[2024-01-24 11:58:20,390] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:20,391] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:20,391] [INFO] DQC Reference Directory: /var/lib/cwl/stg61ac9943-abd1-4bed-86ee-5bd45bc86f72/dqc_reference
[2024-01-24 11:58:21,562] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:21,562] [INFO] Task started: Prodigal
[2024-01-24 11:58:21,563] [INFO] Running command: gunzip -c /var/lib/cwl/stg0258a9bb-ca2e-410c-a83c-e9588c7d3666/GCF_024298845.1_ASM2429884v1_genomic.fna.gz | prodigal -d GCF_024298845.1_ASM2429884v1_genomic.fna/cds.fna -a GCF_024298845.1_ASM2429884v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:58:43,773] [INFO] Task succeeded: Prodigal
[2024-01-24 11:58:43,774] [INFO] Task started: HMMsearch
[2024-01-24 11:58:43,774] [INFO] Running command: hmmsearch --tblout GCF_024298845.1_ASM2429884v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61ac9943-abd1-4bed-86ee-5bd45bc86f72/dqc_reference/reference_markers.hmm GCF_024298845.1_ASM2429884v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:58:44,017] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:58:44,018] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg0258a9bb-ca2e-410c-a83c-e9588c7d3666/GCF_024298845.1_ASM2429884v1_genomic.fna.gz]
[2024-01-24 11:58:44,054] [INFO] Query marker FASTA was written to GCF_024298845.1_ASM2429884v1_genomic.fna/markers.fasta
[2024-01-24 11:58:44,055] [INFO] Task started: Blastn
[2024-01-24 11:58:44,055] [INFO] Running command: blastn -query GCF_024298845.1_ASM2429884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61ac9943-abd1-4bed-86ee-5bd45bc86f72/dqc_reference/reference_markers.fasta -out GCF_024298845.1_ASM2429884v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:58:44,560] [INFO] Task succeeded: Blastn
[2024-01-24 11:58:44,564] [INFO] Selected 15 target genomes.
[2024-01-24 11:58:44,564] [INFO] Target genome list was writen to GCF_024298845.1_ASM2429884v1_genomic.fna/target_genomes.txt
[2024-01-24 11:58:44,595] [INFO] Task started: fastANI
[2024-01-24 11:58:44,595] [INFO] Running command: fastANI --query /var/lib/cwl/stg0258a9bb-ca2e-410c-a83c-e9588c7d3666/GCF_024298845.1_ASM2429884v1_genomic.fna.gz --refList GCF_024298845.1_ASM2429884v1_genomic.fna/target_genomes.txt --output GCF_024298845.1_ASM2429884v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:58:56,289] [INFO] Task succeeded: fastANI
[2024-01-24 11:58:56,290] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61ac9943-abd1-4bed-86ee-5bd45bc86f72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:58:56,290] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61ac9943-abd1-4bed-86ee-5bd45bc86f72/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:58:56,307] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:58:56,307] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:58:56,307] [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
Natronorubrum sulfidifaciens	strain=JCM 14089	GCA_000337735.1	388259	388259	type	True	78.5845	374	1404	95	below_threshold
Natrialba magadii	strain=ATCC 43099	GCA_000025625.1	13769	13769	type	True	78.2431	379	1404	95	below_threshold
Natrialba magadii	strain=MS-3	GCA_000337875.1	13769	13769	type	True	78.2075	366	1404	95	below_threshold
Haloterrigena limicola	strain=JCM 13563	GCA_000337475.1	370323	370323	type	True	78.1494	338	1404	95	below_threshold
Halostagnicola kamekurae	strain=DSM 22427	GCA_900116205.1	619731	619731	type	True	78.1261	335	1404	95	below_threshold
Natronobacterium texcoconense	strain=DSM 24767	GCA_900104065.1	1095778	1095778	type	True	78.0365	403	1404	95	below_threshold
Halopiger xanaduensis	strain=SH-6	GCA_000217715.1	387343	387343	type	True	78.0085	372	1404	95	below_threshold
Natronococcus amylolyticus	strain=DSM 10524	GCA_000337675.1	44470	44470	type	True	77.9796	375	1404	95	below_threshold
Natronococcus pandeyae	strain=LS1_42	GCA_008122205.1	2055836	2055836	type	True	77.928	437	1404	95	below_threshold
Halopiger aswanensis	strain=DSM 13151	GCA_003610195.1	148449	148449	type	True	77.9016	388	1404	95	below_threshold
Natrinema amylolyticum	strain=LT61	GCA_020515625.1	2878679	2878679	type	True	77.8444	382	1404	95	below_threshold
Natrinema versiforme	strain=JCM 10478	GCA_000337195.1	88724	88724	type	True	77.8253	372	1404	95	below_threshold
Natrinema salaciae	strain=DSM 25055	GCA_900110865.1	1186196	1186196	type	True	77.7372	417	1404	95	below_threshold
Haloarcula rubripromontorii	strain=SL3	GCA_001280425.1	1705562	1705562	type	True	76.7831	171	1404	95	below_threshold
Salinarchaeum laminariae	strain=R26	GCA_023204835.1	869888	869888	type	True	76.6559	156	1404	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:58:56,309] [INFO] DFAST Taxonomy check result was written to GCF_024298845.1_ASM2429884v1_genomic.fna/tc_result.tsv
[2024-01-24 11:58:56,309] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:58:56,309] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:58:56,309] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61ac9943-abd1-4bed-86ee-5bd45bc86f72/dqc_reference/checkm_data
[2024-01-24 11:58:56,310] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:58:56,351] [INFO] Task started: CheckM
[2024-01-24 11:58:56,351] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024298845.1_ASM2429884v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024298845.1_ASM2429884v1_genomic.fna/checkm_input GCF_024298845.1_ASM2429884v1_genomic.fna/checkm_result
[2024-01-24 11:59:57,766] [INFO] Task succeeded: CheckM
[2024-01-24 11:59:57,767] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:59:57,790] [INFO] ===== Completeness check finished =====
[2024-01-24 11:59:57,790] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:59:57,791] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024298845.1_ASM2429884v1_genomic.fna/markers.fasta)
[2024-01-24 11:59:57,791] [INFO] Task started: Blastn
[2024-01-24 11:59:57,791] [INFO] Running command: blastn -query GCF_024298845.1_ASM2429884v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61ac9943-abd1-4bed-86ee-5bd45bc86f72/dqc_reference/reference_markers_gtdb.fasta -out GCF_024298845.1_ASM2429884v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:58,252] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:58,256] [INFO] Selected 11 target genomes.
[2024-01-24 11:59:58,256] [INFO] Target genome list was writen to GCF_024298845.1_ASM2429884v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:59:58,264] [INFO] Task started: fastANI
[2024-01-24 11:59:58,265] [INFO] Running command: fastANI --query /var/lib/cwl/stg0258a9bb-ca2e-410c-a83c-e9588c7d3666/GCF_024298845.1_ASM2429884v1_genomic.fna.gz --refList GCF_024298845.1_ASM2429884v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024298845.1_ASM2429884v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:06,224] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:06,238] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:00:06,238] [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_017357105.1	s__Tc-Br11 sp017357105	79.3391	548	1404	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Tc-Br11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003552325.1	s__Tc-Br11 sp003552325	79.1731	288	1404	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Tc-Br11	95.0	98.65	98.65	0.64	0.64	2	-
GCA_001564275.1	s__Tc-Br11 sp001564275	79.1053	430	1404	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Tc-Br11	95.0	99.79	99.79	0.91	0.91	2	-
GCF_000337735.1	s__Natronorubrum sulfidifaciens	78.5876	373	1404	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025625.1	s__Natrialba magadii	78.2364	379	1404	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrialba	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000337475.1	s__Natrinema limicola	78.1185	341	1404	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017357405.1	s__KZCA124 sp017357405	78.0884	421	1404	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__KZCA124	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000690595.2	s__Natrinema mahii	78.0371	370	1404	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008245225.1	s__Natrarchaeobius swarupiae	78.0335	398	1404	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrarchaeobius	95.0	96.49	96.49	0.86	0.86	2	-
GCF_002494345.1	s__Natrinema ejinorense	78.001	379	1404	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	95.42	95.42	0.91	0.91	2	-
GCF_008122205.1	s__Natronococcus sp008122205	77.9005	442	1404	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:06,240] [INFO] GTDB search result was written to GCF_024298845.1_ASM2429884v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:06,241] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:06,247] [INFO] DFAST_QC result json was written to GCF_024298845.1_ASM2429884v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:06,247] [INFO] DFAST_QC completed!
[2024-01-24 12:00:06,247] [INFO] Total running time: 0h1m46s