[2024-01-25 20:21:05,803] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:21:05,805] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:21:05,805] [INFO] DQC Reference Directory: /var/lib/cwl/stge78ecbff-ed5c-47b8-91ff-61e803bc576a/dqc_reference
[2024-01-25 20:21:06,903] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:21:06,904] [INFO] Task started: Prodigal
[2024-01-25 20:21:06,904] [INFO] Running command: gunzip -c /var/lib/cwl/stge4ebfc5d-06ef-44fd-9668-f4a979c99938/GCF_024494645.1_ASM2449464v1_genomic.fna.gz | prodigal -d GCF_024494645.1_ASM2449464v1_genomic.fna/cds.fna -a GCF_024494645.1_ASM2449464v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:21:23,184] [INFO] Task succeeded: Prodigal
[2024-01-25 20:21:23,184] [INFO] Task started: HMMsearch
[2024-01-25 20:21:23,184] [INFO] Running command: hmmsearch --tblout GCF_024494645.1_ASM2449464v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge78ecbff-ed5c-47b8-91ff-61e803bc576a/dqc_reference/reference_markers.hmm GCF_024494645.1_ASM2449464v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:21:23,392] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:21:23,393] [WARNING] Found 3/6 markers. [/var/lib/cwl/stge4ebfc5d-06ef-44fd-9668-f4a979c99938/GCF_024494645.1_ASM2449464v1_genomic.fna.gz]
[2024-01-25 20:21:23,423] [INFO] Query marker FASTA was written to GCF_024494645.1_ASM2449464v1_genomic.fna/markers.fasta
[2024-01-25 20:21:23,423] [INFO] Task started: Blastn
[2024-01-25 20:21:23,423] [INFO] Running command: blastn -query GCF_024494645.1_ASM2449464v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge78ecbff-ed5c-47b8-91ff-61e803bc576a/dqc_reference/reference_markers.fasta -out GCF_024494645.1_ASM2449464v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:23,915] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:23,917] [INFO] Selected 7 target genomes.
[2024-01-25 20:21:23,917] [INFO] Target genome list was writen to GCF_024494645.1_ASM2449464v1_genomic.fna/target_genomes.txt
[2024-01-25 20:21:23,924] [INFO] Task started: fastANI
[2024-01-25 20:21:23,924] [INFO] Running command: fastANI --query /var/lib/cwl/stge4ebfc5d-06ef-44fd-9668-f4a979c99938/GCF_024494645.1_ASM2449464v1_genomic.fna.gz --refList GCF_024494645.1_ASM2449464v1_genomic.fna/target_genomes.txt --output GCF_024494645.1_ASM2449464v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:21:28,392] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:28,392] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge78ecbff-ed5c-47b8-91ff-61e803bc576a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:21:28,392] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge78ecbff-ed5c-47b8-91ff-61e803bc576a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:21:28,398] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:21:28,398] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:21:28,398] [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
Halohasta litchfieldiae	strain=DSM 22187	GCA_900109065.1	1073996	1073996	type	True	83.277	707	1250	95	below_threshold
Halohasta litchfieldiae	strain=tADL	GCA_002788215.1	1073996	1073996	type	True	83.2687	727	1250	95	below_threshold
Halonotius aquaticus	strain=F13-13	GCA_003605575.1	2216978	2216978	type	True	79.6707	383	1250	95	below_threshold
Halonotius roseus	strain=F9-27	GCA_006861655.1	2511997	2511997	type	True	79.67	441	1250	95	below_threshold
Halonotius terrestris	strain=F15B	GCA_006861665.1	2487750	2487750	type	True	79.555	446	1250	95	below_threshold
Halonotius pteroides	strain=CECT 7525	GCA_003605635.1	268735	268735	type	True	78.9916	366	1250	95	below_threshold
Haloferax gibbonsii	strain=ATCC 33959	GCA_000336775.1	35746	35746	type	True	77.48	324	1250	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:21:28,400] [INFO] DFAST Taxonomy check result was written to GCF_024494645.1_ASM2449464v1_genomic.fna/tc_result.tsv
[2024-01-25 20:21:28,401] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:21:28,402] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:21:28,402] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge78ecbff-ed5c-47b8-91ff-61e803bc576a/dqc_reference/checkm_data
[2024-01-25 20:21:28,403] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:21:28,443] [INFO] Task started: CheckM
[2024-01-25 20:21:28,443] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024494645.1_ASM2449464v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024494645.1_ASM2449464v1_genomic.fna/checkm_input GCF_024494645.1_ASM2449464v1_genomic.fna/checkm_result
[2024-01-25 20:22:14,090] [INFO] Task succeeded: CheckM
[2024-01-25 20:22:14,091] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:22:14,127] [INFO] ===== Completeness check finished =====
[2024-01-25 20:22:14,127] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:22:14,128] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024494645.1_ASM2449464v1_genomic.fna/markers.fasta)
[2024-01-25 20:22:14,128] [INFO] Task started: Blastn
[2024-01-25 20:22:14,129] [INFO] Running command: blastn -query GCF_024494645.1_ASM2449464v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge78ecbff-ed5c-47b8-91ff-61e803bc576a/dqc_reference/reference_markers_gtdb.fasta -out GCF_024494645.1_ASM2449464v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:14,647] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:14,651] [INFO] Selected 10 target genomes.
[2024-01-25 20:22:14,651] [INFO] Target genome list was writen to GCF_024494645.1_ASM2449464v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:22:14,673] [INFO] Task started: fastANI
[2024-01-25 20:22:14,674] [INFO] Running command: fastANI --query /var/lib/cwl/stge4ebfc5d-06ef-44fd-9668-f4a979c99938/GCF_024494645.1_ASM2449464v1_genomic.fna.gz --refList GCF_024494645.1_ASM2449464v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024494645.1_ASM2449464v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:22:20,906] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:20,913] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:22:20,913] [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_900109065.1	s__Halohasta litchfieldiae	83.2754	708	1250	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halohasta	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006861655.1	s__Halonotius roseus	79.6607	440	1250	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halonotius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605575.1	s__Halonotius sp003605575	79.6366	386	1250	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halonotius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006861665.1	s__Halonotius terrestris	79.5711	443	1250	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halonotius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000496215.1	s__Halonotius sp000496215	79.4994	357	1250	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halonotius	95.0	96.16	96.16	0.87	0.87	2	-
GCA_003554115.1	s__Halohasta sp003554115	79.3901	257	1250	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halohasta	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605635.1	s__Halonotius pteroides	78.9917	366	1250	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halonotius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001563795.1	s__Halohasta sp001563795	78.9601	372	1250	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halohasta	95.0	99.75	99.75	0.85	0.85	2	-
GCF_000337835.1	s__Haloferax sulfurifontis	77.4749	333	1250	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	96.9285	99.04	99.04	0.92	0.92	2	-
GCF_000336775.1	s__Haloferax gibbonsii	77.4714	325	1250	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	96.8304	98.89	98.78	0.89	0.88	5	-
--------------------------------------------------------------------------------
[2024-01-25 20:22:20,915] [INFO] GTDB search result was written to GCF_024494645.1_ASM2449464v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:22:20,915] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:22:20,918] [INFO] DFAST_QC result json was written to GCF_024494645.1_ASM2449464v1_genomic.fna/dqc_result.json
[2024-01-25 20:22:20,918] [INFO] DFAST_QC completed!
[2024-01-25 20:22:20,918] [INFO] Total running time: 0h1m15s