[2024-01-24 14:05:16,320] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:16,321] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:16,322] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a48fea4-0a7d-4532-9e1a-df38dac1efc2/dqc_reference
[2024-01-24 14:05:17,578] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:17,579] [INFO] Task started: Prodigal
[2024-01-24 14:05:17,579] [INFO] Running command: gunzip -c /var/lib/cwl/stga885c0e1-c30c-4db3-9ddf-ddf21a5d51bc/GCF_002952775.1_ASM295277v1_genomic.fna.gz | prodigal -d GCF_002952775.1_ASM295277v1_genomic.fna/cds.fna -a GCF_002952775.1_ASM295277v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:34,395] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:34,395] [INFO] Task started: HMMsearch
[2024-01-24 14:05:34,396] [INFO] Running command: hmmsearch --tblout GCF_002952775.1_ASM295277v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a48fea4-0a7d-4532-9e1a-df38dac1efc2/dqc_reference/reference_markers.hmm GCF_002952775.1_ASM295277v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:34,654] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:34,656] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga885c0e1-c30c-4db3-9ddf-ddf21a5d51bc/GCF_002952775.1_ASM295277v1_genomic.fna.gz]
[2024-01-24 14:05:34,689] [INFO] Query marker FASTA was written to GCF_002952775.1_ASM295277v1_genomic.fna/markers.fasta
[2024-01-24 14:05:34,690] [INFO] Task started: Blastn
[2024-01-24 14:05:34,690] [INFO] Running command: blastn -query GCF_002952775.1_ASM295277v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a48fea4-0a7d-4532-9e1a-df38dac1efc2/dqc_reference/reference_markers.fasta -out GCF_002952775.1_ASM295277v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:35,249] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:35,252] [INFO] Selected 13 target genomes.
[2024-01-24 14:05:35,253] [INFO] Target genome list was writen to GCF_002952775.1_ASM295277v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:35,285] [INFO] Task started: fastANI
[2024-01-24 14:05:35,285] [INFO] Running command: fastANI --query /var/lib/cwl/stga885c0e1-c30c-4db3-9ddf-ddf21a5d51bc/GCF_002952775.1_ASM295277v1_genomic.fna.gz --refList GCF_002952775.1_ASM295277v1_genomic.fna/target_genomes.txt --output GCF_002952775.1_ASM295277v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:44,339] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:44,339] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a48fea4-0a7d-4532-9e1a-df38dac1efc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:44,340] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a48fea4-0a7d-4532-9e1a-df38dac1efc2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:44,354] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:05:44,354] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:44,354] [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
Halalkaliarchaeum desulfuricum	strain=AArc-Sl	GCA_002952775.1	2055893	2055893	type	True	100.0	1104	1104	95	conclusive
Halorubrum cibi	strain=DSM 19504	GCA_900182635.1	413815	413815	type	True	78.1784	320	1104	95	below_threshold
Halorubrum aethiopicum	strain=SAH-A6	GCA_001542905.1	1758255	1758255	type	True	78.1697	333	1104	95	below_threshold
Halorubrum aquaticum	strain=CGMCC 1.6377	GCA_900113615.1	387340	387340	type	True	78.0978	324	1104	95	below_threshold
Halorubrum salipaludis	strain=WN019	GCA_002286985.1	2032630	2032630	type	True	77.9002	343	1104	95	below_threshold
Halobaculum salinum	strain=NJ-3-1	GCA_013402875.1	2743089	2743089	type	True	77.6419	332	1104	95	below_threshold
Halorubrum coriense	strain=DSM 10284	GCA_000337035.1	64713	64713	type	True	77.5882	336	1104	95	below_threshold
Halegenticoccus tardaugens	strain=SYSU A00711	GCA_004116405.1	2071624	2071624	type	True	77.4547	321	1104	95	below_threshold
Halegenticoccus soli	strain=SYSU A9-0	GCA_002844195.1	1985678	1985678	type	True	77.4272	326	1104	95	below_threshold
Halolamina salifodinae	strain=DSM 26232	GCA_017874235.1	1202767	1202767	type	True	77.3704	222	1104	95	below_threshold
Natronococcus jeotgali	strain=DSM 18795	GCA_000337695.1	413812	413812	type	True	77.2518	290	1104	95	below_threshold
Haloprofundus halophilus	strain=NK23	GCA_003439925.1	2283527	2283527	type	True	77.0544	279	1104	95	below_threshold
Salinirubellus salinus	strain=ZS-35-S2	GCA_025231485.1	1364945	1364945	type	True	76.8285	242	1104	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:44,356] [INFO] DFAST Taxonomy check result was written to GCF_002952775.1_ASM295277v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:44,356] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:44,356] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:44,357] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a48fea4-0a7d-4532-9e1a-df38dac1efc2/dqc_reference/checkm_data
[2024-01-24 14:05:44,357] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:44,392] [INFO] Task started: CheckM
[2024-01-24 14:05:44,393] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002952775.1_ASM295277v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002952775.1_ASM295277v1_genomic.fna/checkm_input GCF_002952775.1_ASM295277v1_genomic.fna/checkm_result
[2024-01-24 14:06:32,272] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:32,273] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:32,300] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:32,301] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:32,302] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002952775.1_ASM295277v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:32,302] [INFO] Task started: Blastn
[2024-01-24 14:06:32,302] [INFO] Running command: blastn -query GCF_002952775.1_ASM295277v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a48fea4-0a7d-4532-9e1a-df38dac1efc2/dqc_reference/reference_markers_gtdb.fasta -out GCF_002952775.1_ASM295277v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:32,842] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:32,846] [INFO] Selected 12 target genomes.
[2024-01-24 14:06:32,846] [INFO] Target genome list was writen to GCF_002952775.1_ASM295277v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:32,858] [INFO] Task started: fastANI
[2024-01-24 14:06:32,858] [INFO] Running command: fastANI --query /var/lib/cwl/stga885c0e1-c30c-4db3-9ddf-ddf21a5d51bc/GCF_002952775.1_ASM295277v1_genomic.fna.gz --refList GCF_002952775.1_ASM295277v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002952775.1_ASM295277v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:41,378] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:41,389] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:41,389] [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_002952775.1	s__Halalkaliarchaeum desulfuricum	100.0	1104	1104	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halalkaliarchaeum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009742825.1	s__Halorubrum sp009742825	78.2686	263	1104	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182635.1	s__Halorubrum cibi	78.168	323	1104	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113615.1	s__Halorubrum aquaticum	78.0928	325	1104	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003697845.1	s__Halorubrum sp003697845	77.9959	350	1104	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002286985.1	s__Halorubrum sp002286985	77.912	341	1104	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	98.74	98.74	0.87	0.87	2	-
GCF_000336995.1	s__Halorubrum aidingense	77.8751	306	1104	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000495475.1	s__Halobaculum tyrrellense	77.7058	320	1104	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004116405.1	s__Halegenticoccus sp004116405	77.4723	318	1104	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halegenticoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002844195.1	s__Halegenticoccus soli	77.4303	327	1104	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halegenticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874235.1	s__Halolamina salifodinae	77.3851	221	1104	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halolamina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337695.1	s__Natronococcus jeotgali	77.2444	290	1104	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	95.54	95.54	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:41,391] [INFO] GTDB search result was written to GCF_002952775.1_ASM295277v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:41,392] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:41,395] [INFO] DFAST_QC result json was written to GCF_002952775.1_ASM295277v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:41,396] [INFO] DFAST_QC completed!
[2024-01-24 14:06:41,396] [INFO] Total running time: 0h1m25s