[2024-01-24 14:13:01,013] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:13:01,014] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:13:01,015] [INFO] DQC Reference Directory: /var/lib/cwl/stg12a5cf2e-a641-4225-91a7-1f9c1e01364e/dqc_reference
[2024-01-24 14:13:02,254] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:13:02,255] [INFO] Task started: Prodigal
[2024-01-24 14:13:02,256] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a7cf19c-d2e8-4fdc-a363-21981c4ed01e/GCF_020700235.1_ASM2070023v1_genomic.fna.gz | prodigal -d GCF_020700235.1_ASM2070023v1_genomic.fna/cds.fna -a GCF_020700235.1_ASM2070023v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:35,574] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:35,575] [INFO] Task started: HMMsearch
[2024-01-24 14:13:35,575] [INFO] Running command: hmmsearch --tblout GCF_020700235.1_ASM2070023v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12a5cf2e-a641-4225-91a7-1f9c1e01364e/dqc_reference/reference_markers.hmm GCF_020700235.1_ASM2070023v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:35,929] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:35,931] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg3a7cf19c-d2e8-4fdc-a363-21981c4ed01e/GCF_020700235.1_ASM2070023v1_genomic.fna.gz]
[2024-01-24 14:13:35,993] [INFO] Query marker FASTA was written to GCF_020700235.1_ASM2070023v1_genomic.fna/markers.fasta
[2024-01-24 14:13:35,993] [INFO] Task started: Blastn
[2024-01-24 14:13:35,993] [INFO] Running command: blastn -query GCF_020700235.1_ASM2070023v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12a5cf2e-a641-4225-91a7-1f9c1e01364e/dqc_reference/reference_markers.fasta -out GCF_020700235.1_ASM2070023v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:36,546] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:36,550] [INFO] Selected 7 target genomes.
[2024-01-24 14:13:36,550] [INFO] Target genome list was writen to GCF_020700235.1_ASM2070023v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:36,554] [INFO] Task started: fastANI
[2024-01-24 14:13:36,554] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a7cf19c-d2e8-4fdc-a363-21981c4ed01e/GCF_020700235.1_ASM2070023v1_genomic.fna.gz --refList GCF_020700235.1_ASM2070023v1_genomic.fna/target_genomes.txt --output GCF_020700235.1_ASM2070023v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:45,060] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:45,060] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12a5cf2e-a641-4225-91a7-1f9c1e01364e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:45,060] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12a5cf2e-a641-4225-91a7-1f9c1e01364e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:45,067] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:45,068] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:45,068] [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
Haladaptatus pallidirubidus	strain=YIM 93656	GCA_020700235.1	1008152	1008152	type	True	100.0	1992	2087	95	conclusive
Haladaptatus cibarius	strain=D43	GCA_000710615.1	453847	453847	type	True	87.273	969	2087	95	below_threshold
Haladaptatus litoreus	strain=CGMCC 1.7737	GCA_900156425.1	553468	553468	type	True	86.8926	1177	2087	95	below_threshold
Haladaptatus paucihalophilus	strain=DX253	GCA_000376445.1	367189	367189	type	True	81.0353	768	2087	95	below_threshold
Haladaptatus paucihalophilus	strain=DX253	GCA_000187225.2	367189	367189	type	True	80.9907	771	2087	95	below_threshold
Haloferax gibbonsii	strain=ATCC 33959	GCA_000336775.1	35746	35746	type	True	77.412	312	2087	95	below_threshold
Haloferax marisrubri	strain=SB3	GCA_001469875.2	1544719	1544719	type	True	77.3372	305	2087	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:45,070] [INFO] DFAST Taxonomy check result was written to GCF_020700235.1_ASM2070023v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:45,070] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:45,070] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:45,071] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12a5cf2e-a641-4225-91a7-1f9c1e01364e/dqc_reference/checkm_data
[2024-01-24 14:13:45,072] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:45,132] [INFO] Task started: CheckM
[2024-01-24 14:13:45,132] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020700235.1_ASM2070023v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020700235.1_ASM2070023v1_genomic.fna/checkm_input GCF_020700235.1_ASM2070023v1_genomic.fna/checkm_result
[2024-01-24 14:15:12,475] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:12,477] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:12,513] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:12,514] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:12,514] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020700235.1_ASM2070023v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:12,515] [INFO] Task started: Blastn
[2024-01-24 14:15:12,515] [INFO] Running command: blastn -query GCF_020700235.1_ASM2070023v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12a5cf2e-a641-4225-91a7-1f9c1e01364e/dqc_reference/reference_markers_gtdb.fasta -out GCF_020700235.1_ASM2070023v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:12,972] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:12,976] [INFO] Selected 8 target genomes.
[2024-01-24 14:15:12,977] [INFO] Target genome list was writen to GCF_020700235.1_ASM2070023v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:12,986] [INFO] Task started: fastANI
[2024-01-24 14:15:12,986] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a7cf19c-d2e8-4fdc-a363-21981c4ed01e/GCF_020700235.1_ASM2070023v1_genomic.fna.gz --refList GCF_020700235.1_ASM2070023v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020700235.1_ASM2070023v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:21,680] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:21,688] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:15:21,688] [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_000710615.1	s__Haladaptatus cibarius	87.2857	968	2087	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Haladaptatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156425.1	s__Haladaptatus litoreus	86.9019	1176	2087	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Haladaptatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000376445.1	s__Haladaptatus paucihalophilus	81.0519	766	2087	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Haladaptatus	95.0	98.84	96.52	0.92	0.76	4	-
GCF_001625445.1	s__Haladaptatus sp001625445	80.3807	779	2087	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Haladaptatus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003298465.1	s__Haladaptatus sp003298465	78.7041	532	2087	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Haladaptatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000336775.1	s__Haloferax gibbonsii	77.3975	314	2087	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	96.8304	98.89	98.78	0.89	0.88	5	-
GCF_001469875.2	s__Haloferax marisrubri	77.3185	307	2087	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	95.85	95.85	0.83	0.83	2	-
GCF_001482285.1	s__Haloferax sp001482285	77.3098	297	2087	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:21,690] [INFO] GTDB search result was written to GCF_020700235.1_ASM2070023v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:21,690] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:21,693] [INFO] DFAST_QC result json was written to GCF_020700235.1_ASM2070023v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:21,693] [INFO] DFAST_QC completed!
[2024-01-24 14:15:21,693] [INFO] Total running time: 0h2m21s