[2024-01-25 17:53:20,553] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:53:20,554] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:53:20,554] [INFO] DQC Reference Directory: /var/lib/cwl/stg11ebf1ed-29bd-4562-a67c-f90cee27662a/dqc_reference
[2024-01-25 17:53:21,686] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:53:21,687] [INFO] Task started: Prodigal
[2024-01-25 17:53:21,687] [INFO] Running command: gunzip -c /var/lib/cwl/stg3033ed39-2d6e-470f-a96c-289ec5623c16/GCF_024494575.1_ASM2449457v1_genomic.fna.gz | prodigal -d GCF_024494575.1_ASM2449457v1_genomic.fna/cds.fna -a GCF_024494575.1_ASM2449457v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:53:32,334] [INFO] Task succeeded: Prodigal
[2024-01-25 17:53:32,334] [INFO] Task started: HMMsearch
[2024-01-25 17:53:32,334] [INFO] Running command: hmmsearch --tblout GCF_024494575.1_ASM2449457v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11ebf1ed-29bd-4562-a67c-f90cee27662a/dqc_reference/reference_markers.hmm GCF_024494575.1_ASM2449457v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:53:32,535] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:53:32,536] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg3033ed39-2d6e-470f-a96c-289ec5623c16/GCF_024494575.1_ASM2449457v1_genomic.fna.gz]
[2024-01-25 17:53:32,560] [INFO] Query marker FASTA was written to GCF_024494575.1_ASM2449457v1_genomic.fna/markers.fasta
[2024-01-25 17:53:32,561] [INFO] Task started: Blastn
[2024-01-25 17:53:32,561] [INFO] Running command: blastn -query GCF_024494575.1_ASM2449457v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11ebf1ed-29bd-4562-a67c-f90cee27662a/dqc_reference/reference_markers.fasta -out GCF_024494575.1_ASM2449457v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:53:33,052] [INFO] Task succeeded: Blastn
[2024-01-25 17:53:33,054] [INFO] Selected 10 target genomes.
[2024-01-25 17:53:33,055] [INFO] Target genome list was writen to GCF_024494575.1_ASM2449457v1_genomic.fna/target_genomes.txt
[2024-01-25 17:53:33,076] [INFO] Task started: fastANI
[2024-01-25 17:53:33,077] [INFO] Running command: fastANI --query /var/lib/cwl/stg3033ed39-2d6e-470f-a96c-289ec5623c16/GCF_024494575.1_ASM2449457v1_genomic.fna.gz --refList GCF_024494575.1_ASM2449457v1_genomic.fna/target_genomes.txt --output GCF_024494575.1_ASM2449457v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:53:41,785] [INFO] Task succeeded: fastANI
[2024-01-25 17:53:41,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11ebf1ed-29bd-4562-a67c-f90cee27662a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:53:41,786] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11ebf1ed-29bd-4562-a67c-f90cee27662a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:53:41,793] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:53:41,793] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:53:41,793] [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
Halorubrum salinum	strain=GX71	GCA_024494575.1	767517	767517	type	True	100.0	892	905	95	conclusive
Halorubrum salsamenti	strain=Y69	GCA_007671685.1	2583990	2583990	type	True	85.0383	626	905	95	below_threshold
Halorubrum depositum	strain=Y78	GCA_007671725.1	2583992	2583992	type	True	84.9619	660	905	95	below_threshold
Halorubrum salipaludis	strain=WN019	GCA_002286985.1	2032630	2032630	type	True	84.8395	660	905	95	below_threshold
Halorubrum lipolyticum	strain=DSM 21995	GCA_000337375.1	368624	368624	type	True	84.8321	621	905	95	below_threshold
Halorubrum rutilum	strain=YJ-18-S1	GCA_024494565.1	1364933	1364933	type	True	84.8293	643	905	95	below_threshold
Halorubrum halophilum	strain=B8	GCA_000739595.1	413816	413816	type	True	84.782	635	905	95	below_threshold
Halorubrum saccharovorum	strain=DSM 1137	GCA_000337915.1	2248	2248	type	True	84.7787	638	905	95	below_threshold
Halorubrum kocurii	strain=JCM 14978	GCA_000337355.1	478441	478441	type	True	84.6655	610	905	95	below_threshold
Halorubrum aidingense	strain=JCM 13560	GCA_000336995.1	368623	368623	type	True	84.3222	610	905	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:53:41,794] [INFO] DFAST Taxonomy check result was written to GCF_024494575.1_ASM2449457v1_genomic.fna/tc_result.tsv
[2024-01-25 17:53:41,795] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:53:41,795] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:53:41,795] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11ebf1ed-29bd-4562-a67c-f90cee27662a/dqc_reference/checkm_data
[2024-01-25 17:53:41,796] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:53:41,824] [INFO] Task started: CheckM
[2024-01-25 17:53:41,824] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024494575.1_ASM2449457v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024494575.1_ASM2449457v1_genomic.fna/checkm_input GCF_024494575.1_ASM2449457v1_genomic.fna/checkm_result
[2024-01-25 17:54:13,176] [INFO] Task succeeded: CheckM
[2024-01-25 17:54:13,177] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-25 17:54:13,194] [INFO] ===== Completeness check finished =====
[2024-01-25 17:54:13,195] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:54:13,195] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024494575.1_ASM2449457v1_genomic.fna/markers.fasta)
[2024-01-25 17:54:13,195] [INFO] Task started: Blastn
[2024-01-25 17:54:13,195] [INFO] Running command: blastn -query GCF_024494575.1_ASM2449457v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11ebf1ed-29bd-4562-a67c-f90cee27662a/dqc_reference/reference_markers_gtdb.fasta -out GCF_024494575.1_ASM2449457v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:13,731] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:13,734] [INFO] Selected 10 target genomes.
[2024-01-25 17:54:13,734] [INFO] Target genome list was writen to GCF_024494575.1_ASM2449457v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:54:13,744] [INFO] Task started: fastANI
[2024-01-25 17:54:13,744] [INFO] Running command: fastANI --query /var/lib/cwl/stg3033ed39-2d6e-470f-a96c-289ec5623c16/GCF_024494575.1_ASM2449457v1_genomic.fna.gz --refList GCF_024494575.1_ASM2449457v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024494575.1_ASM2449457v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:54:22,294] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:22,300] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:54:22,301] [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_000746205.1	s__Halorubrum sp000746205	93.244	733	905	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007671685.1	s__Halorubrum salsamenti	85.0492	626	905	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007671725.1	s__Halorubrum depositum	84.949	659	905	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003781945.1	s__Halorubrum sp003781945	84.8565	633	905	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337915.1	s__Halorubrum saccharovorum	84.855	631	905	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739595.1	s__Halorubrum halophilum	84.8273	631	905	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	98.11	98.11	0.88	0.88	2	-
GCF_000337375.1	s__Halorubrum lipolyticum	84.8258	622	905	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002286985.1	s__Halorubrum sp002286985	84.7958	663	905	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	98.74	98.74	0.87	0.87	2	-
GCF_000337355.1	s__Halorubrum kocurii	84.6726	609	905	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000336995.1	s__Halorubrum aidingense	84.2904	613	905	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:54:22,302] [INFO] GTDB search result was written to GCF_024494575.1_ASM2449457v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:54:22,303] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:54:22,306] [INFO] DFAST_QC result json was written to GCF_024494575.1_ASM2449457v1_genomic.fna/dqc_result.json
[2024-01-25 17:54:22,306] [INFO] DFAST_QC completed!
[2024-01-25 17:54:22,306] [INFO] Total running time: 0h1m2s