[2024-01-24 13:40:44,129] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:44,131] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:44,131] [INFO] DQC Reference Directory: /var/lib/cwl/stg5845995e-2944-46b1-bc9f-713eb439f302/dqc_reference
[2024-01-24 13:40:45,590] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:45,592] [INFO] Task started: Prodigal
[2024-01-24 13:40:45,592] [INFO] Running command: gunzip -c /var/lib/cwl/stg47fff3a8-fa25-49f5-b0cb-dbc4e98cfd38/GCF_024218775.1_ASM2421877v1_genomic.fna.gz | prodigal -d GCF_024218775.1_ASM2421877v1_genomic.fna/cds.fna -a GCF_024218775.1_ASM2421877v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:05,947] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:05,948] [INFO] Task started: HMMsearch
[2024-01-24 13:41:05,948] [INFO] Running command: hmmsearch --tblout GCF_024218775.1_ASM2421877v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5845995e-2944-46b1-bc9f-713eb439f302/dqc_reference/reference_markers.hmm GCF_024218775.1_ASM2421877v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:06,207] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:06,208] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg47fff3a8-fa25-49f5-b0cb-dbc4e98cfd38/GCF_024218775.1_ASM2421877v1_genomic.fna.gz]
[2024-01-24 13:41:06,243] [INFO] Query marker FASTA was written to GCF_024218775.1_ASM2421877v1_genomic.fna/markers.fasta
[2024-01-24 13:41:06,244] [INFO] Task started: Blastn
[2024-01-24 13:41:06,244] [INFO] Running command: blastn -query GCF_024218775.1_ASM2421877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5845995e-2944-46b1-bc9f-713eb439f302/dqc_reference/reference_markers.fasta -out GCF_024218775.1_ASM2421877v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:06,781] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:06,785] [INFO] Selected 10 target genomes.
[2024-01-24 13:41:06,785] [INFO] Target genome list was writen to GCF_024218775.1_ASM2421877v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:06,789] [INFO] Task started: fastANI
[2024-01-24 13:41:06,790] [INFO] Running command: fastANI --query /var/lib/cwl/stg47fff3a8-fa25-49f5-b0cb-dbc4e98cfd38/GCF_024218775.1_ASM2421877v1_genomic.fna.gz --refList GCF_024218775.1_ASM2421877v1_genomic.fna/target_genomes.txt --output GCF_024218775.1_ASM2421877v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:16,550] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:16,551] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5845995e-2944-46b1-bc9f-713eb439f302/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:16,551] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5845995e-2944-46b1-bc9f-713eb439f302/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:16,561] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:16,561] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:16,562] [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
Halomicroarcula rubra	strain=F13	GCA_019599465.1	2487747	2487747	type	True	84.7081	886	1246	95	below_threshold
Halomicroarcula pellucida	strain=CECT 7537	GCA_019599515.1	1427151	1427151	type	True	84.4228	867	1246	95	below_threshold
Halomicroarcula pellucida	strain=JCM 17820	GCA_014647235.1	1427151	1427151	type	True	84.3112	871	1246	95	below_threshold
Halomicroarcula nitratireducens	strain=F27	GCA_019599505.1	2487749	2487749	type	True	83.3985	791	1246	95	below_threshold
Halomicroarcula limicola	strain=YGHS32	GCA_010119205.1	1429915	1429915	type	True	83.3539	787	1246	95	below_threshold
Halomicroarcula amylolytica	strain=LR21	GCA_004681185.1	2562280	2562280	type	True	82.5406	812	1246	95	below_threshold
Halomicroarcula salina	strain=JCM 18369	GCA_019061225.1	1429914	1429914	type	True	81.8046	686	1246	95	below_threshold
Halomicroarcula salina	strain=YGHS18	GCA_010119195.1	1429914	1429914	type	True	81.7843	696	1246	95	below_threshold
Haloarcula rubripromontorii	strain=SL3	GCA_001280425.1	1705562	1705562	type	True	80.7867	611	1246	95	below_threshold
Haloarcula salaria	strain=JCM 15759	GCA_014647095.1	575195	575195	type	True	80.1946	587	1246	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:16,564] [INFO] DFAST Taxonomy check result was written to GCF_024218775.1_ASM2421877v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:16,565] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:16,565] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:16,566] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5845995e-2944-46b1-bc9f-713eb439f302/dqc_reference/checkm_data
[2024-01-24 13:41:16,567] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:16,610] [INFO] Task started: CheckM
[2024-01-24 13:41:16,610] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024218775.1_ASM2421877v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024218775.1_ASM2421877v1_genomic.fna/checkm_input GCF_024218775.1_ASM2421877v1_genomic.fna/checkm_result
[2024-01-24 13:42:10,060] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:10,062] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:10,085] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:10,085] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:10,086] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024218775.1_ASM2421877v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:10,086] [INFO] Task started: Blastn
[2024-01-24 13:42:10,087] [INFO] Running command: blastn -query GCF_024218775.1_ASM2421877v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5845995e-2944-46b1-bc9f-713eb439f302/dqc_reference/reference_markers_gtdb.fasta -out GCF_024218775.1_ASM2421877v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:10,576] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:10,579] [INFO] Selected 9 target genomes.
[2024-01-24 13:42:10,579] [INFO] Target genome list was writen to GCF_024218775.1_ASM2421877v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:10,597] [INFO] Task started: fastANI
[2024-01-24 13:42:10,597] [INFO] Running command: fastANI --query /var/lib/cwl/stg47fff3a8-fa25-49f5-b0cb-dbc4e98cfd38/GCF_024218775.1_ASM2421877v1_genomic.fna.gz --refList GCF_024218775.1_ASM2421877v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024218775.1_ASM2421877v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:18,712] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:18,725] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:42:18,725] [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_014647235.1	s__Halomicroarcula pellucida	84.3291	870	1246	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	96.63	96.63	0.87	0.87	2	-
GCF_010119205.1	s__Halomicroarcula limicola	83.3639	788	1246	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004681185.1	s__Halomicroarcula amylolytica	82.5204	814	1246	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119195.1	s__Haloarcula salina	81.7915	695	1246	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003021755.1	s__Halomicroarcula sp003021755	81.5275	399	1246	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicroarcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005406125.1	s__Haloarcula sp005406125	80.9277	634	1246	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002844335.1	s__Haloarcula taiwanensis	80.7948	585	1246	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	99.00	98.44	0.94	0.92	4	-
GCF_001280425.1	s__Haloarcula rubripromontorii	80.7862	612	1246	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	99.01	99.01	0.90	0.90	2	-
GCF_008729015.1	s__Haloarcula sp008729015	80.5648	608	1246	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:18,727] [INFO] GTDB search result was written to GCF_024218775.1_ASM2421877v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:18,727] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:18,731] [INFO] DFAST_QC result json was written to GCF_024218775.1_ASM2421877v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:18,731] [INFO] DFAST_QC completed!
[2024-01-24 13:42:18,731] [INFO] Total running time: 0h1m35s