[2024-01-24 11:51:11,319] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:11,321] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:11,321] [INFO] DQC Reference Directory: /var/lib/cwl/stgc07317cc-1cd6-4dbc-a022-932eda51c79f/dqc_reference
[2024-01-24 11:51:12,773] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:12,774] [INFO] Task started: Prodigal
[2024-01-24 11:51:12,775] [INFO] Running command: gunzip -c /var/lib/cwl/stg463784e8-0357-48c0-8a07-4e7e6b090a9a/GCF_024362405.1_ASM2436240v1_genomic.fna.gz | prodigal -d GCF_024362405.1_ASM2436240v1_genomic.fna/cds.fna -a GCF_024362405.1_ASM2436240v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:34,741] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:34,742] [INFO] Task started: HMMsearch
[2024-01-24 11:51:34,742] [INFO] Running command: hmmsearch --tblout GCF_024362405.1_ASM2436240v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc07317cc-1cd6-4dbc-a022-932eda51c79f/dqc_reference/reference_markers.hmm GCF_024362405.1_ASM2436240v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:35,005] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:35,006] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg463784e8-0357-48c0-8a07-4e7e6b090a9a/GCF_024362405.1_ASM2436240v1_genomic.fna.gz]
[2024-01-24 11:51:35,045] [INFO] Query marker FASTA was written to GCF_024362405.1_ASM2436240v1_genomic.fna/markers.fasta
[2024-01-24 11:51:35,046] [INFO] Task started: Blastn
[2024-01-24 11:51:35,046] [INFO] Running command: blastn -query GCF_024362405.1_ASM2436240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc07317cc-1cd6-4dbc-a022-932eda51c79f/dqc_reference/reference_markers.fasta -out GCF_024362405.1_ASM2436240v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:35,581] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:35,586] [INFO] Selected 10 target genomes.
[2024-01-24 11:51:35,587] [INFO] Target genome list was writen to GCF_024362405.1_ASM2436240v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:35,593] [INFO] Task started: fastANI
[2024-01-24 11:51:35,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg463784e8-0357-48c0-8a07-4e7e6b090a9a/GCF_024362405.1_ASM2436240v1_genomic.fna.gz --refList GCF_024362405.1_ASM2436240v1_genomic.fna/target_genomes.txt --output GCF_024362405.1_ASM2436240v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:43,604] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:43,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc07317cc-1cd6-4dbc-a022-932eda51c79f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:43,605] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc07317cc-1cd6-4dbc-a022-932eda51c79f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:43,614] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:51:43,615] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:51:43,615] [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
Salinirubellus salinus	strain=ZS-35-S2	GCA_025231485.1	1364945	1364945	type	True	79.7944	624	1389	95	below_threshold
Halosegnis rubeus	strain=F17-44	GCA_009184545.1	2212850	2212850	type	True	79.4905	453	1389	95	below_threshold
Halosegnis longus	strain=F12-1	GCA_009663395.1	2216012	2216012	type	True	79.4751	468	1389	95	below_threshold
Natronomonas salina	strain=YPL13	GCA_013391105.1	1710540	1710540	type	True	79.1421	512	1389	95	below_threshold
Halomicroarcula nitratireducens	strain=F27	GCA_019599505.1	2487749	2487749	type	True	78.9322	466	1389	95	below_threshold
Haloglomus irregulare	strain=F16-60	GCA_007421925.1	2234134	2234134	type	True	78.5541	486	1389	95	below_threshold
Natronomonas halophila	strain=C90	GCA_013391085.1	2747817	2747817	type	True	78.3975	413	1389	95	below_threshold
Salinigranum halophilum	strain=YJ-53	GCA_007004735.1	2565931	2565931	type	True	78.2822	458	1389	95	below_threshold
Haloferax gibbonsii	strain=ATCC 33959	GCA_000336775.1	35746	35746	type	True	78.1733	490	1389	95	below_threshold
Halomicroarcula limicola	strain=YGHS32	GCA_010119205.1	1429915	1429915	type	True	77.9553	446	1389	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:43,617] [INFO] DFAST Taxonomy check result was written to GCF_024362405.1_ASM2436240v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:43,618] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:43,618] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:43,618] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc07317cc-1cd6-4dbc-a022-932eda51c79f/dqc_reference/checkm_data
[2024-01-24 11:51:43,620] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:43,660] [INFO] Task started: CheckM
[2024-01-24 11:51:43,661] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024362405.1_ASM2436240v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024362405.1_ASM2436240v1_genomic.fna/checkm_input GCF_024362405.1_ASM2436240v1_genomic.fna/checkm_result
[2024-01-24 11:52:41,241] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:41,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:41,263] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:41,263] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:41,264] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024362405.1_ASM2436240v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:41,264] [INFO] Task started: Blastn
[2024-01-24 11:52:41,264] [INFO] Running command: blastn -query GCF_024362405.1_ASM2436240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc07317cc-1cd6-4dbc-a022-932eda51c79f/dqc_reference/reference_markers_gtdb.fasta -out GCF_024362405.1_ASM2436240v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:41,736] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:41,739] [INFO] Selected 13 target genomes.
[2024-01-24 11:52:41,740] [INFO] Target genome list was writen to GCF_024362405.1_ASM2436240v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:41,748] [INFO] Task started: fastANI
[2024-01-24 11:52:41,749] [INFO] Running command: fastANI --query /var/lib/cwl/stg463784e8-0357-48c0-8a07-4e7e6b090a9a/GCF_024362405.1_ASM2436240v1_genomic.fna.gz --refList GCF_024362405.1_ASM2436240v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024362405.1_ASM2436240v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:50,636] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:50,647] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:52:50,648] [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
GCA_003021175.1	s__CBA1134 sp003021175	79.7712	467	1389	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__CBA1134	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001950595.1	s__CBA1134 sp001950595	79.5316	463	1389	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__CBA1134	95.0	99.03	98.86	0.91	0.88	3	-
GCF_009184545.1	s__CBA1134 sp009184545	79.4797	454	1389	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__CBA1134	95.0	99.60	99.56	0.94	0.94	3	-
GCF_013391105.1	s__Natronomonas salina	79.1249	512	1389	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391635.1	s__Natronomonas gomsonensis	78.6453	446	1389	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009741925.1	s__Natronomonas sp009741925	78.6204	433	1389	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021785.1	s__CBA1134 sp003021785	78.518	370	1389	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__CBA1134	95.0	97.75	97.59	0.93	0.92	3	-
GCF_007421925.1	s__Haloglomus irregulare	78.5158	488	1389	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloglomus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004735.1	s__Salinigranum halophilum	78.2402	462	1389	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Salinigranum	95.0	97.81	97.63	0.88	0.87	3	-
GCF_000336775.1	s__Haloferax gibbonsii	78.2319	481	1389	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	96.8304	98.89	98.78	0.89	0.88	5	-
GCF_900112175.1	s__Halogeometricum rufum	77.9584	471	1389	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogeometricum	95.0	98.26	98.26	0.87	0.87	2	-
GCA_003020945.1	s__Halobaculum sp003020945	77.9552	375	1389	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119205.1	s__Halomicroarcula limicola	77.9542	446	1389	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:50,649] [INFO] GTDB search result was written to GCF_024362405.1_ASM2436240v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:50,650] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:50,654] [INFO] DFAST_QC result json was written to GCF_024362405.1_ASM2436240v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:50,654] [INFO] DFAST_QC completed!
[2024-01-24 11:52:50,654] [INFO] Total running time: 0h1m39s