[2024-01-24 12:36:35,253] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:35,256] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:35,256] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b6a6ffa-fff6-4abc-8e4f-313b52b3cbd3/dqc_reference
[2024-01-24 12:36:36,488] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:36,489] [INFO] Task started: Prodigal
[2024-01-24 12:36:36,489] [INFO] Running command: gunzip -c /var/lib/cwl/stg91911e86-9344-4a69-aa6d-26148efc7ab3/GCF_024449025.1_ASM2444902v1_genomic.fna.gz | prodigal -d GCF_024449025.1_ASM2444902v1_genomic.fna/cds.fna -a GCF_024449025.1_ASM2444902v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:50,888] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:50,888] [INFO] Task started: HMMsearch
[2024-01-24 12:36:50,889] [INFO] Running command: hmmsearch --tblout GCF_024449025.1_ASM2444902v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b6a6ffa-fff6-4abc-8e4f-313b52b3cbd3/dqc_reference/reference_markers.hmm GCF_024449025.1_ASM2444902v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:51,193] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:51,194] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg91911e86-9344-4a69-aa6d-26148efc7ab3/GCF_024449025.1_ASM2444902v1_genomic.fna.gz]
[2024-01-24 12:36:51,224] [INFO] Query marker FASTA was written to GCF_024449025.1_ASM2444902v1_genomic.fna/markers.fasta
[2024-01-24 12:36:51,225] [INFO] Task started: Blastn
[2024-01-24 12:36:51,225] [INFO] Running command: blastn -query GCF_024449025.1_ASM2444902v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b6a6ffa-fff6-4abc-8e4f-313b52b3cbd3/dqc_reference/reference_markers.fasta -out GCF_024449025.1_ASM2444902v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:51,810] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:51,815] [INFO] Selected 9 target genomes.
[2024-01-24 12:36:51,816] [INFO] Target genome list was writen to GCF_024449025.1_ASM2444902v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:51,829] [INFO] Task started: fastANI
[2024-01-24 12:36:51,829] [INFO] Running command: fastANI --query /var/lib/cwl/stg91911e86-9344-4a69-aa6d-26148efc7ab3/GCF_024449025.1_ASM2444902v1_genomic.fna.gz --refList GCF_024449025.1_ASM2444902v1_genomic.fna/target_genomes.txt --output GCF_024449025.1_ASM2444902v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:36:57,986] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:57,987] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b6a6ffa-fff6-4abc-8e4f-313b52b3cbd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:36:57,988] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b6a6ffa-fff6-4abc-8e4f-313b52b3cbd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:36:57,997] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:36:57,997] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:36:57,998] [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
Natronomonas moolapensis	strain=8.8.11	GCA_000591055.1	416273	416273	type	True	80.6381	488	1032	95	below_threshold
Natronomonas salsuginis	strain=F20-122	GCA_005239135.1	2217661	2217661	type	True	80.1964	475	1032	95	below_threshold
Natronomonas salina	strain=YPL13	GCA_013391105.1	1710540	1710540	type	True	79.5417	450	1032	95	below_threshold
Natronomonas gomsonensis	strain=KCTC 4088	GCA_024300825.1	1046043	1046043	type	True	79.0677	418	1032	95	below_threshold
Natronomonas pharaonis	strain=Gabara	GCA_000026045.1	2257	2257	type	True	79.0221	378	1032	95	below_threshold
Natronomonas halophila	strain=C90	GCA_013391085.1	2747817	2747817	type	True	78.9339	395	1032	95	below_threshold
Halomicroarcula rubra	strain=F13	GCA_019599465.1	2487747	2487747	type	True	77.2551	276	1032	95	below_threshold
Halorientalis pallida	strain=F13-25	GCA_004118325.1	2479928	2479928	type	True	77.0378	300	1032	95	below_threshold
Salinigranum halophilum	strain=YJ-53	GCA_007004735.1	2565931	2565931	type	True	76.8442	237	1032	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:36:58,000] [INFO] DFAST Taxonomy check result was written to GCF_024449025.1_ASM2444902v1_genomic.fna/tc_result.tsv
[2024-01-24 12:36:58,001] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:36:58,001] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:36:58,001] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b6a6ffa-fff6-4abc-8e4f-313b52b3cbd3/dqc_reference/checkm_data
[2024-01-24 12:36:58,003] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:36:58,039] [INFO] Task started: CheckM
[2024-01-24 12:36:58,039] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024449025.1_ASM2444902v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024449025.1_ASM2444902v1_genomic.fna/checkm_input GCF_024449025.1_ASM2444902v1_genomic.fna/checkm_result
[2024-01-24 12:37:40,975] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:40,976] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.15%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:40,998] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:40,998] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:40,999] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024449025.1_ASM2444902v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:40,999] [INFO] Task started: Blastn
[2024-01-24 12:37:40,999] [INFO] Running command: blastn -query GCF_024449025.1_ASM2444902v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b6a6ffa-fff6-4abc-8e4f-313b52b3cbd3/dqc_reference/reference_markers_gtdb.fasta -out GCF_024449025.1_ASM2444902v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:41,756] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:41,760] [INFO] Selected 9 target genomes.
[2024-01-24 12:37:41,760] [INFO] Target genome list was writen to GCF_024449025.1_ASM2444902v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:41,792] [INFO] Task started: fastANI
[2024-01-24 12:37:41,792] [INFO] Running command: fastANI --query /var/lib/cwl/stg91911e86-9344-4a69-aa6d-26148efc7ab3/GCF_024449025.1_ASM2444902v1_genomic.fna.gz --refList GCF_024449025.1_ASM2444902v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024449025.1_ASM2444902v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:46,861] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:46,874] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:37:46,874] [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_000591055.1	s__Natronomonas moolapensis	80.6773	485	1032	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013839515.1	s__Natronomonas sp013839515	80.5566	484	1032	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005239135.1	s__Natronomonas salsuginis	80.1823	477	1032	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391105.1	s__Natronomonas salina	79.5412	450	1032	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003023535.1	s__Natronomonas sp003023535	79.0574	284	1032	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003020965.1	s__Natronomonas sp003020965	79.0481	402	1032	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003022945.1	s__Natronomonas sp003022945	78.5787	350	1032	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007121575.1	s__Natronomonas sp007121575	78.3259	200	1032	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021325.1	s__Natronomonas sp003021325	78.3055	258	1032	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:37:46,876] [INFO] GTDB search result was written to GCF_024449025.1_ASM2444902v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:46,876] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:46,879] [INFO] DFAST_QC result json was written to GCF_024449025.1_ASM2444902v1_genomic.fna/dqc_result.json
[2024-01-24 12:37:46,879] [INFO] DFAST_QC completed!
[2024-01-24 12:37:46,879] [INFO] Total running time: 0h1m12s