[2024-01-24 13:56:27,070] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:27,072] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:27,072] [INFO] DQC Reference Directory: /var/lib/cwl/stg66dab8cb-c8e3-4de0-bf03-f6193449bdb3/dqc_reference
[2024-01-24 13:56:28,309] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:28,310] [INFO] Task started: Prodigal
[2024-01-24 13:56:28,310] [INFO] Running command: gunzip -c /var/lib/cwl/stg94b3f829-9ba1-45a4-88ef-685ed503119c/GCF_009674625.1_ASM967462v1_genomic.fna.gz | prodigal -d GCF_009674625.1_ASM967462v1_genomic.fna/cds.fna -a GCF_009674625.1_ASM967462v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:47,245] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:47,245] [INFO] Task started: HMMsearch
[2024-01-24 13:56:47,245] [INFO] Running command: hmmsearch --tblout GCF_009674625.1_ASM967462v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66dab8cb-c8e3-4de0-bf03-f6193449bdb3/dqc_reference/reference_markers.hmm GCF_009674625.1_ASM967462v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:47,473] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:47,474] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg94b3f829-9ba1-45a4-88ef-685ed503119c/GCF_009674625.1_ASM967462v1_genomic.fna.gz]
[2024-01-24 13:56:47,516] [INFO] Query marker FASTA was written to GCF_009674625.1_ASM967462v1_genomic.fna/markers.fasta
[2024-01-24 13:56:47,516] [INFO] Task started: Blastn
[2024-01-24 13:56:47,516] [INFO] Running command: blastn -query GCF_009674625.1_ASM967462v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66dab8cb-c8e3-4de0-bf03-f6193449bdb3/dqc_reference/reference_markers.fasta -out GCF_009674625.1_ASM967462v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:48,021] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:48,025] [INFO] Selected 7 target genomes.
[2024-01-24 13:56:48,025] [INFO] Target genome list was writen to GCF_009674625.1_ASM967462v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:48,030] [INFO] Task started: fastANI
[2024-01-24 13:56:48,031] [INFO] Running command: fastANI --query /var/lib/cwl/stg94b3f829-9ba1-45a4-88ef-685ed503119c/GCF_009674625.1_ASM967462v1_genomic.fna.gz --refList GCF_009674625.1_ASM967462v1_genomic.fna/target_genomes.txt --output GCF_009674625.1_ASM967462v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:54,151] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:54,152] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66dab8cb-c8e3-4de0-bf03-f6193449bdb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:54,152] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66dab8cb-c8e3-4de0-bf03-f6193449bdb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:54,162] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:54,162] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:54,163] [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
Haloferax marinum	strain=MBLA0078	GCA_009674625.1	2666143	2666143	type	True	100.0	1158	1159	95	conclusive
Haloferax marinisediminis	strain=MBLA0077	GCA_009674585.1	2666142	2666142	type	True	86.0181	891	1159	95	below_threshold
Haloferax profundi	strain=SB29	GCA_001469865.1	1544718	1544718	type	True	85.8842	776	1159	95	below_threshold
Haloferax litoreum	strain=MBLA0076	GCA_009674605.1	2666140	2666140	type	True	85.7731	879	1159	95	below_threshold
Haloferax marisrubri	strain=SB3	GCA_001469875.2	1544719	1544719	type	True	83.4362	765	1159	95	below_threshold
Haloferax massiliensis	strain=Arc-Hr	GCA_001368915.1	1476858	1476858	type	True	83.0552	742	1159	95	below_threshold
Haloferax mucosum	strain=ATCC BAA-1512	GCA_000337815.1	403181	403181	type	True	82.712	691	1159	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:54,178] [INFO] DFAST Taxonomy check result was written to GCF_009674625.1_ASM967462v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:54,178] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:54,179] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:54,179] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66dab8cb-c8e3-4de0-bf03-f6193449bdb3/dqc_reference/checkm_data
[2024-01-24 13:56:54,181] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:54,219] [INFO] Task started: CheckM
[2024-01-24 13:56:54,220] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009674625.1_ASM967462v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009674625.1_ASM967462v1_genomic.fna/checkm_input GCF_009674625.1_ASM967462v1_genomic.fna/checkm_result
[2024-01-24 13:57:48,700] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:48,701] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:48,725] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:48,726] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:48,726] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009674625.1_ASM967462v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:48,727] [INFO] Task started: Blastn
[2024-01-24 13:57:48,727] [INFO] Running command: blastn -query GCF_009674625.1_ASM967462v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66dab8cb-c8e3-4de0-bf03-f6193449bdb3/dqc_reference/reference_markers_gtdb.fasta -out GCF_009674625.1_ASM967462v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:49,249] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:49,254] [INFO] Selected 7 target genomes.
[2024-01-24 13:57:49,255] [INFO] Target genome list was writen to GCF_009674625.1_ASM967462v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:49,260] [INFO] Task started: fastANI
[2024-01-24 13:57:49,260] [INFO] Running command: fastANI --query /var/lib/cwl/stg94b3f829-9ba1-45a4-88ef-685ed503119c/GCF_009674625.1_ASM967462v1_genomic.fna.gz --refList GCF_009674625.1_ASM967462v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009674625.1_ASM967462v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:55,893] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:55,910] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:55,910] [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_009674625.1	s__Haloferax sp009674625	100.0	1158	1159	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_009674585.1	s__Haloferax sp009674585	86.0312	890	1159	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001469865.1	s__Haloferax profundi	85.8839	776	1159	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674605.1	s__Haloferax sp009674605	85.7948	879	1159	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001469875.2	s__Haloferax marisrubri	83.4302	765	1159	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	95.85	95.85	0.83	0.83	2	-
GCF_001368915.1	s__Haloferax massiliensis	83.0437	743	1159	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.2845	98.47	96.94	0.94	0.88	3	-
GCF_000337815.1	s__Haloferax mucosum	82.712	691	1159	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:55,913] [INFO] GTDB search result was written to GCF_009674625.1_ASM967462v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:55,914] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:55,921] [INFO] DFAST_QC result json was written to GCF_009674625.1_ASM967462v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:55,921] [INFO] DFAST_QC completed!
[2024-01-24 13:57:55,922] [INFO] Total running time: 0h1m29s