090] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:34,130] [INFO] Task started: CheckM
[2024-01-24 14:06:34,130] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000093085.1_ASM9308v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000093085.1_ASM9308v1_genomic.fna/checkm_input GCF_000093085.1_ASM9308v1_genomic.fna/checkm_result
[2024-01-24 14:07:09,746] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:09,748] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:09,764] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:09,765] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:09,765] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000093085.1_ASM9308v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:09,766] [INFO] Task started: Blastn
[2024-01-24 14:07:09,766] [INFO] Running command: blastn -query GCF_000093085.1_ASM9308v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg923d648e-d22a-4ae2-8e20-c1fe913baa54/dqc_reference/reference_markers_gtdb.fasta -out GCF_000093085.1_ASM9308v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:10,566] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:10,573] [INFO] Selected 22 target genomes.
[2024-01-24 14:07:10,574] [INFO] Target genome list was writen to GCF_000093085.1_ASM9308v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:10,588] [INFO] Task started: fastANI
[2024-01-24 14:07:10,589] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb97ede5-30ab-4f06-9c5b-5cac02b14733/GCF_000093085.1_ASM9308v1_genomic.fna.gz --refList GCF_000093085.1_ASM9308v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000093085.1_ASM9308v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:24,081] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:24,088] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:24,088] [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
GCA_000093085.1	s__Salisediminibacterium selenitireducens	100.0	1195	1197	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Salisediminibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001721685.1	s__Salisediminibacterium beveridgei	78.9155	322	1197	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Salisediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003226345.1	s__Alteribacter lacisalsi	77.5276	63	1197	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002993335.1	s__Alkalicoccus urumqiensis	77.3963	78	1197	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_006007885.1	s__Alteribacter natronophilus	77.1419	63	1197	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429725.1	s__Alkalicoccus chagannorensis	76.8515	74	1197	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:24,090] [INFO] GTDB search result was written to GCF_000093085.1_ASM9308v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:24,091] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:24,093] [INFO] DFAST_QC result json was written to GCF_000093085.1_ASM9308v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:24,094] [INFO] DFAST_QC completed!
[2024-01-24 14:07:24,094] [INFO] Total running time: 0h1m17s