[2024-01-24 13:32:26,091] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:26,093] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:26,093] [INFO] DQC Reference Directory: /var/lib/cwl/stg98532565-b94d-4d68-a97a-0392cb41aa37/dqc_reference
[2024-01-24 13:32:27,284] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:27,285] [INFO] Task started: Prodigal
[2024-01-24 13:32:27,285] [INFO] Running command: gunzip -c /var/lib/cwl/stgdbc001ed-aca3-4c3b-a34c-c2eb2f62fa02/GCF_005543295.1_ASM554329v1_genomic.fna.gz | prodigal -d GCF_005543295.1_ASM554329v1_genomic.fna/cds.fna -a GCF_005543295.1_ASM554329v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:46,005] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:46,006] [INFO] Task started: HMMsearch
[2024-01-24 13:32:46,006] [INFO] Running command: hmmsearch --tblout GCF_005543295.1_ASM554329v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98532565-b94d-4d68-a97a-0392cb41aa37/dqc_reference/reference_markers.hmm GCF_005543295.1_ASM554329v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:46,266] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:46,268] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgdbc001ed-aca3-4c3b-a34c-c2eb2f62fa02/GCF_005543295.1_ASM554329v1_genomic.fna.gz]
[2024-01-24 13:32:46,316] [INFO] Query marker FASTA was written to GCF_005543295.1_ASM554329v1_genomic.fna/markers.fasta
[2024-01-24 13:32:46,317] [INFO] Task started: Blastn
[2024-01-24 13:32:46,317] [INFO] Running command: blastn -query GCF_005543295.1_ASM554329v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98532565-b94d-4d68-a97a-0392cb41aa37/dqc_reference/reference_markers.fasta -out GCF_005543295.1_ASM554329v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:46,836] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:46,840] [INFO] Selected 11 target genomes.
[2024-01-24 13:32:46,841] [INFO] Target genome list was writen to GCF_005543295.1_ASM554329v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:46,879] [INFO] Task started: fastANI
[2024-01-24 13:32:46,880] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbc001ed-aca3-4c3b-a34c-c2eb2f62fa02/GCF_005543295.1_ASM554329v1_genomic.fna.gz --refList GCF_005543295.1_ASM554329v1_genomic.fna/target_genomes.txt --output GCF_005543295.1_ASM554329v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:53,697] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:53,698] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98532565-b94d-4d68-a97a-0392cb41aa37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:53,699] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98532565-b94d-4d68-a97a-0392cb41aa37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:53,715] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:53,715] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:53,715] [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
Halalkalirubrum salinum	strain=N1521	GCA_005543295.1	2563889	2563889	type	True	100.0	1102	1106	95	conclusive
Haloprofundus halophilus	strain=NK23	GCA_003439925.1	2283527	2283527	type	True	77.3822	219	1106	95	below_threshold
Halorubrum tebenquichense	strain=DSM 14210	GCA_000337415.1	119434	119434	type	True	77.1913	214	1106	95	below_threshold
Halonotius terrestris	strain=F15B	GCA_006861665.1	2487750	2487750	type	True	77.1779	163	1106	95	below_threshold
Haloferax volcanii	strain=DS2	GCA_000337315.1	2246	2246	type	True	77.0288	209	1106	95	below_threshold
Haloferax volcanii	strain=DS2	GCA_000025685.1	2246	2246	type	True	77.0224	210	1106	95	below_threshold
Haloprofundus marisrubri	strain=SB9	GCA_001469955.1	1514971	1514971	type	True	76.8789	223	1106	95	below_threshold
Halalkaliarchaeum desulfuricum	strain=AArc-Sl	GCA_002952775.1	2055893	2055893	type	True	76.8193	186	1106	95	below_threshold
Halogranum salarium	strain=B-1	GCA_000283335.1	693851	693851	type	True	76.7237	176	1106	95	below_threshold
Haloferax mucosum	strain=ATCC BAA-1512	GCA_000337815.1	403181	403181	type	True	76.655	142	1106	95	below_threshold
Halostella limicola	strain=LT12	GCA_003675875.1	2448456	2448456	type	True	76.2029	173	1106	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:53,717] [INFO] DFAST Taxonomy check result was written to GCF_005543295.1_ASM554329v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:53,717] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:53,718] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:53,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98532565-b94d-4d68-a97a-0392cb41aa37/dqc_reference/checkm_data
[2024-01-24 13:32:53,719] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:53,755] [INFO] Task started: CheckM
[2024-01-24 13:32:53,756] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005543295.1_ASM554329v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005543295.1_ASM554329v1_genomic.fna/checkm_input GCF_005543295.1_ASM554329v1_genomic.fna/checkm_result
[2024-01-24 13:33:47,568] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:47,569] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:47,590] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:47,591] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:47,591] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005543295.1_ASM554329v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:47,592] [INFO] Task started: Blastn
[2024-01-24 13:33:47,592] [INFO] Running command: blastn -query GCF_005543295.1_ASM554329v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98532565-b94d-4d68-a97a-0392cb41aa37/dqc_reference/reference_markers_gtdb.fasta -out GCF_005543295.1_ASM554329v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:48,095] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:48,099] [INFO] Selected 11 target genomes.
[2024-01-24 13:33:48,099] [INFO] Target genome list was writen to GCF_005543295.1_ASM554329v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:48,189] [INFO] Task started: fastANI
[2024-01-24 13:33:48,189] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbc001ed-aca3-4c3b-a34c-c2eb2f62fa02/GCF_005543295.1_ASM554329v1_genomic.fna.gz --refList GCF_005543295.1_ASM554329v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005543295.1_ASM554329v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:55,302] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:55,319] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:55,319] [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_005543295.1	s__Halalkalirubrum salinum	100.0	1102	1106	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halalkalirubrum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_005239175.1	s__Halalkalirubrum sp005239175	91.9646	858	1106	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halalkalirubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003781945.1	s__Halorubrum sp003781945	77.3741	214	1106	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006861665.1	s__Halonotius terrestris	77.162	164	1106	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halonotius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009806985.1	s__Halorubrum sp009806985	77.08	231	1106	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000336815.1	s__Haloferax prahovense	77.0138	214	1106	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	96.8304	99.29	99.22	0.91	0.91	5	-
GCF_000025685.1	s__Haloferax volcanii	77.0112	211	1106	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	98.27	96.62	0.93	0.89	21	-
GCF_002952775.1	s__Halalkaliarchaeum desulfuricum	76.8193	186	1106	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halalkaliarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337815.1	s__Haloferax mucosum	76.655	142	1106	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003675875.1	s__Halostella sp003675875	76.2132	172	1106	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013402815.1	s__Natrinema sp013402815	76.1979	112	1106	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:55,321] [INFO] GTDB search result was written to GCF_005543295.1_ASM554329v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:55,322] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:55,325] [INFO] DFAST_QC result json was written to GCF_005543295.1_ASM554329v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:55,326] [INFO] DFAST_QC completed!
[2024-01-24 13:33:55,326] [INFO] Total running time: 0h1m29s