[2024-01-24 13:37:27,858] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:27,860] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:27,860] [INFO] DQC Reference Directory: /var/lib/cwl/stg42396327-ea64-4f44-946c-371883ea185b/dqc_reference
[2024-01-24 13:37:29,095] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:29,095] [INFO] Task started: Prodigal
[2024-01-24 13:37:29,096] [INFO] Running command: gunzip -c /var/lib/cwl/stg87702e6b-ec5a-4567-ab90-74b1c66cdbf4/GCF_000337435.1_ASM33743v1_genomic.fna.gz | prodigal -d GCF_000337435.1_ASM33743v1_genomic.fna/cds.fna -a GCF_000337435.1_ASM33743v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:43,593] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:43,594] [INFO] Task started: HMMsearch
[2024-01-24 13:37:43,594] [INFO] Running command: hmmsearch --tblout GCF_000337435.1_ASM33743v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42396327-ea64-4f44-946c-371883ea185b/dqc_reference/reference_markers.hmm GCF_000337435.1_ASM33743v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:43,828] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:43,830] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg87702e6b-ec5a-4567-ab90-74b1c66cdbf4/GCF_000337435.1_ASM33743v1_genomic.fna.gz]
[2024-01-24 13:37:43,859] [INFO] Query marker FASTA was written to GCF_000337435.1_ASM33743v1_genomic.fna/markers.fasta
[2024-01-24 13:37:43,860] [INFO] Task started: Blastn
[2024-01-24 13:37:43,860] [INFO] Running command: blastn -query GCF_000337435.1_ASM33743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42396327-ea64-4f44-946c-371883ea185b/dqc_reference/reference_markers.fasta -out GCF_000337435.1_ASM33743v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:44,385] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:44,392] [INFO] Selected 6 target genomes.
[2024-01-24 13:37:44,393] [INFO] Target genome list was writen to GCF_000337435.1_ASM33743v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:44,398] [INFO] Task started: fastANI
[2024-01-24 13:37:44,398] [INFO] Running command: fastANI --query /var/lib/cwl/stg87702e6b-ec5a-4567-ab90-74b1c66cdbf4/GCF_000337435.1_ASM33743v1_genomic.fna.gz --refList GCF_000337435.1_ASM33743v1_genomic.fna/target_genomes.txt --output GCF_000337435.1_ASM33743v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:51,596] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:51,596] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42396327-ea64-4f44-946c-371883ea185b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:51,596] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42396327-ea64-4f44-946c-371883ea185b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:51,603] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:37:51,603] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:37:51,604] [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
Halorubrum distributum	strain=JCM 9100	GCA_000337055.1	29283	29283	suspected-type	True	98.1391	917	1090	95	inconclusive
Halorubrum distributum	strain=JCM 10118	GCA_000337335.1	29283	29283	suspected-type	True	98.1044	931	1090	95	inconclusive
Halorubrum arcis	strain=JCM 13916	GCA_000337015.1	368454	368454	type	True	97.7183	912	1090	95	inconclusive
Halorubrum ezzemoulense	strain=DSM 17463	GCA_000421805.1	337243	337243	type	True	89.9647	846	1090	95	below_threshold
Halorubrum ezzemoulense	strain=DSM 17463	GCA_002114285.1	337243	337243	type	True	89.9232	814	1090	95	below_threshold
Halorubrum coriense	strain=DSM 10284	GCA_000337035.1	64713	64713	type	True	89.3896	833	1090	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:51,605] [INFO] DFAST Taxonomy check result was written to GCF_000337435.1_ASM33743v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:51,606] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:51,606] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:51,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42396327-ea64-4f44-946c-371883ea185b/dqc_reference/checkm_data
[2024-01-24 13:37:51,608] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:51,650] [INFO] Task started: CheckM
[2024-01-24 13:37:51,650] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000337435.1_ASM33743v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000337435.1_ASM33743v1_genomic.fna/checkm_input GCF_000337435.1_ASM33743v1_genomic.fna/checkm_result
[2024-01-24 13:38:33,488] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:33,490] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:33,518] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:33,518] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:33,519] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000337435.1_ASM33743v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:33,519] [INFO] Task started: Blastn
[2024-01-24 13:38:33,520] [INFO] Running command: blastn -query GCF_000337435.1_ASM33743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42396327-ea64-4f44-946c-371883ea185b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000337435.1_ASM33743v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:34,049] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:34,053] [INFO] Selected 8 target genomes.
[2024-01-24 13:38:34,054] [INFO] Target genome list was writen to GCF_000337435.1_ASM33743v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:34,095] [INFO] Task started: fastANI
[2024-01-24 13:38:34,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg87702e6b-ec5a-4567-ab90-74b1c66cdbf4/GCF_000337435.1_ASM33743v1_genomic.fna.gz --refList GCF_000337435.1_ASM33743v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000337435.1_ASM33743v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:44,608] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:44,615] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:44,616] [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_000337335.1	s__Halorubrum distributum	98.0676	932	1090	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	98.52	97.80	0.88	0.83	7	conclusive
GCF_003666015.1	s__Halorubrum sp003666015	93.264	877	1090	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018228765.1	s__Halorubrum sp000296615	93.2297	856	1090	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	99.09	99.09	0.95	0.95	2	-
GCF_002355655.1	s__Halorubrum trapanicum_A	92.555	834	1090	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102375.1	s__Halorubrum xinjiangense	91.226	853	1090	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000336875.1	s__Halorubrum californiense	90.8175	834	1090	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	99.69	99.69	0.88	0.88	2	-
GCF_001280455.1	s__Halorubrum tropicale	90.5673	852	1090	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	97.18	95.21	0.82	0.77	8	-
GCF_017873555.1	s__Halorubrum trapanicum	90.3635	786	1090	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halorubrum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:44,617] [INFO] GTDB search result was written to GCF_000337435.1_ASM33743v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:44,618] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:44,620] [INFO] DFAST_QC result json was written to GCF_000337435.1_ASM33743v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:44,621] [INFO] DFAST_QC completed!
[2024-01-24 13:38:44,621] [INFO] Total running time: 0h1m17s