[2024-01-24 13:18:46,417] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:46,419] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:46,419] [INFO] DQC Reference Directory: /var/lib/cwl/stg9adf47d7-041e-4ce2-9c63-c41c514b6041/dqc_reference
[2024-01-24 13:18:47,800] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:47,801] [INFO] Task started: Prodigal
[2024-01-24 13:18:47,802] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f04cad9-8daa-4e52-8fb9-887598ad3011/GCF_009674585.1_ASM967458v1_genomic.fna.gz | prodigal -d GCF_009674585.1_ASM967458v1_genomic.fna/cds.fna -a GCF_009674585.1_ASM967458v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:07,222] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:07,223] [INFO] Task started: HMMsearch
[2024-01-24 13:19:07,223] [INFO] Running command: hmmsearch --tblout GCF_009674585.1_ASM967458v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9adf47d7-041e-4ce2-9c63-c41c514b6041/dqc_reference/reference_markers.hmm GCF_009674585.1_ASM967458v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:07,498] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:07,500] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg7f04cad9-8daa-4e52-8fb9-887598ad3011/GCF_009674585.1_ASM967458v1_genomic.fna.gz]
[2024-01-24 13:19:07,540] [INFO] Query marker FASTA was written to GCF_009674585.1_ASM967458v1_genomic.fna/markers.fasta
[2024-01-24 13:19:07,541] [INFO] Task started: Blastn
[2024-01-24 13:19:07,541] [INFO] Running command: blastn -query GCF_009674585.1_ASM967458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9adf47d7-041e-4ce2-9c63-c41c514b6041/dqc_reference/reference_markers.fasta -out GCF_009674585.1_ASM967458v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:08,086] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:08,089] [INFO] Selected 8 target genomes.
[2024-01-24 13:19:08,090] [INFO] Target genome list was writen to GCF_009674585.1_ASM967458v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:08,096] [INFO] Task started: fastANI
[2024-01-24 13:19:08,096] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f04cad9-8daa-4e52-8fb9-887598ad3011/GCF_009674585.1_ASM967458v1_genomic.fna.gz --refList GCF_009674585.1_ASM967458v1_genomic.fna/target_genomes.txt --output GCF_009674585.1_ASM967458v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:14,950] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:14,951] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9adf47d7-041e-4ce2-9c63-c41c514b6041/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:14,951] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9adf47d7-041e-4ce2-9c63-c41c514b6041/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:14,960] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:14,960] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:14,960] [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 marinisediminis	strain=MBLA0077	GCA_009674585.1	2666142	2666142	type	True	100.0	1154	1159	95	conclusive
Haloferax profundi	strain=SB29	GCA_001469865.1	1544718	1544718	type	True	86.9479	793	1159	95	below_threshold
Haloferax litoreum	strain=MBLA0076	GCA_009674605.1	2666140	2666140	type	True	86.8208	906	1159	95	below_threshold
Haloferax marinum	strain=MBLA0078	GCA_009674625.1	2666143	2666143	type	True	86.1068	885	1159	95	below_threshold
Haloferax massiliensis	strain=Arc-Hr	GCA_001368915.1	1476858	1476858	type	True	83.4452	752	1159	95	below_threshold
Haloferax mediterranei	strain=CGMCC 1.2087	GCA_000306765.2	2252	2252	type	True	83.2819	740	1159	95	below_threshold
Haloferax larsenii	strain=JCM 13917	GCA_000336955.1	302484	302484	type	True	83.2236	742	1159	95	below_threshold
Haloferax mediterranei	strain=ATCC 33500	GCA_000685635.1	2252	2252	type	True	83.1947	736	1159	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:14,962] [INFO] DFAST Taxonomy check result was written to GCF_009674585.1_ASM967458v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:14,963] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:14,963] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:14,963] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9adf47d7-041e-4ce2-9c63-c41c514b6041/dqc_reference/checkm_data
[2024-01-24 13:19:14,965] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:15,001] [INFO] Task started: CheckM
[2024-01-24 13:19:15,001] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009674585.1_ASM967458v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009674585.1_ASM967458v1_genomic.fna/checkm_input GCF_009674585.1_ASM967458v1_genomic.fna/checkm_result
[2024-01-24 13:20:09,588] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:09,589] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:09,607] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:09,608] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:09,608] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009674585.1_ASM967458v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:09,608] [INFO] Task started: Blastn
[2024-01-24 13:20:09,609] [INFO] Running command: blastn -query GCF_009674585.1_ASM967458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9adf47d7-041e-4ce2-9c63-c41c514b6041/dqc_reference/reference_markers_gtdb.fasta -out GCF_009674585.1_ASM967458v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:10,126] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:10,129] [INFO] Selected 7 target genomes.
[2024-01-24 13:20:10,129] [INFO] Target genome list was writen to GCF_009674585.1_ASM967458v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:10,145] [INFO] Task started: fastANI
[2024-01-24 13:20:10,145] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f04cad9-8daa-4e52-8fb9-887598ad3011/GCF_009674585.1_ASM967458v1_genomic.fna.gz --refList GCF_009674585.1_ASM967458v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009674585.1_ASM967458v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:16,383] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:16,392] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:16,393] [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_009674585.1	s__Haloferax sp009674585	100.0	1153	1159	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_001469865.1	s__Haloferax profundi	86.9553	792	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	86.8074	907	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_009674625.1	s__Haloferax sp009674625	86.1241	887	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_001368915.1	s__Haloferax massiliensis	83.42	753	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_000306765.2	s__Haloferax mediterranei	83.2906	739	1159	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	99.99	99.97	1.00	0.99	4	-
GCF_000336955.1	s__Haloferax larsenii	83.2266	741	1159	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	96.49	96.49	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:16,402] [INFO] GTDB search result was written to GCF_009674585.1_ASM967458v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:16,403] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:16,405] [INFO] DFAST_QC result json was written to GCF_009674585.1_ASM967458v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:16,406] [INFO] DFAST_QC completed!
[2024-01-24 13:20:16,406] [INFO] Total running time: 0h1m30s