[2024-01-24 15:18:26,985] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:26,987] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:26,987] [INFO] DQC Reference Directory: /var/lib/cwl/stg329c3531-582d-4788-b8bf-e3ad771abb3e/dqc_reference
[2024-01-24 15:18:28,434] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:28,435] [INFO] Task started: Prodigal
[2024-01-24 15:18:28,436] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b36eb92-830e-4d0a-b988-a6b853da99b3/GCF_007004735.1_ASM700473v1_genomic.fna.gz | prodigal -d GCF_007004735.1_ASM700473v1_genomic.fna/cds.fna -a GCF_007004735.1_ASM700473v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:51,264] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:51,264] [INFO] Task started: HMMsearch
[2024-01-24 15:18:51,264] [INFO] Running command: hmmsearch --tblout GCF_007004735.1_ASM700473v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg329c3531-582d-4788-b8bf-e3ad771abb3e/dqc_reference/reference_markers.hmm GCF_007004735.1_ASM700473v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:51,582] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:51,583] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg6b36eb92-830e-4d0a-b988-a6b853da99b3/GCF_007004735.1_ASM700473v1_genomic.fna.gz]
[2024-01-24 15:18:51,625] [INFO] Query marker FASTA was written to GCF_007004735.1_ASM700473v1_genomic.fna/markers.fasta
[2024-01-24 15:18:51,625] [INFO] Task started: Blastn
[2024-01-24 15:18:51,625] [INFO] Running command: blastn -query GCF_007004735.1_ASM700473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg329c3531-582d-4788-b8bf-e3ad771abb3e/dqc_reference/reference_markers.fasta -out GCF_007004735.1_ASM700473v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:52,206] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:52,210] [INFO] Selected 8 target genomes.
[2024-01-24 15:18:52,211] [INFO] Target genome list was writen to GCF_007004735.1_ASM700473v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:52,216] [INFO] Task started: fastANI
[2024-01-24 15:18:52,217] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b36eb92-830e-4d0a-b988-a6b853da99b3/GCF_007004735.1_ASM700473v1_genomic.fna.gz --refList GCF_007004735.1_ASM700473v1_genomic.fna/target_genomes.txt --output GCF_007004735.1_ASM700473v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:01,495] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:01,495] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg329c3531-582d-4788-b8bf-e3ad771abb3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:01,496] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg329c3531-582d-4788-b8bf-e3ad771abb3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:01,503] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:01,504] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:01,504] [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
Salinigranum halophilum	strain=YJ-53	GCA_007004735.1	2565931	2565931	type	True	100.0	1395	1395	95	conclusive
Salinigranum rubrum	strain=GX10	GCA_002906575.1	755307	755307	type	True	86.4444	954	1395	95	below_threshold
Salinigranum salinum	strain=YJ-50-S2	GCA_009176545.1	1364937	1364937	type	True	82.8071	866	1395	95	below_threshold
Haloferax gibbonsii	strain=ATCC 33959	GCA_000336775.1	35746	35746	type	True	79.3432	608	1395	95	below_threshold
Haloferax prahovense	strain=DSM 18310	GCA_000336815.1	381852	381852	type	True	79.2403	585	1395	95	below_threshold
Haloferax marisrubri	strain=SB3	GCA_001469875.2	1544719	1544719	type	True	79.24	601	1395	95	below_threshold
Halogranum gelatinilyticum	strain=CGMCC 1.10119	GCA_900103715.1	660521	660521	type	True	79.0033	575	1395	95	below_threshold
Halegenticoccus tardaugens	strain=SYSU A00711	GCA_004116405.1	2071624	2071624	type	True	78.6705	517	1395	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:01,506] [INFO] DFAST Taxonomy check result was written to GCF_007004735.1_ASM700473v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:01,506] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:01,506] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:01,506] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg329c3531-582d-4788-b8bf-e3ad771abb3e/dqc_reference/checkm_data
[2024-01-24 15:19:01,508] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:01,550] [INFO] Task started: CheckM
[2024-01-24 15:19:01,550] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007004735.1_ASM700473v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007004735.1_ASM700473v1_genomic.fna/checkm_input GCF_007004735.1_ASM700473v1_genomic.fna/checkm_result
[2024-01-24 15:20:00,594] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:00,595] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:00,617] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:00,618] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:00,618] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007004735.1_ASM700473v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:00,618] [INFO] Task started: Blastn
[2024-01-24 15:20:00,619] [INFO] Running command: blastn -query GCF_007004735.1_ASM700473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg329c3531-582d-4788-b8bf-e3ad771abb3e/dqc_reference/reference_markers_gtdb.fasta -out GCF_007004735.1_ASM700473v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:01,147] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:01,151] [INFO] Selected 8 target genomes.
[2024-01-24 15:20:01,151] [INFO] Target genome list was writen to GCF_007004735.1_ASM700473v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:01,157] [INFO] Task started: fastANI
[2024-01-24 15:20:01,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b36eb92-830e-4d0a-b988-a6b853da99b3/GCF_007004735.1_ASM700473v1_genomic.fna.gz --refList GCF_007004735.1_ASM700473v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007004735.1_ASM700473v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:09,426] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:09,440] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:09,440] [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_007004735.1	s__Salinigranum halophilum	100.0	1395	1395	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Salinigranum	95.0	97.81	97.63	0.88	0.87	3	conclusive
GCF_002906575.1	s__Salinigranum rubrum	86.4311	954	1395	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Salinigranum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009176545.1	s__Salinigranum salinum	82.7837	868	1395	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Salinigranum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000336775.1	s__Haloferax gibbonsii	79.3587	605	1395	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	96.8304	98.89	98.78	0.89	0.88	5	-
GCF_001469875.2	s__Haloferax marisrubri	79.2329	602	1395	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	95.85	95.85	0.83	0.83	2	-
GCF_000336815.1	s__Haloferax prahovense	79.2173	588	1395	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	96.8304	99.29	99.22	0.91	0.91	5	-
GCF_900103715.1	s__Halogranum gelatinilyticum	78.9775	577	1395	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004116405.1	s__Halegenticoccus sp004116405	78.6823	516	1395	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halegenticoccus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:09,442] [INFO] GTDB search result was written to GCF_007004735.1_ASM700473v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:09,443] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:09,452] [INFO] DFAST_QC result json was written to GCF_007004735.1_ASM700473v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:09,452] [INFO] DFAST_QC completed!
[2024-01-24 15:20:09,452] [INFO] Total running time: 0h1m42s