[2024-01-25 19:39:05,668] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:39:05,673] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:39:05,673] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1de5209-3566-40c4-8d7d-97833674224f/dqc_reference
[2024-01-25 19:39:06,911] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:39:06,915] [INFO] Task started: Prodigal
[2024-01-25 19:39:06,915] [INFO] Running command: gunzip -c /var/lib/cwl/stge17c5f16-6ce2-45c9-a012-1a074d82dc3d/GCF_002788215.1_ASM278821v1_genomic.fna.gz | prodigal -d GCF_002788215.1_ASM278821v1_genomic.fna/cds.fna -a GCF_002788215.1_ASM278821v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:39:15,161] [INFO] Task succeeded: Prodigal
[2024-01-25 19:39:15,161] [INFO] Task started: HMMsearch
[2024-01-25 19:39:15,161] [INFO] Running command: hmmsearch --tblout GCF_002788215.1_ASM278821v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1de5209-3566-40c4-8d7d-97833674224f/dqc_reference/reference_markers.hmm GCF_002788215.1_ASM278821v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:39:15,361] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:39:15,362] [WARNING] Found 3/6 markers. [/var/lib/cwl/stge17c5f16-6ce2-45c9-a012-1a074d82dc3d/GCF_002788215.1_ASM278821v1_genomic.fna.gz]
[2024-01-25 19:39:15,389] [INFO] Query marker FASTA was written to GCF_002788215.1_ASM278821v1_genomic.fna/markers.fasta
[2024-01-25 19:39:15,389] [INFO] Task started: Blastn
[2024-01-25 19:39:15,389] [INFO] Running command: blastn -query GCF_002788215.1_ASM278821v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1de5209-3566-40c4-8d7d-97833674224f/dqc_reference/reference_markers.fasta -out GCF_002788215.1_ASM278821v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:15,858] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:15,861] [INFO] Selected 7 target genomes.
[2024-01-25 19:39:15,861] [INFO] Target genome list was writen to GCF_002788215.1_ASM278821v1_genomic.fna/target_genomes.txt
[2024-01-25 19:39:15,864] [INFO] Task started: fastANI
[2024-01-25 19:39:15,864] [INFO] Running command: fastANI --query /var/lib/cwl/stge17c5f16-6ce2-45c9-a012-1a074d82dc3d/GCF_002788215.1_ASM278821v1_genomic.fna.gz --refList GCF_002788215.1_ASM278821v1_genomic.fna/target_genomes.txt --output GCF_002788215.1_ASM278821v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:39:21,180] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:21,181] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1de5209-3566-40c4-8d7d-97833674224f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:39:21,181] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1de5209-3566-40c4-8d7d-97833674224f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:39:21,187] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:39:21,187] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:39:21,187] [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
Halohasta litchfieldiae	strain=tADL	GCA_002788215.1	1073996	1073996	type	True	100.0	1109	1110	95	conclusive
Halohasta litchfieldiae	strain=DSM 22187	GCA_900109065.1	1073996	1073996	type	True	99.9367	1046	1110	95	conclusive
Halonotius roseus	strain=F9-27	GCA_006861655.1	2511997	2511997	type	True	78.8781	378	1110	95	below_threshold
Halonotius aquaticus	strain=F13-13	GCA_003605575.1	2216978	2216978	type	True	78.7451	351	1110	95	below_threshold
Halonotius terrestris	strain=F15B	GCA_006861665.1	2487750	2487750	type	True	78.6741	397	1110	95	below_threshold
Halonotius pteroides	strain=CECT 7525	GCA_003605635.1	268735	268735	type	True	78.5045	324	1110	95	below_threshold
Haloferax gibbonsii	strain=ATCC 33959	GCA_000336775.1	35746	35746	type	True	77.4847	258	1110	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:39:21,188] [INFO] DFAST Taxonomy check result was written to GCF_002788215.1_ASM278821v1_genomic.fna/tc_result.tsv
[2024-01-25 19:39:21,189] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:39:21,189] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:39:21,189] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1de5209-3566-40c4-8d7d-97833674224f/dqc_reference/checkm_data
[2024-01-25 19:39:21,190] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:39:21,224] [INFO] Task started: CheckM
[2024-01-25 19:39:21,225] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002788215.1_ASM278821v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002788215.1_ASM278821v1_genomic.fna/checkm_input GCF_002788215.1_ASM278821v1_genomic.fna/checkm_result
[2024-01-25 19:39:47,673] [INFO] Task succeeded: CheckM
[2024-01-25 19:39:47,674] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:39:47,693] [INFO] ===== Completeness check finished =====
[2024-01-25 19:39:47,694] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:39:47,694] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002788215.1_ASM278821v1_genomic.fna/markers.fasta)
[2024-01-25 19:39:47,694] [INFO] Task started: Blastn
[2024-01-25 19:39:47,694] [INFO] Running command: blastn -query GCF_002788215.1_ASM278821v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1de5209-3566-40c4-8d7d-97833674224f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002788215.1_ASM278821v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:48,156] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:48,158] [INFO] Selected 8 target genomes.
[2024-01-25 19:39:48,158] [INFO] Target genome list was writen to GCF_002788215.1_ASM278821v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:39:48,168] [INFO] Task started: fastANI
[2024-01-25 19:39:48,168] [INFO] Running command: fastANI --query /var/lib/cwl/stge17c5f16-6ce2-45c9-a012-1a074d82dc3d/GCF_002788215.1_ASM278821v1_genomic.fna.gz --refList GCF_002788215.1_ASM278821v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002788215.1_ASM278821v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:39:53,791] [INFO] Task succeeded: fastANI
[2024-01-25 19:39:53,798] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:39:53,798] [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_900109065.1	s__Halohasta litchfieldiae	99.9367	1046	1110	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halohasta	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006861655.1	s__Halonotius roseus	78.8668	379	1110	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halonotius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605575.1	s__Halonotius sp003605575	78.7489	352	1110	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halonotius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006861665.1	s__Halonotius terrestris	78.6953	395	1110	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halonotius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000496215.1	s__Halonotius sp000496215	78.5997	322	1110	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halonotius	95.0	96.16	96.16	0.87	0.87	2	-
GCF_003605635.1	s__Halonotius pteroides	78.5117	324	1110	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halonotius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000336775.1	s__Haloferax gibbonsii	77.5083	256	1110	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	96.8304	98.89	98.78	0.89	0.88	5	-
GCF_000336815.1	s__Haloferax prahovense	77.2139	250	1110	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	96.8304	99.29	99.22	0.91	0.91	5	-
--------------------------------------------------------------------------------
[2024-01-25 19:39:53,801] [INFO] GTDB search result was written to GCF_002788215.1_ASM278821v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:39:53,802] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:39:53,804] [INFO] DFAST_QC result json was written to GCF_002788215.1_ASM278821v1_genomic.fna/dqc_result.json
[2024-01-25 19:39:53,805] [INFO] DFAST_QC completed!
[2024-01-25 19:39:53,805] [INFO] Total running time: 0h0m48s