[2024-01-25 18:47:20,817] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:47:20,819] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:47:20,819] [INFO] DQC Reference Directory: /var/lib/cwl/stg8427fde0-07e5-4b35-b6d0-e109df909afa/dqc_reference
[2024-01-25 18:47:21,973] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:47:21,973] [INFO] Task started: Prodigal
[2024-01-25 18:47:21,973] [INFO] Running command: gunzip -c /var/lib/cwl/stgb01ded12-3425-4a12-a58d-18b02b9fc117/GCF_026586665.1_ASM2658666v1_genomic.fna.gz | prodigal -d GCF_026586665.1_ASM2658666v1_genomic.fna/cds.fna -a GCF_026586665.1_ASM2658666v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:47:38,909] [INFO] Task succeeded: Prodigal
[2024-01-25 18:47:38,910] [INFO] Task started: HMMsearch
[2024-01-25 18:47:38,910] [INFO] Running command: hmmsearch --tblout GCF_026586665.1_ASM2658666v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8427fde0-07e5-4b35-b6d0-e109df909afa/dqc_reference/reference_markers.hmm GCF_026586665.1_ASM2658666v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:47:39,130] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:47:39,131] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgb01ded12-3425-4a12-a58d-18b02b9fc117/GCF_026586665.1_ASM2658666v1_genomic.fna.gz]
[2024-01-25 18:47:39,159] [INFO] Query marker FASTA was written to GCF_026586665.1_ASM2658666v1_genomic.fna/markers.fasta
[2024-01-25 18:47:39,160] [INFO] Task started: Blastn
[2024-01-25 18:47:39,160] [INFO] Running command: blastn -query GCF_026586665.1_ASM2658666v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8427fde0-07e5-4b35-b6d0-e109df909afa/dqc_reference/reference_markers.fasta -out GCF_026586665.1_ASM2658666v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:47:39,617] [INFO] Task succeeded: Blastn
[2024-01-25 18:47:39,620] [INFO] Selected 10 target genomes.
[2024-01-25 18:47:39,620] [INFO] Target genome list was writen to GCF_026586665.1_ASM2658666v1_genomic.fna/target_genomes.txt
[2024-01-25 18:47:39,632] [INFO] Task started: fastANI
[2024-01-25 18:47:39,632] [INFO] Running command: fastANI --query /var/lib/cwl/stgb01ded12-3425-4a12-a58d-18b02b9fc117/GCF_026586665.1_ASM2658666v1_genomic.fna.gz --refList GCF_026586665.1_ASM2658666v1_genomic.fna/target_genomes.txt --output GCF_026586665.1_ASM2658666v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:47:45,969] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:45,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8427fde0-07e5-4b35-b6d0-e109df909afa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:47:45,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8427fde0-07e5-4b35-b6d0-e109df909afa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:47:45,978] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:47:45,978] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:47:45,978] [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
Halorientalis litorea	strain=ZY14	GCA_023028225.1	2931977	2931977	type	True	79.044	110	1167	95	below_threshold
Halovenus aranensis	strain=IBRC-M10015	GCA_900100385.1	890420	890420	type	True	78.2669	383	1167	95	below_threshold
Halostella salina	strain=CBA1114	GCA_003675855.1	1547897	1547897	type	True	77.2668	86	1167	95	below_threshold
Halostella limicola	strain=LT12	GCA_003675875.1	2448456	2448456	type	True	76.5579	59	1167	95	below_threshold
Halovenus carboxidivorans	strain=WSH3	GCA_009831575.1	2692199	2692199	type	True	76.4869	116	1167	95	below_threshold
Halomicrobium mukohataei	strain=DSM 12286	GCA_000023965.1	57705	57705	type	True	76.4541	99	1167	95	below_threshold
Natronococcus jeotgali	strain=DSM 18795	GCA_000337695.1	413812	413812	type	True	76.2758	68	1167	95	below_threshold
Halapricum desulfuricans	strain=HSR12-2	GCA_017094525.1	2841257	2841257	type	True	76.17	85	1167	95	below_threshold
Halorientalis brevis	strain=YC89	GCA_023077655.1	1126241	1126241	type	True	76.0661	87	1167	95	below_threshold
Halorientalis pallida	strain=F13-25	GCA_004118325.1	2479928	2479928	type	True	75.9711	94	1167	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:47:45,980] [INFO] DFAST Taxonomy check result was written to GCF_026586665.1_ASM2658666v1_genomic.fna/tc_result.tsv
[2024-01-25 18:47:45,980] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:47:45,980] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:47:45,981] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8427fde0-07e5-4b35-b6d0-e109df909afa/dqc_reference/checkm_data
[2024-01-25 18:47:45,981] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:47:46,021] [INFO] Task started: CheckM
[2024-01-25 18:47:46,021] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026586665.1_ASM2658666v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026586665.1_ASM2658666v1_genomic.fna/checkm_input GCF_026586665.1_ASM2658666v1_genomic.fna/checkm_result
[2024-01-25 18:48:33,563] [INFO] Task succeeded: CheckM
[2024-01-25 18:48:33,564] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:48:33,593] [INFO] ===== Completeness check finished =====
[2024-01-25 18:48:33,593] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:48:33,594] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026586665.1_ASM2658666v1_genomic.fna/markers.fasta)
[2024-01-25 18:48:33,595] [INFO] Task started: Blastn
[2024-01-25 18:48:33,595] [INFO] Running command: blastn -query GCF_026586665.1_ASM2658666v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8427fde0-07e5-4b35-b6d0-e109df909afa/dqc_reference/reference_markers_gtdb.fasta -out GCF_026586665.1_ASM2658666v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:34,049] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:34,053] [INFO] Selected 13 target genomes.
[2024-01-25 18:48:34,054] [INFO] Target genome list was writen to GCF_026586665.1_ASM2658666v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:48:34,068] [INFO] Task started: fastANI
[2024-01-25 18:48:34,068] [INFO] Running command: fastANI --query /var/lib/cwl/stgb01ded12-3425-4a12-a58d-18b02b9fc117/GCF_026586665.1_ASM2658666v1_genomic.fna.gz --refList GCF_026586665.1_ASM2658666v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026586665.1_ASM2658666v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:48:40,885] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:40,892] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:48:40,893] [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_900100385.1	s__Halovenus aranensis	78.2669	383	1167	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halovenus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003675855.1	s__Halostella salina	77.2668	86	1167	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021285.1	s__Halovenus sp003021285	76.9022	117	1167	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halovenus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003551265.1	s__Halovenus sp003551265	76.845	128	1167	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halovenus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004015825.1	s__Halovenus sp004015825	76.5777	128	1167	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halovenus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003551945.1	s__Halovenus sp003551945	76.5177	57	1167	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halovenus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009831575.1	s__Halovenus sp009831575	76.4869	116	1167	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halovenus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001564135.1	s__Halovenus sp001564135	76.4805	61	1167	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halovenus	95.0	98.32	98.32	0.71	0.71	2	-
GCF_000023965.1	s__Halomicrobium mukohataei	76.4541	99	1167	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicrobium	96.8107	100.00	100.00	1.00	1.00	4	-
GCF_000337695.1	s__Natronococcus jeotgali	76.2488	69	1167	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	95.54	95.54	0.86	0.86	2	-
GCA_017094525.1	s__Halapricum sp017094525	76.17	85	1167	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halapricum	95.0	98.12	98.12	0.88	0.88	2	-
GCF_004118325.1	s__Halorientalis sp004118325	75.9711	94	1167	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorientalis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:48:40,894] [INFO] GTDB search result was written to GCF_026586665.1_ASM2658666v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:48:40,895] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:48:40,901] [INFO] DFAST_QC result json was written to GCF_026586665.1_ASM2658666v1_genomic.fna/dqc_result.json
[2024-01-25 18:48:40,901] [INFO] DFAST_QC completed!
[2024-01-25 18:48:40,901] [INFO] Total running time: 0h1m20s