[2024-01-24 15:06:36,561] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:06:36,566] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:06:36,567] [INFO] DQC Reference Directory: /var/lib/cwl/stg09819562-6c95-4321-bea7-db727519fd9a/dqc_reference
[2024-01-24 15:06:37,935] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:06:37,936] [INFO] Task started: Prodigal
[2024-01-24 15:06:37,937] [INFO] Running command: gunzip -c /var/lib/cwl/stgc457f88a-322a-4452-939a-dcb9c64da08d/GCF_005049285.1_ASM504928v1_genomic.fna.gz | prodigal -d GCF_005049285.1_ASM504928v1_genomic.fna/cds.fna -a GCF_005049285.1_ASM504928v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:06:57,589] [INFO] Task succeeded: Prodigal
[2024-01-24 15:06:57,589] [INFO] Task started: HMMsearch
[2024-01-24 15:06:57,589] [INFO] Running command: hmmsearch --tblout GCF_005049285.1_ASM504928v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09819562-6c95-4321-bea7-db727519fd9a/dqc_reference/reference_markers.hmm GCF_005049285.1_ASM504928v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:06:57,857] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:06:57,859] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc457f88a-322a-4452-939a-dcb9c64da08d/GCF_005049285.1_ASM504928v1_genomic.fna.gz]
[2024-01-24 15:06:57,895] [INFO] Query marker FASTA was written to GCF_005049285.1_ASM504928v1_genomic.fna/markers.fasta
[2024-01-24 15:06:57,895] [INFO] Task started: Blastn
[2024-01-24 15:06:57,895] [INFO] Running command: blastn -query GCF_005049285.1_ASM504928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09819562-6c95-4321-bea7-db727519fd9a/dqc_reference/reference_markers.fasta -out GCF_005049285.1_ASM504928v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:06:58,450] [INFO] Task succeeded: Blastn
[2024-01-24 15:06:58,453] [INFO] Selected 8 target genomes.
[2024-01-24 15:06:58,454] [INFO] Target genome list was writen to GCF_005049285.1_ASM504928v1_genomic.fna/target_genomes.txt
[2024-01-24 15:06:58,462] [INFO] Task started: fastANI
[2024-01-24 15:06:58,462] [INFO] Running command: fastANI --query /var/lib/cwl/stgc457f88a-322a-4452-939a-dcb9c64da08d/GCF_005049285.1_ASM504928v1_genomic.fna.gz --refList GCF_005049285.1_ASM504928v1_genomic.fna/target_genomes.txt --output GCF_005049285.1_ASM504928v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:07:06,795] [INFO] Task succeeded: fastANI
[2024-01-24 15:07:06,795] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09819562-6c95-4321-bea7-db727519fd9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:07:06,796] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09819562-6c95-4321-bea7-db727519fd9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:07:06,809] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:07:06,809] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:07:06,809] [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
Halorientalis salina	strain=NEN8	GCA_023566035.1	2932266	2932266	type	True	100.0	1210	1210	95	conclusive
Halorientalis salina	strain=NEN8	GCA_005049285.1	2932266	2932266	type	True	100.0	1210	1210	95	conclusive
Halorientalis brevis	strain=YC89	GCA_023077655.1	1126241	1126241	type	True	83.757	842	1210	95	below_threshold
Halorientalis marina	strain=GDY88	GCA_023028345.1	2931976	2931976	type	True	81.0911	689	1210	95	below_threshold
Halorientalis regularis	strain=TNN28	GCA_023698535.1	660518	660518	type	True	81.0093	663	1210	95	below_threshold
Halorientalis pallida	strain=F13-25	GCA_004118325.1	2479928	2479928	type	True	80.9205	670	1210	95	below_threshold
Halosimplex halophilum	strain=TH32	GCA_004698125.1	2559572	2559572	type	True	78.7962	507	1210	95	below_threshold
Halapricum salinum	strain=CBA1105	GCA_000755225.1	1457250	1457250	type	True	78.2407	375	1210	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:07:06,811] [INFO] DFAST Taxonomy check result was written to GCF_005049285.1_ASM504928v1_genomic.fna/tc_result.tsv
[2024-01-24 15:07:06,812] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:07:06,812] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:07:06,812] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09819562-6c95-4321-bea7-db727519fd9a/dqc_reference/checkm_data
[2024-01-24 15:07:06,813] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:07:06,855] [INFO] Task started: CheckM
[2024-01-24 15:07:06,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005049285.1_ASM504928v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005049285.1_ASM504928v1_genomic.fna/checkm_input GCF_005049285.1_ASM504928v1_genomic.fna/checkm_result
[2024-01-24 15:07:57,746] [INFO] Task succeeded: CheckM
[2024-01-24 15:07:57,748] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:07:57,772] [INFO] ===== Completeness check finished =====
[2024-01-24 15:07:57,773] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:07:57,774] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005049285.1_ASM504928v1_genomic.fna/markers.fasta)
[2024-01-24 15:07:57,774] [INFO] Task started: Blastn
[2024-01-24 15:07:57,774] [INFO] Running command: blastn -query GCF_005049285.1_ASM504928v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09819562-6c95-4321-bea7-db727519fd9a/dqc_reference/reference_markers_gtdb.fasta -out GCF_005049285.1_ASM504928v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:07:58,314] [INFO] Task succeeded: Blastn
[2024-01-24 15:07:58,319] [INFO] Selected 8 target genomes.
[2024-01-24 15:07:58,319] [INFO] Target genome list was writen to GCF_005049285.1_ASM504928v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:07:58,340] [INFO] Task started: fastANI
[2024-01-24 15:07:58,341] [INFO] Running command: fastANI --query /var/lib/cwl/stgc457f88a-322a-4452-939a-dcb9c64da08d/GCF_005049285.1_ASM504928v1_genomic.fna.gz --refList GCF_005049285.1_ASM504928v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005049285.1_ASM504928v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:08:05,567] [INFO] Task succeeded: fastANI
[2024-01-24 15:08:05,579] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:08:05,579] [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_005049285.1	s__Halorientalis sp005049285	100.0	1210	1210	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorientalis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001989615.1	s__Halorientalis sp001989615	81.0998	669	1210	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorientalis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110215.1	s__Halorientalis persicus	81.0888	682	1210	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorientalis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102305.1	s__Halorientalis regularis	80.9449	665	1210	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorientalis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004118325.1	s__Halorientalis sp004118325	80.874	674	1210	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorientalis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013415885.1	s__Halosimplex rubrum	78.9162	521	1210	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004698125.1	s__Halosimplex halophilum	78.7914	507	1210	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799665.1	s__Halapricum salinum	78.2725	368	1210	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halapricum	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:08:05,583] [INFO] GTDB search result was written to GCF_005049285.1_ASM504928v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:08:05,584] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:08:05,587] [INFO] DFAST_QC result json was written to GCF_005049285.1_ASM504928v1_genomic.fna/dqc_result.json
[2024-01-24 15:08:05,587] [INFO] DFAST_QC completed!
[2024-01-24 15:08:05,587] [INFO] Total running time: 0h1m29s