[2024-01-24 12:06:24,669] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:24,675] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:24,675] [INFO] DQC Reference Directory: /var/lib/cwl/stg80128c34-4fb6-49f1-b903-8c93a02bfde3/dqc_reference
[2024-01-24 12:06:26,039] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:26,045] [INFO] Task started: Prodigal
[2024-01-24 12:06:26,046] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd90b322-9e54-424c-b533-ca5da2766e14/GCF_013402815.2_ASM1340281v2_genomic.fna.gz | prodigal -d GCF_013402815.2_ASM1340281v2_genomic.fna/cds.fna -a GCF_013402815.2_ASM1340281v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:50,390] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:50,390] [INFO] Task started: HMMsearch
[2024-01-24 12:06:50,390] [INFO] Running command: hmmsearch --tblout GCF_013402815.2_ASM1340281v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80128c34-4fb6-49f1-b903-8c93a02bfde3/dqc_reference/reference_markers.hmm GCF_013402815.2_ASM1340281v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:50,621] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:50,622] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgcd90b322-9e54-424c-b533-ca5da2766e14/GCF_013402815.2_ASM1340281v2_genomic.fna.gz]
[2024-01-24 12:06:50,669] [INFO] Query marker FASTA was written to GCF_013402815.2_ASM1340281v2_genomic.fna/markers.fasta
[2024-01-24 12:06:50,670] [INFO] Task started: Blastn
[2024-01-24 12:06:50,670] [INFO] Running command: blastn -query GCF_013402815.2_ASM1340281v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg80128c34-4fb6-49f1-b903-8c93a02bfde3/dqc_reference/reference_markers.fasta -out GCF_013402815.2_ASM1340281v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:51,173] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:51,177] [INFO] Selected 9 target genomes.
[2024-01-24 12:06:51,177] [INFO] Target genome list was writen to GCF_013402815.2_ASM1340281v2_genomic.fna/target_genomes.txt
[2024-01-24 12:06:51,181] [INFO] Task started: fastANI
[2024-01-24 12:06:51,182] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd90b322-9e54-424c-b533-ca5da2766e14/GCF_013402815.2_ASM1340281v2_genomic.fna.gz --refList GCF_013402815.2_ASM1340281v2_genomic.fna/target_genomes.txt --output GCF_013402815.2_ASM1340281v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:59,092] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:59,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80128c34-4fb6-49f1-b903-8c93a02bfde3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:59,093] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80128c34-4fb6-49f1-b903-8c93a02bfde3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:59,101] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:06:59,101] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:06:59,102] [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
Natrinema salaciae	strain=DSM 25055	GCA_900110865.1	1186196	1186196	type	True	81.1648	884	1612	95	below_threshold
Natrinema amylolyticum	strain=LT61	GCA_020515625.1	2878679	2878679	type	True	80.9734	841	1612	95	below_threshold
Natrinema altunense	strain=AJ2	GCA_000731985.1	222984	222984	type	True	80.8191	729	1612	95	below_threshold
Natrinema altunense	strain=JCM 12890	GCA_000337155.1	222984	222984	type	True	80.8033	727	1612	95	below_threshold
Haloterrigena limicola	strain=JCM 13563	GCA_000337475.1	370323	370323	type	True	80.6015	645	1612	95	below_threshold
Halopiger salifodinae	strain=CGMCC 1.12284	GCA_900110455.1	1202768	1202768	type	True	80.5531	776	1612	95	below_threshold
Halopiger salifodinae	strain=KCY07-B2	GCA_000784335.1	1202768	1202768	type	True	80.5418	762	1612	95	below_threshold
Natrinema pallidum	strain=DSM 3751	GCA_000337615.1	69527	69527	type	True	80.5168	715	1612	95	below_threshold
Natrinema gari	strain=JCM 14663	GCA_000337175.1	419186	419186	type	True	80.4618	711	1612	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:59,106] [INFO] DFAST Taxonomy check result was written to GCF_013402815.2_ASM1340281v2_genomic.fna/tc_result.tsv
[2024-01-24 12:06:59,106] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:59,107] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:59,107] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80128c34-4fb6-49f1-b903-8c93a02bfde3/dqc_reference/checkm_data
[2024-01-24 12:06:59,108] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:59,158] [INFO] Task started: CheckM
[2024-01-24 12:06:59,158] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013402815.2_ASM1340281v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013402815.2_ASM1340281v2_genomic.fna/checkm_input GCF_013402815.2_ASM1340281v2_genomic.fna/checkm_result
[2024-01-24 12:08:01,808] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:01,809] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:01,831] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:01,831] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:01,831] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013402815.2_ASM1340281v2_genomic.fna/markers.fasta)
[2024-01-24 12:08:01,832] [INFO] Task started: Blastn
[2024-01-24 12:08:01,832] [INFO] Running command: blastn -query GCF_013402815.2_ASM1340281v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg80128c34-4fb6-49f1-b903-8c93a02bfde3/dqc_reference/reference_markers_gtdb.fasta -out GCF_013402815.2_ASM1340281v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:02,303] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:02,306] [INFO] Selected 9 target genomes.
[2024-01-24 12:08:02,306] [INFO] Target genome list was writen to GCF_013402815.2_ASM1340281v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:02,313] [INFO] Task started: fastANI
[2024-01-24 12:08:02,313] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd90b322-9e54-424c-b533-ca5da2766e14/GCF_013402815.2_ASM1340281v2_genomic.fna.gz --refList GCF_013402815.2_ASM1340281v2_genomic.fna/target_genomes_gtdb.txt --output GCF_013402815.2_ASM1340281v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:10,883] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:10,892] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:10,892] [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_013402815.1	s__Natrinema sp013402815	100.0	1453	1612	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005576615.1	s__Natrinema versiforme_A	81.1684	805	1612	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110865.1	s__Natrinema salaciae	81.1623	884	1612	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000731985.1	s__Natrinema altunense	80.8158	729	1612	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	98.98	98.00	0.96	0.93	4	-
GCF_000337475.1	s__Natrinema limicola	80.5576	650	1612	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110455.1	s__Natrinema salifodinae	80.5325	779	1612	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	100.00	100.00	0.98	0.98	2	-
GCF_000337615.1	s__Natrinema pallidum	80.4944	717	1612	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	98.94	98.94	0.86	0.86	2	-
GCF_000337175.1	s__Natrinema gari	80.4661	711	1612	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	98.50	98.45	0.93	0.92	3	-
GCF_900111485.1	s__Natrinema hispanicum_A	80.3383	670	1612	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	99.65	99.65	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:10,894] [INFO] GTDB search result was written to GCF_013402815.2_ASM1340281v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:10,894] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:10,897] [INFO] DFAST_QC result json was written to GCF_013402815.2_ASM1340281v2_genomic.fna/dqc_result.json
[2024-01-24 12:08:10,897] [INFO] DFAST_QC completed!
[2024-01-24 12:08:10,898] [INFO] Total running time: 0h1m46s