[2024-01-24 11:12:39,855] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:39,857] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:39,857] [INFO] DQC Reference Directory: /var/lib/cwl/stge95c83d9-254f-4f10-b3c9-1e7a4c9f4bdb/dqc_reference
[2024-01-24 11:12:41,256] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:41,257] [INFO] Task started: Prodigal
[2024-01-24 11:12:41,257] [INFO] Running command: gunzip -c /var/lib/cwl/stg660df749-5d98-47e2-bf9b-df10a0bb23e1/GCF_024362525.1_ASM2436252v1_genomic.fna.gz | prodigal -d GCF_024362525.1_ASM2436252v1_genomic.fna/cds.fna -a GCF_024362525.1_ASM2436252v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:59,133] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:59,134] [INFO] Task started: HMMsearch
[2024-01-24 11:12:59,134] [INFO] Running command: hmmsearch --tblout GCF_024362525.1_ASM2436252v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge95c83d9-254f-4f10-b3c9-1e7a4c9f4bdb/dqc_reference/reference_markers.hmm GCF_024362525.1_ASM2436252v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:59,413] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:59,414] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg660df749-5d98-47e2-bf9b-df10a0bb23e1/GCF_024362525.1_ASM2436252v1_genomic.fna.gz]
[2024-01-24 11:12:59,460] [INFO] Query marker FASTA was written to GCF_024362525.1_ASM2436252v1_genomic.fna/markers.fasta
[2024-01-24 11:12:59,460] [INFO] Task started: Blastn
[2024-01-24 11:12:59,460] [INFO] Running command: blastn -query GCF_024362525.1_ASM2436252v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge95c83d9-254f-4f10-b3c9-1e7a4c9f4bdb/dqc_reference/reference_markers.fasta -out GCF_024362525.1_ASM2436252v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:00,070] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:00,073] [INFO] Selected 15 target genomes.
[2024-01-24 11:13:00,073] [INFO] Target genome list was writen to GCF_024362525.1_ASM2436252v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:00,099] [INFO] Task started: fastANI
[2024-01-24 11:13:00,099] [INFO] Running command: fastANI --query /var/lib/cwl/stg660df749-5d98-47e2-bf9b-df10a0bb23e1/GCF_024362525.1_ASM2436252v1_genomic.fna.gz --refList GCF_024362525.1_ASM2436252v1_genomic.fna/target_genomes.txt --output GCF_024362525.1_ASM2436252v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:15,847] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:15,847] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge95c83d9-254f-4f10-b3c9-1e7a4c9f4bdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:15,848] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge95c83d9-254f-4f10-b3c9-1e7a4c9f4bdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:15,860] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:13:15,861] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:13:15,861] [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
Natronococcus jeotgali	strain=DSM 18795	GCA_000337695.1	413812	413812	type	True	80.7738	640	1328	95	below_threshold
Natronococcus amylolyticus	strain=DSM 10524	GCA_000337675.1	44470	44470	type	True	80.6671	680	1328	95	below_threshold
Natronococcus pandeyae	strain=LS1_42	GCA_008122205.1	2055836	2055836	type	True	80.4251	756	1328	95	below_threshold
Halopiger xanaduensis	strain=SH-6	GCA_000217715.1	387343	387343	type	True	80.2269	655	1328	95	below_threshold
Halobiforma lacisalsi	strain=AJ5	GCA_000226975.3	229731	229731	type	True	80.2031	643	1328	95	below_threshold
Halobiforma lacisalsi	strain=AJ5	GCA_000336655.1	229731	229731	type	True	80.1757	645	1328	95	below_threshold
Halobiforma haloterrestris	strain=DSM 13078	GCA_900112205.1	148448	148448	type	True	80.1009	653	1328	95	below_threshold
Halopiger goleimassiliensis	strain=IIH3	GCA_000455345.1	1293048	1293048	type	True	80.0818	631	1328	95	below_threshold
Halopiger salifodinae	strain=CGMCC 1.12284	GCA_900110455.1	1202768	1202768	type	True	80.0471	617	1328	95	below_threshold
Halopiger salifodinae	strain=KCY07-B2	GCA_000784335.1	1202768	1202768	type	True	79.9632	623	1328	95	below_threshold
Natrinema amylolyticum	strain=LT61	GCA_020515625.1	2878679	2878679	type	True	79.8746	616	1328	95	below_threshold
Natrinema salaciae	strain=DSM 25055	GCA_900110865.1	1186196	1186196	type	True	79.7441	644	1328	95	below_threshold
Natronorubrum halalkaliphilum	strain=JWXQ-INN-674	GCA_009834785.1	2691917	2691917	type	True	79.539	646	1328	95	below_threshold
Natrinema gari	strain=JCM 14663	GCA_000337175.1	419186	419186	type	True	79.5153	522	1328	95	below_threshold
Natrinema pallidum	strain=DSM 3751	GCA_000337615.1	69527	69527	type	True	79.3963	548	1328	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:15,862] [INFO] DFAST Taxonomy check result was written to GCF_024362525.1_ASM2436252v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:15,863] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:15,863] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:15,863] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge95c83d9-254f-4f10-b3c9-1e7a4c9f4bdb/dqc_reference/checkm_data
[2024-01-24 11:13:15,864] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:15,905] [INFO] Task started: CheckM
[2024-01-24 11:13:15,906] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024362525.1_ASM2436252v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024362525.1_ASM2436252v1_genomic.fna/checkm_input GCF_024362525.1_ASM2436252v1_genomic.fna/checkm_result
[2024-01-24 11:14:06,108] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:06,112] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:06,136] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:06,136] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:06,137] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024362525.1_ASM2436252v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:06,137] [INFO] Task started: Blastn
[2024-01-24 11:14:06,138] [INFO] Running command: blastn -query GCF_024362525.1_ASM2436252v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge95c83d9-254f-4f10-b3c9-1e7a4c9f4bdb/dqc_reference/reference_markers_gtdb.fasta -out GCF_024362525.1_ASM2436252v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:06,662] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:06,666] [INFO] Selected 14 target genomes.
[2024-01-24 11:14:06,667] [INFO] Target genome list was writen to GCF_024362525.1_ASM2436252v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:06,677] [INFO] Task started: fastANI
[2024-01-24 11:14:06,678] [INFO] Running command: fastANI --query /var/lib/cwl/stg660df749-5d98-47e2-bf9b-df10a0bb23e1/GCF_024362525.1_ASM2436252v1_genomic.fna.gz --refList GCF_024362525.1_ASM2436252v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024362525.1_ASM2436252v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:20,112] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:20,136] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:14:20,137] [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_000337695.1	s__Natronococcus jeotgali	80.79	639	1328	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	95.54	95.54	0.86	0.86	2	-
GCA_003559215.1	s__Natronococcus sp003559215	80.7596	630	1328	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	99.83	99.81	0.98	0.98	4	-
GCF_000337675.1	s__Natronococcus amylolyticus	80.7223	674	1328	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008122205.1	s__Natronococcus sp008122205	80.428	754	1328	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000217715.1	s__Halopiger xanaduensis	80.2562	654	1328	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017357105.1	s__Tc-Br11 sp017357105	80.2486	630	1328	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Tc-Br11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953745.1	s__Natrinema saccharevitans	80.2457	619	1328	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000226975.2	s__Halobiforma lacisalsi	80.195	644	1328	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halobiforma	95.4693	99.98	99.98	1.00	1.00	2	-
GCF_900112205.1	s__Halobiforma haloterrestris	80.1418	649	1328	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halobiforma	95.4693	N/A	N/A	N/A	N/A	1	-
GCF_900110455.1	s__Natrinema salifodinae	80.0296	618	1328	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	100.00	100.00	0.98	0.98	2	-
GCF_900110865.1	s__Natrinema salaciae	79.7877	640	1328	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002494345.1	s__Natrinema ejinorense	79.6271	570	1328	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	95.42	95.42	0.91	0.91	2	-
GCF_009834785.1	s__Natronorubrum halalkaliphilum	79.5248	647	1328	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337615.1	s__Natrinema pallidum	79.3997	548	1328	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	98.94	98.94	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:20,138] [INFO] GTDB search result was written to GCF_024362525.1_ASM2436252v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:20,139] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:20,143] [INFO] DFAST_QC result json was written to GCF_024362525.1_ASM2436252v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:20,143] [INFO] DFAST_QC completed!
[2024-01-24 11:14:20,143] [INFO] Total running time: 0h1m40s