[2024-01-24 13:01:39,586] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:39,593] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:39,594] [INFO] DQC Reference Directory: /var/lib/cwl/stgd9390f5d-07c6-4fc9-9dd5-0c600a73cc55/dqc_reference
[2024-01-24 13:01:41,262] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:41,263] [INFO] Task started: Prodigal
[2024-01-24 13:01:41,263] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb023cb4-aed6-429d-83fd-e3ecb77e8020/GCF_900113245.1_IMG-taxon_2617270917_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113245.1_IMG-taxon_2617270917_annotated_assembly_genomic.fna/cds.fna -a GCF_900113245.1_IMG-taxon_2617270917_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:58,410] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:58,411] [INFO] Task started: HMMsearch
[2024-01-24 13:01:58,411] [INFO] Running command: hmmsearch --tblout GCF_900113245.1_IMG-taxon_2617270917_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd9390f5d-07c6-4fc9-9dd5-0c600a73cc55/dqc_reference/reference_markers.hmm GCF_900113245.1_IMG-taxon_2617270917_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:58,668] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:58,670] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgcb023cb4-aed6-429d-83fd-e3ecb77e8020/GCF_900113245.1_IMG-taxon_2617270917_annotated_assembly_genomic.fna.gz]
[2024-01-24 13:01:58,703] [INFO] Query marker FASTA was written to GCF_900113245.1_IMG-taxon_2617270917_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:01:58,703] [INFO] Task started: Blastn
[2024-01-24 13:01:58,703] [INFO] Running command: blastn -query GCF_900113245.1_IMG-taxon_2617270917_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9390f5d-07c6-4fc9-9dd5-0c600a73cc55/dqc_reference/reference_markers.fasta -out GCF_900113245.1_IMG-taxon_2617270917_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:59,278] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:59,281] [INFO] Selected 7 target genomes.
[2024-01-24 13:01:59,281] [INFO] Target genome list was writen to GCF_900113245.1_IMG-taxon_2617270917_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:01:59,284] [INFO] Task started: fastANI
[2024-01-24 13:01:59,284] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb023cb4-aed6-429d-83fd-e3ecb77e8020/GCF_900113245.1_IMG-taxon_2617270917_annotated_assembly_genomic.fna.gz --refList GCF_900113245.1_IMG-taxon_2617270917_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113245.1_IMG-taxon_2617270917_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:06,439] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:06,439] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd9390f5d-07c6-4fc9-9dd5-0c600a73cc55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:06,440] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd9390f5d-07c6-4fc9-9dd5-0c600a73cc55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:06,447] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:06,447] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:06,447] [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
Halopelagius inordinatus	strain=CGMCC 1.7739	GCA_900113245.1	553467	553467	type	True	100.0	1170	1170	95	conclusive
Halopelagius longus	strain=CGMCC 1.12397	GCA_900100875.1	1236180	1236180	type	True	87.2094	899	1170	95	below_threshold
Halopelagius longus	strain=BC12-B1	GCA_003351065.1	1236180	1236180	type	True	87.2024	906	1170	95	below_threshold
Halogeometricum limi	strain=CGMCC 1.8711	GCA_900115785.1	555875	555875	type	True	81.7881	686	1170	95	below_threshold
Halogeometricum rufum	strain=CGMCC 1.7736	GCA_900112175.1	553469	553469	type	True	81.6113	751	1170	95	below_threshold
Haloferax prahovense	strain=DSM 18310	GCA_000336815.1	381852	381852	type	True	79.666	599	1170	95	below_threshold
Haloferax profundi	strain=SB29	GCA_001469865.1	1544718	1544718	type	True	79.0424	469	1170	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:06,458] [INFO] DFAST Taxonomy check result was written to GCF_900113245.1_IMG-taxon_2617270917_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:02:06,459] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:06,459] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:06,459] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd9390f5d-07c6-4fc9-9dd5-0c600a73cc55/dqc_reference/checkm_data
[2024-01-24 13:02:06,460] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:06,496] [INFO] Task started: CheckM
[2024-01-24 13:02:06,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113245.1_IMG-taxon_2617270917_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113245.1_IMG-taxon_2617270917_annotated_assembly_genomic.fna/checkm_input GCF_900113245.1_IMG-taxon_2617270917_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:02:53,850] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:53,852] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:53,878] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:53,878] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:53,879] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113245.1_IMG-taxon_2617270917_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:02:53,879] [INFO] Task started: Blastn
[2024-01-24 13:02:53,879] [INFO] Running command: blastn -query GCF_900113245.1_IMG-taxon_2617270917_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgd9390f5d-07c6-4fc9-9dd5-0c600a73cc55/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113245.1_IMG-taxon_2617270917_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:54,446] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:54,451] [INFO] Selected 9 target genomes.
[2024-01-24 13:02:54,451] [INFO] Target genome list was writen to GCF_900113245.1_IMG-taxon_2617270917_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:54,459] [INFO] Task started: fastANI
[2024-01-24 13:02:54,460] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb023cb4-aed6-429d-83fd-e3ecb77e8020/GCF_900113245.1_IMG-taxon_2617270917_annotated_assembly_genomic.fna.gz --refList GCF_900113245.1_IMG-taxon_2617270917_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113245.1_IMG-taxon_2617270917_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:02,795] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:02,812] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:02,812] [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_900113245.1	s__Halopelagius inordinatus	100.0	1170	1170	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halopelagius	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900100875.1	s__Halopelagius longus	87.1895	901	1170	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halopelagius	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900115785.1	s__Halogeometricum limi	81.7801	688	1170	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogeometricum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112175.1	s__Halogeometricum rufum	81.6244	748	1170	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogeometricum	95.0	98.26	98.26	0.87	0.87	2	-
GCF_000337095.1	s__Halogeometricum pallidum	81.3998	710	1170	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogeometricum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000336775.1	s__Haloferax gibbonsii	79.8126	582	1170	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	96.8304	98.89	98.78	0.89	0.88	5	-
GCF_000336815.1	s__Haloferax prahovense	79.6643	599	1170	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	96.8304	99.29	99.22	0.91	0.91	5	-
GCF_003665935.1	s__Halobellus sp003665935	79.1057	447	1170	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halobellus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001469865.1	s__Haloferax profundi	79.0078	473	1170	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 13:03:02,814] [INFO] GTDB search result was written to GCF_900113245.1_IMG-taxon_2617270917_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:02,815] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:02,820] [INFO] DFAST_QC result json was written to GCF_900113245.1_IMG-taxon_2617270917_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:03:02,820] [INFO] DFAST_QC completed!
[2024-01-24 13:03:02,820] [INFO] Total running time: 0h1m23s