[2024-01-24 11:58:20,665] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:20,667] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:20,667] [INFO] DQC Reference Directory: /var/lib/cwl/stg934897c2-16a2-46e3-9e15-bb2da0dbe92e/dqc_reference
[2024-01-24 11:58:21,873] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:21,873] [INFO] Task started: Prodigal
[2024-01-24 11:58:21,874] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9acddab-91ea-4b10-87ca-f6c3408b7d3b/GCF_002156705.1_ASM215670v1_genomic.fna.gz | prodigal -d GCF_002156705.1_ASM215670v1_genomic.fna/cds.fna -a GCF_002156705.1_ASM215670v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:58:40,459] [INFO] Task succeeded: Prodigal
[2024-01-24 11:58:40,459] [INFO] Task started: HMMsearch
[2024-01-24 11:58:40,459] [INFO] Running command: hmmsearch --tblout GCF_002156705.1_ASM215670v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg934897c2-16a2-46e3-9e15-bb2da0dbe92e/dqc_reference/reference_markers.hmm GCF_002156705.1_ASM215670v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:58:40,707] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:58:40,708] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgb9acddab-91ea-4b10-87ca-f6c3408b7d3b/GCF_002156705.1_ASM215670v1_genomic.fna.gz]
[2024-01-24 11:58:40,740] [INFO] Query marker FASTA was written to GCF_002156705.1_ASM215670v1_genomic.fna/markers.fasta
[2024-01-24 11:58:40,741] [INFO] Task started: Blastn
[2024-01-24 11:58:40,741] [INFO] Running command: blastn -query GCF_002156705.1_ASM215670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg934897c2-16a2-46e3-9e15-bb2da0dbe92e/dqc_reference/reference_markers.fasta -out GCF_002156705.1_ASM215670v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:58:41,306] [INFO] Task succeeded: Blastn
[2024-01-24 11:58:41,312] [INFO] Selected 12 target genomes.
[2024-01-24 11:58:41,313] [INFO] Target genome list was writen to GCF_002156705.1_ASM215670v1_genomic.fna/target_genomes.txt
[2024-01-24 11:58:41,321] [INFO] Task started: fastANI
[2024-01-24 11:58:41,322] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9acddab-91ea-4b10-87ca-f6c3408b7d3b/GCF_002156705.1_ASM215670v1_genomic.fna.gz --refList GCF_002156705.1_ASM215670v1_genomic.fna/target_genomes.txt --output GCF_002156705.1_ASM215670v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:58:52,118] [INFO] Task succeeded: fastANI
[2024-01-24 11:58:52,119] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg934897c2-16a2-46e3-9e15-bb2da0dbe92e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:58:52,119] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg934897c2-16a2-46e3-9e15-bb2da0dbe92e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:58:52,130] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:58:52,130] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:58:52,131] [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
Halopiger goleimassiliensis	strain=IIH3	GCA_000455345.1	1293048	1293048	type	True	80.9903	726	1310	95	below_threshold
Haloterrigena salina	strain=JCM 13891	GCA_000337495.1	504937	504937	type	True	80.3797	680	1310	95	below_threshold
Halopiger xanaduensis	strain=SH-6	GCA_000217715.1	387343	387343	type	True	80.3392	654	1310	95	below_threshold
Halopiger aswanensis	strain=DSM 13151	GCA_003610195.1	148449	148449	type	True	80.3269	665	1310	95	below_threshold
Natrinema pellirubrum	strain=DSM 15624	GCA_000337635.1	69525	69525	type	True	80.1611	606	1310	95	below_threshold
Natrinema pellirubrum	strain=DSM 15624	GCA_000230735.3	69525	69525	type	True	80.1407	632	1310	95	below_threshold
Haloterrigena salifodinae	strain=ZY19	GCA_003977755.1	2675099	2675099	type	True	80.1219	655	1310	95	below_threshold
Natrinema amylolyticum	strain=LT61	GCA_020515625.1	2878679	2878679	type	True	79.8737	643	1310	95	below_threshold
Haloterrigena hispanica	strain=DSM 18328	GCA_004217335.1	392421	392421	type	True	79.8586	548	1310	95	below_threshold
Natronococcus jeotgali	strain=DSM 18795	GCA_000337695.1	413812	413812	type	True	79.838	618	1310	95	below_threshold
Haloterrigena limicola	strain=JCM 13563	GCA_000337475.1	370323	370323	type	True	79.8343	538	1310	95	below_threshold
Natronolimnobius baerhuensis	strain=CGMCC 1.3597	GCA_002177135.1	253108	253108	type	True	79.2385	547	1310	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:58:52,132] [INFO] DFAST Taxonomy check result was written to GCF_002156705.1_ASM215670v1_genomic.fna/tc_result.tsv
[2024-01-24 11:58:52,132] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:58:52,132] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:58:52,133] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg934897c2-16a2-46e3-9e15-bb2da0dbe92e/dqc_reference/checkm_data
[2024-01-24 11:58:52,133] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:58:52,170] [INFO] Task started: CheckM
[2024-01-24 11:58:52,170] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002156705.1_ASM215670v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002156705.1_ASM215670v1_genomic.fna/checkm_input GCF_002156705.1_ASM215670v1_genomic.fna/checkm_result
[2024-01-24 11:59:43,933] [INFO] Task succeeded: CheckM
[2024-01-24 11:59:43,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:59:43,952] [INFO] ===== Completeness check finished =====
[2024-01-24 11:59:43,952] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:59:43,953] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002156705.1_ASM215670v1_genomic.fna/markers.fasta)
[2024-01-24 11:59:43,953] [INFO] Task started: Blastn
[2024-01-24 11:59:43,953] [INFO] Running command: blastn -query GCF_002156705.1_ASM215670v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg934897c2-16a2-46e3-9e15-bb2da0dbe92e/dqc_reference/reference_markers_gtdb.fasta -out GCF_002156705.1_ASM215670v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:44,458] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:44,462] [INFO] Selected 10 target genomes.
[2024-01-24 11:59:44,462] [INFO] Target genome list was writen to GCF_002156705.1_ASM215670v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:59:44,470] [INFO] Task started: fastANI
[2024-01-24 11:59:44,471] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9acddab-91ea-4b10-87ca-f6c3408b7d3b/GCF_002156705.1_ASM215670v1_genomic.fna.gz --refList GCF_002156705.1_ASM215670v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002156705.1_ASM215670v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:59:54,073] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:54,088] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:59:54,088] [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_002156705.1	s__Natrarchaeobaculum aegyptiacum	100.0	1310	1310	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrarchaeobaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001563805.1	s__Natrarchaeobaculum sp001563805	81.9575	555	1310	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrarchaeobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003430825.1	s__Natrarchaeobaculum sulfurireducens	81.1677	741	1310	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrarchaeobaculum	95.0	99.22	99.22	0.92	0.92	2	-
GCF_000455345.1	s__Halopiger_A goleimassiliensis	80.9839	728	1310	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610195.1	s__Halopiger aswanensis	80.3325	663	1310	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003841505.1	s__Natrarchaeobius chitinivorans	80.1084	635	1310	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrarchaeobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003977755.1	s__Haloterrigena salifodinae	80.1073	656	1310	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	98.23	98.23	0.92	0.92	2	-
GCF_000337475.1	s__Natrinema limicola	79.8475	536	1310	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217335.1	s__Natrinema hispanicum	79.8471	552	1310	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002177135.1	s__Natronolimnobius baerhuensis	79.2387	547	1310	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronolimnobius	95.0	99.89	99.89	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:59:54,089] [INFO] GTDB search result was written to GCF_002156705.1_ASM215670v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:59:54,090] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:59:54,092] [INFO] DFAST_QC result json was written to GCF_002156705.1_ASM215670v1_genomic.fna/dqc_result.json
[2024-01-24 11:59:54,093] [INFO] DFAST_QC completed!
[2024-01-24 11:59:54,093] [INFO] Total running time: 0h1m33s