[2024-01-25 19:43:50,786] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:43:50,788] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:43:50,788] [INFO] DQC Reference Directory: /var/lib/cwl/stg0534e11a-bcc7-4de5-acaa-be5cff8be742/dqc_reference
[2024-01-25 19:43:51,941] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:43:51,942] [INFO] Task started: Prodigal
[2024-01-25 19:43:51,943] [INFO] Running command: gunzip -c /var/lib/cwl/stg47ba98e4-5e54-4f16-890d-a58a7e7aacff/GCF_002177135.1_ASM217713v1_genomic.fna.gz | prodigal -d GCF_002177135.1_ASM217713v1_genomic.fna/cds.fna -a GCF_002177135.1_ASM217713v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:44:09,538] [INFO] Task succeeded: Prodigal
[2024-01-25 19:44:09,539] [INFO] Task started: HMMsearch
[2024-01-25 19:44:09,539] [INFO] Running command: hmmsearch --tblout GCF_002177135.1_ASM217713v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0534e11a-bcc7-4de5-acaa-be5cff8be742/dqc_reference/reference_markers.hmm GCF_002177135.1_ASM217713v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:44:09,793] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:44:09,794] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg47ba98e4-5e54-4f16-890d-a58a7e7aacff/GCF_002177135.1_ASM217713v1_genomic.fna.gz]
[2024-01-25 19:44:09,828] [INFO] Query marker FASTA was written to GCF_002177135.1_ASM217713v1_genomic.fna/markers.fasta
[2024-01-25 19:44:09,828] [INFO] Task started: Blastn
[2024-01-25 19:44:09,828] [INFO] Running command: blastn -query GCF_002177135.1_ASM217713v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0534e11a-bcc7-4de5-acaa-be5cff8be742/dqc_reference/reference_markers.fasta -out GCF_002177135.1_ASM217713v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:44:10,308] [INFO] Task succeeded: Blastn
[2024-01-25 19:44:10,310] [INFO] Selected 10 target genomes.
[2024-01-25 19:44:10,311] [INFO] Target genome list was writen to GCF_002177135.1_ASM217713v1_genomic.fna/target_genomes.txt
[2024-01-25 19:44:10,315] [INFO] Task started: fastANI
[2024-01-25 19:44:10,315] [INFO] Running command: fastANI --query /var/lib/cwl/stg47ba98e4-5e54-4f16-890d-a58a7e7aacff/GCF_002177135.1_ASM217713v1_genomic.fna.gz --refList GCF_002177135.1_ASM217713v1_genomic.fna/target_genomes.txt --output GCF_002177135.1_ASM217713v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:44:20,351] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:20,351] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0534e11a-bcc7-4de5-acaa-be5cff8be742/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:44:20,351] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0534e11a-bcc7-4de5-acaa-be5cff8be742/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:44:20,359] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:44:20,359] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:44:20,359] [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
Natronolimnobius baerhuensis	strain=CGMCC 1.3597	GCA_002177135.1	253108	253108	type	True	100.0	1302	1302	95	conclusive
Halopiger aswanensis	strain=DSM 13151	GCA_003610195.1	148449	148449	type	True	80.519	740	1302	95	below_threshold
Halopiger xanaduensis	strain=SH-6	GCA_000217715.1	387343	387343	type	True	80.5012	719	1302	95	below_threshold
Haloterrigena alkaliphila	strain=KZCA68	GCA_017352155.2	2816475	2816475	type	True	79.8991	573	1302	95	below_threshold
Natronorubrum aibiense	strain=7-3	GCA_009392895.1	348826	348826	type	True	79.7651	566	1302	95	below_threshold
Haloterrigena salina	strain=JCM 13891	GCA_000337495.1	504937	504937	type	True	79.6743	616	1302	95	below_threshold
Haloterrigena limicola	strain=JCM 13563	GCA_000337475.1	370323	370323	type	True	79.64	498	1302	95	below_threshold
Natrinema amylolyticum	strain=LT61	GCA_020515625.1	2878679	2878679	type	True	79.4837	595	1302	95	below_threshold
Halopiger salifodinae	strain=CGMCC 1.12284	GCA_900110455.1	1202768	1202768	type	True	79.4406	551	1302	95	below_threshold
Halopiger djelfimassiliensis	strain=IIH2	GCA_000455365.1	1293047	1293047	type	True	79.3317	570	1302	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:44:20,360] [INFO] DFAST Taxonomy check result was written to GCF_002177135.1_ASM217713v1_genomic.fna/tc_result.tsv
[2024-01-25 19:44:20,361] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:44:20,361] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:44:20,361] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0534e11a-bcc7-4de5-acaa-be5cff8be742/dqc_reference/checkm_data
[2024-01-25 19:44:20,362] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:44:20,401] [INFO] Task started: CheckM
[2024-01-25 19:44:20,401] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002177135.1_ASM217713v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002177135.1_ASM217713v1_genomic.fna/checkm_input GCF_002177135.1_ASM217713v1_genomic.fna/checkm_result
[2024-01-25 19:45:10,181] [INFO] Task succeeded: CheckM
[2024-01-25 19:45:10,182] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:45:10,208] [INFO] ===== Completeness check finished =====
[2024-01-25 19:45:10,209] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:45:10,209] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002177135.1_ASM217713v1_genomic.fna/markers.fasta)
[2024-01-25 19:45:10,209] [INFO] Task started: Blastn
[2024-01-25 19:45:10,209] [INFO] Running command: blastn -query GCF_002177135.1_ASM217713v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0534e11a-bcc7-4de5-acaa-be5cff8be742/dqc_reference/reference_markers_gtdb.fasta -out GCF_002177135.1_ASM217713v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:10,754] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:10,757] [INFO] Selected 10 target genomes.
[2024-01-25 19:45:10,757] [INFO] Target genome list was writen to GCF_002177135.1_ASM217713v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:45:10,772] [INFO] Task started: fastANI
[2024-01-25 19:45:10,772] [INFO] Running command: fastANI --query /var/lib/cwl/stg47ba98e4-5e54-4f16-890d-a58a7e7aacff/GCF_002177135.1_ASM217713v1_genomic.fna.gz --refList GCF_002177135.1_ASM217713v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002177135.1_ASM217713v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:45:20,421] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:20,430] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:45:20,430] [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_002177135.1	s__Natronolimnobius baerhuensis	100.0	1302	1302	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronolimnobius	95.0	99.89	99.89	1.00	1.00	2	conclusive
GCF_011043775.1	s__Natronolimnobius sp011043775	87.2286	1065	1302	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronolimnobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000217715.1	s__Halopiger xanaduensis	80.5207	716	1302	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610195.1	s__Halopiger aswanensis	80.5108	741	1302	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017352155.1	s__Haloterrigena sp017352155	79.973	550	1302	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013342135.1	s__Haloterrigena sp013342135	79.7544	630	1302	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	99.13	99.13	0.91	0.91	2	-
GCF_000337495.1	s__Haloterrigena salina	79.6614	617	1302	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337475.1	s__Natrinema limicola	79.6611	496	1302	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002494345.1	s__Natrinema ejinorense	79.3855	559	1302	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	95.42	95.42	0.91	0.91	2	-
GCF_000455365.1	s__Halopiger_B djelfimassiliensis	79.3154	572	1302	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:45:20,432] [INFO] GTDB search result was written to GCF_002177135.1_ASM217713v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:45:20,432] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:45:20,435] [INFO] DFAST_QC result json was written to GCF_002177135.1_ASM217713v1_genomic.fna/dqc_result.json
[2024-01-25 19:45:20,435] [INFO] DFAST_QC completed!
[2024-01-25 19:45:20,435] [INFO] Total running time: 0h1m30s