[2024-01-25 18:44:05,727] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:44:05,729] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:44:05,729] [INFO] DQC Reference Directory: /var/lib/cwl/stg19b97ec9-1afa-4ef5-9ead-d7e0ea464033/dqc_reference
[2024-01-25 18:44:06,855] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:44:06,856] [INFO] Task started: Prodigal
[2024-01-25 18:44:06,856] [INFO] Running command: gunzip -c /var/lib/cwl/stgadde384c-8826-4c7a-93af-fdc066c1a83f/GCF_014647415.1_ASM1464741v1_genomic.fna.gz | prodigal -d GCF_014647415.1_ASM1464741v1_genomic.fna/cds.fna -a GCF_014647415.1_ASM1464741v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:44:25,304] [INFO] Task succeeded: Prodigal
[2024-01-25 18:44:25,304] [INFO] Task started: HMMsearch
[2024-01-25 18:44:25,304] [INFO] Running command: hmmsearch --tblout GCF_014647415.1_ASM1464741v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19b97ec9-1afa-4ef5-9ead-d7e0ea464033/dqc_reference/reference_markers.hmm GCF_014647415.1_ASM1464741v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:44:25,523] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:44:25,524] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgadde384c-8826-4c7a-93af-fdc066c1a83f/GCF_014647415.1_ASM1464741v1_genomic.fna.gz]
[2024-01-25 18:44:25,562] [INFO] Query marker FASTA was written to GCF_014647415.1_ASM1464741v1_genomic.fna/markers.fasta
[2024-01-25 18:44:25,562] [INFO] Task started: Blastn
[2024-01-25 18:44:25,562] [INFO] Running command: blastn -query GCF_014647415.1_ASM1464741v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19b97ec9-1afa-4ef5-9ead-d7e0ea464033/dqc_reference/reference_markers.fasta -out GCF_014647415.1_ASM1464741v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:26,038] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:26,041] [INFO] Selected 7 target genomes.
[2024-01-25 18:44:26,041] [INFO] Target genome list was writen to GCF_014647415.1_ASM1464741v1_genomic.fna/target_genomes.txt
[2024-01-25 18:44:26,045] [INFO] Task started: fastANI
[2024-01-25 18:44:26,045] [INFO] Running command: fastANI --query /var/lib/cwl/stgadde384c-8826-4c7a-93af-fdc066c1a83f/GCF_014647415.1_ASM1464741v1_genomic.fna.gz --refList GCF_014647415.1_ASM1464741v1_genomic.fna/target_genomes.txt --output GCF_014647415.1_ASM1464741v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:44:33,443] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:33,443] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19b97ec9-1afa-4ef5-9ead-d7e0ea464033/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:44:33,444] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19b97ec9-1afa-4ef5-9ead-d7e0ea464033/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:44:33,449] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:44:33,450] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 18:44:33,450] [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
Haloarcula sebkhae	strain=JCM 19018	GCA_014647415.1	932660	932660	type	True	100.0	1376	1378	95	inconclusive
Haloarcula salaria	strain=JCM 15759	GCA_014647095.1	575195	575195	type	True	95.37	1061	1378	95	inconclusive
Haloarcula japonica	strain=DSM 6131	GCA_000336635.1	29282	29282	type	True	91.8937	1123	1378	95	below_threshold
Haloarcula marismortui	strain=ATCC 43049	GCA_000011085.1	2238	2238	suspected-type	True	90.1976	1117	1378	95	below_threshold
Haloarcula sinaiiensis	strain=ATCC 33800	GCA_000337275.1	35742	35742	suspected-type	True	90.1347	1080	1378	95	below_threshold
Haloarcula marismortui	strain=ATCC 43049	GCA_005310945.1	2238	2238	suspected-type	True	90.1044	1132	1378	95	below_threshold
Haloarcula sinaiiensis	strain=ATCC 33800	GCA_018200015.1	35742	35742	suspected-type	True	90.1034	1108	1378	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:44:33,451] [INFO] DFAST Taxonomy check result was written to GCF_014647415.1_ASM1464741v1_genomic.fna/tc_result.tsv
[2024-01-25 18:44:33,451] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:44:33,452] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:44:33,452] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19b97ec9-1afa-4ef5-9ead-d7e0ea464033/dqc_reference/checkm_data
[2024-01-25 18:44:33,452] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:44:33,507] [INFO] Task started: CheckM
[2024-01-25 18:44:33,507] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014647415.1_ASM1464741v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014647415.1_ASM1464741v1_genomic.fna/checkm_input GCF_014647415.1_ASM1464741v1_genomic.fna/checkm_result
[2024-01-25 18:45:24,482] [INFO] Task succeeded: CheckM
[2024-01-25 18:45:24,483] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:45:24,498] [INFO] ===== Completeness check finished =====
[2024-01-25 18:45:24,498] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:45:24,499] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014647415.1_ASM1464741v1_genomic.fna/markers.fasta)
[2024-01-25 18:45:24,499] [INFO] Task started: Blastn
[2024-01-25 18:45:24,499] [INFO] Running command: blastn -query GCF_014647415.1_ASM1464741v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg19b97ec9-1afa-4ef5-9ead-d7e0ea464033/dqc_reference/reference_markers_gtdb.fasta -out GCF_014647415.1_ASM1464741v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:24,997] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:24,999] [INFO] Selected 5 target genomes.
[2024-01-25 18:45:24,999] [INFO] Target genome list was writen to GCF_014647415.1_ASM1464741v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:45:25,003] [INFO] Task started: fastANI
[2024-01-25 18:45:25,003] [INFO] Running command: fastANI --query /var/lib/cwl/stgadde384c-8826-4c7a-93af-fdc066c1a83f/GCF_014647415.1_ASM1464741v1_genomic.fna.gz --refList GCF_014647415.1_ASM1464741v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014647415.1_ASM1464741v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:45:30,489] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:30,494] [INFO] Found 5 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-25 18:45:30,494] [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_014647415.1	s__Haloarcula sebkhae	100.0	1376	1378	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.2413	95.97	95.97	0.88	0.88	2	inconclusive
GCA_000336895.1	s__Haloarcula argentinensis	95.2587	1164	1378	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.2413	99.05	99.05	0.91	0.91	2	inconclusive
GCF_001485575.1	s__Haloarcula sp001485575	91.9825	1119	1378	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000336635.1	s__Haloarcula japonica	91.9072	1122	1378	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011085.1	s__Haloarcula marismortui	90.2305	1114	1378	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloarcula	95.0	98.41	98.12	0.88	0.85	9	-
--------------------------------------------------------------------------------
[2024-01-25 18:45:30,496] [INFO] GTDB search result was written to GCF_014647415.1_ASM1464741v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:45:30,496] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:45:30,499] [INFO] DFAST_QC result json was written to GCF_014647415.1_ASM1464741v1_genomic.fna/dqc_result.json
[2024-01-25 18:45:30,499] [INFO] DFAST_QC completed!
[2024-01-25 18:45:30,499] [INFO] Total running time: 0h1m25s