[2024-01-25 19:46:06,088] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:46:06,090] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:46:06,090] [INFO] DQC Reference Directory: /var/lib/cwl/stgacc93295-d51a-4184-92fa-f6d76a260040/dqc_reference
[2024-01-25 19:46:07,247] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:46:07,248] [INFO] Task started: Prodigal
[2024-01-25 19:46:07,248] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ea7677b-00da-4d37-a4b4-e8650de44cd9/GCF_024464655.1_ASM2446465v1_genomic.fna.gz | prodigal -d GCF_024464655.1_ASM2446465v1_genomic.fna/cds.fna -a GCF_024464655.1_ASM2446465v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:46:20,842] [INFO] Task succeeded: Prodigal
[2024-01-25 19:46:20,843] [INFO] Task started: HMMsearch
[2024-01-25 19:46:20,843] [INFO] Running command: hmmsearch --tblout GCF_024464655.1_ASM2446465v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgacc93295-d51a-4184-92fa-f6d76a260040/dqc_reference/reference_markers.hmm GCF_024464655.1_ASM2446465v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:46:21,124] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:46:21,126] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg1ea7677b-00da-4d37-a4b4-e8650de44cd9/GCF_024464655.1_ASM2446465v1_genomic.fna.gz]
[2024-01-25 19:46:21,168] [INFO] Query marker FASTA was written to GCF_024464655.1_ASM2446465v1_genomic.fna/markers.fasta
[2024-01-25 19:46:21,168] [INFO] Task started: Blastn
[2024-01-25 19:46:21,169] [INFO] Running command: blastn -query GCF_024464655.1_ASM2446465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacc93295-d51a-4184-92fa-f6d76a260040/dqc_reference/reference_markers.fasta -out GCF_024464655.1_ASM2446465v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:21,688] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:21,690] [INFO] Selected 8 target genomes.
[2024-01-25 19:46:21,691] [INFO] Target genome list was writen to GCF_024464655.1_ASM2446465v1_genomic.fna/target_genomes.txt
[2024-01-25 19:46:21,703] [INFO] Task started: fastANI
[2024-01-25 19:46:21,703] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ea7677b-00da-4d37-a4b4-e8650de44cd9/GCF_024464655.1_ASM2446465v1_genomic.fna.gz --refList GCF_024464655.1_ASM2446465v1_genomic.fna/target_genomes.txt --output GCF_024464655.1_ASM2446465v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:46:28,247] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:28,247] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgacc93295-d51a-4184-92fa-f6d76a260040/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:46:28,248] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgacc93295-d51a-4184-92fa-f6d76a260040/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:46:28,254] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:46:28,254] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:46:28,254] [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
Halobellus limi	strain=CGMCC 1.10331	GCA_900108165.1	699433	699433	type	True	84.2854	706	1126	95	below_threshold
Halobellus limi	strain=CGMCC 1.10331	GCA_004799685.1	699433	699433	type	True	84.2101	715	1126	95	below_threshold
Halobellus rarus	strain=YC21	GCA_024494595.1	1126237	1126237	type	True	84.1008	705	1126	95	below_threshold
Halobellus litoreus	strain=GX31	GCA_024464595.1	755310	755310	type	True	83.7885	734	1126	95	below_threshold
Halobellus rufus	strain=CBA1103	GCA_000739575.1	1448860	1448860	type	True	83.6093	683	1126	95	below_threshold
Halobellus captivus	strain=ZY21	GCA_007655485.1	2592614	2592614	type	True	82.8161	658	1126	95	below_threshold
Halobellus clavatus	strain=CGMCC 1.10118	GCA_900107195.1	660517	660517	type	True	82.358	656	1126	95	below_threshold
Halobellus ruber	strain=MBLA0160	GCA_014212355.1	2761102	2761102	type	True	80.929	565	1126	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:46:28,256] [INFO] DFAST Taxonomy check result was written to GCF_024464655.1_ASM2446465v1_genomic.fna/tc_result.tsv
[2024-01-25 19:46:28,256] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:46:28,256] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:46:28,256] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgacc93295-d51a-4184-92fa-f6d76a260040/dqc_reference/checkm_data
[2024-01-25 19:46:28,257] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:46:28,293] [INFO] Task started: CheckM
[2024-01-25 19:46:28,293] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024464655.1_ASM2446465v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024464655.1_ASM2446465v1_genomic.fna/checkm_input GCF_024464655.1_ASM2446465v1_genomic.fna/checkm_result
[2024-01-25 19:47:07,093] [INFO] Task succeeded: CheckM
[2024-01-25 19:47:07,094] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:47:07,111] [INFO] ===== Completeness check finished =====
[2024-01-25 19:47:07,111] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:47:07,111] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024464655.1_ASM2446465v1_genomic.fna/markers.fasta)
[2024-01-25 19:47:07,112] [INFO] Task started: Blastn
[2024-01-25 19:47:07,112] [INFO] Running command: blastn -query GCF_024464655.1_ASM2446465v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacc93295-d51a-4184-92fa-f6d76a260040/dqc_reference/reference_markers_gtdb.fasta -out GCF_024464655.1_ASM2446465v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:07,653] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:07,655] [INFO] Selected 6 target genomes.
[2024-01-25 19:47:07,655] [INFO] Target genome list was writen to GCF_024464655.1_ASM2446465v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:47:07,661] [INFO] Task started: fastANI
[2024-01-25 19:47:07,661] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ea7677b-00da-4d37-a4b4-e8650de44cd9/GCF_024464655.1_ASM2446465v1_genomic.fna.gz --refList GCF_024464655.1_ASM2446465v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024464655.1_ASM2446465v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:47:13,238] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:13,243] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:47:13,244] [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_003665925.1	s__Halobellus sp003665925	96.307	979	1126	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobellus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003665935.1	s__Halobellus sp003665935	86.2833	772	1126	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobellus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799685.1	s__Halobellus limi	84.1888	717	1126	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobellus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000739575.1	s__Halobellus rufus	83.5564	687	1126	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobellus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007655485.1	s__Halobellus captivus	82.8033	659	1126	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobellus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107195.1	s__Halobellus clavatus	82.3533	657	1126	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobellus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:47:13,245] [INFO] GTDB search result was written to GCF_024464655.1_ASM2446465v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:47:13,245] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:47:13,247] [INFO] DFAST_QC result json was written to GCF_024464655.1_ASM2446465v1_genomic.fna/dqc_result.json
[2024-01-25 19:47:13,248] [INFO] DFAST_QC completed!
[2024-01-25 19:47:13,248] [INFO] Total running time: 0h1m7s