[2024-01-24 12:16:03,293] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:16:03,295] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:16:03,295] [INFO] DQC Reference Directory: /var/lib/cwl/stg90e5aae0-79ff-422c-855a-7fe331c54002/dqc_reference
[2024-01-24 12:16:04,522] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:16:04,523] [INFO] Task started: Prodigal
[2024-01-24 12:16:04,523] [INFO] Running command: gunzip -c /var/lib/cwl/stg0418444d-efc1-4d16-b0ad-0796c950a5bd/GCF_024296665.1_ASM2429666v1_genomic.fna.gz | prodigal -d GCF_024296665.1_ASM2429666v1_genomic.fna/cds.fna -a GCF_024296665.1_ASM2429666v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:16:19,680] [INFO] Task succeeded: Prodigal
[2024-01-24 12:16:19,681] [INFO] Task started: HMMsearch
[2024-01-24 12:16:19,681] [INFO] Running command: hmmsearch --tblout GCF_024296665.1_ASM2429666v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90e5aae0-79ff-422c-855a-7fe331c54002/dqc_reference/reference_markers.hmm GCF_024296665.1_ASM2429666v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:16:19,893] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:16:19,895] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg0418444d-efc1-4d16-b0ad-0796c950a5bd/GCF_024296665.1_ASM2429666v1_genomic.fna.gz]
[2024-01-24 12:16:19,929] [INFO] Query marker FASTA was written to GCF_024296665.1_ASM2429666v1_genomic.fna/markers.fasta
[2024-01-24 12:16:19,929] [INFO] Task started: Blastn
[2024-01-24 12:16:19,929] [INFO] Running command: blastn -query GCF_024296665.1_ASM2429666v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90e5aae0-79ff-422c-855a-7fe331c54002/dqc_reference/reference_markers.fasta -out GCF_024296665.1_ASM2429666v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:20,475] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:20,479] [INFO] Selected 11 target genomes.
[2024-01-24 12:16:20,480] [INFO] Target genome list was writen to GCF_024296665.1_ASM2429666v1_genomic.fna/target_genomes.txt
[2024-01-24 12:16:20,482] [INFO] Task started: fastANI
[2024-01-24 12:16:20,482] [INFO] Running command: fastANI --query /var/lib/cwl/stg0418444d-efc1-4d16-b0ad-0796c950a5bd/GCF_024296665.1_ASM2429666v1_genomic.fna.gz --refList GCF_024296665.1_ASM2429666v1_genomic.fna/target_genomes.txt --output GCF_024296665.1_ASM2429666v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:31,861] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:31,862] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90e5aae0-79ff-422c-855a-7fe331c54002/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:31,862] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90e5aae0-79ff-422c-855a-7fe331c54002/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:31,875] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:16:31,875] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:16:31,875] [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 xanaduensis	strain=SH-6	GCA_000217715.1	387343	387343	type	True	81.1795	697	1207	95	below_threshold
Haloterrigena alkaliphila	strain=KZCA68	GCA_017352155.2	2816475	2816475	type	True	81.0497	710	1207	95	below_threshold
Halopiger goleimassiliensis	strain=IIH3	GCA_000455345.1	1293048	1293048	type	True	81.0252	679	1207	95	below_threshold
Halopiger aswanensis	strain=DSM 13151	GCA_003610195.1	148449	148449	type	True	80.9822	715	1207	95	below_threshold
Natrinema pellirubrum	strain=DSM 15624	GCA_000337635.1	69525	69525	type	True	80.6511	643	1207	95	below_threshold
Haloterrigena salifodinae	strain=ZY19	GCA_003977755.1	2675099	2675099	type	True	80.6129	718	1207	95	below_threshold
Natronococcus pandeyae	strain=LS1_42	GCA_008122205.1	2055836	2055836	type	True	80.5691	726	1207	95	below_threshold
Natrinema amylolyticum	strain=LT61	GCA_020515625.1	2878679	2878679	type	True	80.5418	683	1207	95	below_threshold
Natrinema salaciae	strain=DSM 25055	GCA_900110865.1	1186196	1186196	type	True	80.4774	717	1207	95	below_threshold
Natronobacterium texcoconense	strain=DSM 24767	GCA_900104065.1	1095778	1095778	type	True	80.261	659	1207	95	below_threshold
Natronorubrum halalkaliphilum	strain=JWXQ-INN-674	GCA_009834785.1	2691917	2691917	type	True	79.5884	635	1207	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:31,876] [INFO] DFAST Taxonomy check result was written to GCF_024296665.1_ASM2429666v1_genomic.fna/tc_result.tsv
[2024-01-24 12:16:31,877] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:31,877] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:31,877] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90e5aae0-79ff-422c-855a-7fe331c54002/dqc_reference/checkm_data
[2024-01-24 12:16:31,878] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:31,913] [INFO] Task started: CheckM
[2024-01-24 12:16:31,914] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024296665.1_ASM2429666v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024296665.1_ASM2429666v1_genomic.fna/checkm_input GCF_024296665.1_ASM2429666v1_genomic.fna/checkm_result
[2024-01-24 12:17:15,061] [INFO] Task succeeded: CheckM
[2024-01-24 12:17:15,063] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:17:15,084] [INFO] ===== Completeness check finished =====
[2024-01-24 12:17:15,084] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:17:15,085] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024296665.1_ASM2429666v1_genomic.fna/markers.fasta)
[2024-01-24 12:17:15,085] [INFO] Task started: Blastn
[2024-01-24 12:17:15,085] [INFO] Running command: blastn -query GCF_024296665.1_ASM2429666v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90e5aae0-79ff-422c-855a-7fe331c54002/dqc_reference/reference_markers_gtdb.fasta -out GCF_024296665.1_ASM2429666v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:17:15,613] [INFO] Task succeeded: Blastn
[2024-01-24 12:17:15,617] [INFO] Selected 13 target genomes.
[2024-01-24 12:17:15,617] [INFO] Target genome list was writen to GCF_024296665.1_ASM2429666v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:17:15,628] [INFO] Task started: fastANI
[2024-01-24 12:17:15,629] [INFO] Running command: fastANI --query /var/lib/cwl/stg0418444d-efc1-4d16-b0ad-0796c950a5bd/GCF_024296665.1_ASM2429666v1_genomic.fna.gz --refList GCF_024296665.1_ASM2429666v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024296665.1_ASM2429666v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:27,575] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:27,598] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:17:27,599] [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_000217715.1	s__Halopiger xanaduensis	81.1925	697	1207	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455345.1	s__Halopiger_A goleimassiliensis	81.0849	672	1207	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_017352155.1	s__Haloterrigena sp017352155	81.0347	684	1207	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610195.1	s__Halopiger aswanensis	80.9734	716	1207	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953745.1	s__Natrinema saccharevitans	80.9714	674	1207	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000690595.2	s__Natrinema mahii	80.8751	648	1207	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005576615.1	s__Natrinema versiforme_A	80.7179	668	1207	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001563805.1	s__Natrarchaeobaculum sp001563805	80.5539	494	1207	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrarchaeobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003977755.1	s__Haloterrigena salifodinae	80.5161	730	1207	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	98.23	98.23	0.92	0.92	2	-
GCF_900110865.1	s__Natrinema salaciae	80.4536	720	1207	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	80.2429	645	1207	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	95.42	95.42	0.91	0.91	2	-
GCF_003841465.1	s__Natrarchaeobius chitinivorans_A	80.1751	633	1207	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrarchaeobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834785.1	s__Natronorubrum halalkaliphilum	79.6129	632	1207	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:27,600] [INFO] GTDB search result was written to GCF_024296665.1_ASM2429666v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:27,601] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:27,604] [INFO] DFAST_QC result json was written to GCF_024296665.1_ASM2429666v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:27,604] [INFO] DFAST_QC completed!
[2024-01-24 12:17:27,604] [INFO] Total running time: 0h1m24s