[2024-01-24 10:57:08,968] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:08,973] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:08,974] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f2cc0f8-8b49-4d3a-ad8b-bb1234498889/dqc_reference
[2024-01-24 10:57:10,643] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:10,644] [INFO] Task started: Prodigal
[2024-01-24 10:57:10,645] [INFO] Running command: gunzip -c /var/lib/cwl/stg91716263-a137-47ed-b415-a6bd32379058/GCF_024494695.1_ASM2449469v1_genomic.fna.gz | prodigal -d GCF_024494695.1_ASM2449469v1_genomic.fna/cds.fna -a GCF_024494695.1_ASM2449469v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:29,312] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:29,313] [INFO] Task started: HMMsearch
[2024-01-24 10:57:29,313] [INFO] Running command: hmmsearch --tblout GCF_024494695.1_ASM2449469v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f2cc0f8-8b49-4d3a-ad8b-bb1234498889/dqc_reference/reference_markers.hmm GCF_024494695.1_ASM2449469v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:29,621] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:29,622] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg91716263-a137-47ed-b415-a6bd32379058/GCF_024494695.1_ASM2449469v1_genomic.fna.gz]
[2024-01-24 10:57:29,657] [INFO] Query marker FASTA was written to GCF_024494695.1_ASM2449469v1_genomic.fna/markers.fasta
[2024-01-24 10:57:29,658] [INFO] Task started: Blastn
[2024-01-24 10:57:29,658] [INFO] Running command: blastn -query GCF_024494695.1_ASM2449469v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f2cc0f8-8b49-4d3a-ad8b-bb1234498889/dqc_reference/reference_markers.fasta -out GCF_024494695.1_ASM2449469v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:30,418] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:30,421] [INFO] Selected 7 target genomes.
[2024-01-24 10:57:30,421] [INFO] Target genome list was writen to GCF_024494695.1_ASM2449469v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:30,426] [INFO] Task started: fastANI
[2024-01-24 10:57:30,427] [INFO] Running command: fastANI --query /var/lib/cwl/stg91716263-a137-47ed-b415-a6bd32379058/GCF_024494695.1_ASM2449469v1_genomic.fna.gz --refList GCF_024494695.1_ASM2449469v1_genomic.fna/target_genomes.txt --output GCF_024494695.1_ASM2449469v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:38,232] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:38,233] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f2cc0f8-8b49-4d3a-ad8b-bb1234498889/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:38,233] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f2cc0f8-8b49-4d3a-ad8b-bb1234498889/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:38,241] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:57:38,241] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:38,241] [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
Natronoarchaeum rubrum	strain=GX48	GCA_024494695.1	755311	755311	type	True	100.0	1278	1337	95	conclusive
Natronoarchaeum philippinense	strain=DSM 27208	GCA_900215575.1	558529	558529	type	True	85.9472	838	1337	95	below_threshold
Halostella litorea	strain=DLLS-108	GCA_004785955.1	2528831	2528831	type	True	79.7065	598	1337	95	below_threshold
Halostella limicola	strain=LT12	GCA_003675875.1	2448456	2448456	type	True	79.6801	604	1337	95	below_threshold
Natranaeroarchaeum aerophilus	strain=AArc-St1-1	GCA_023638055.1	2917711	2917711	type	True	79.2557	463	1337	95	below_threshold
Natranaeroarchaeum sulfidigenes	strain=AArc-S	GCA_017094485.1	2784880	2784880	type	True	79.1573	432	1337	95	below_threshold
Halorussus rarus	strain=TBN4	GCA_003369835.1	660515	660515	type	True	78.5272	557	1337	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:38,242] [INFO] DFAST Taxonomy check result was written to GCF_024494695.1_ASM2449469v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:38,243] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:38,243] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:38,243] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f2cc0f8-8b49-4d3a-ad8b-bb1234498889/dqc_reference/checkm_data
[2024-01-24 10:57:38,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:38,284] [INFO] Task started: CheckM
[2024-01-24 10:57:38,284] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024494695.1_ASM2449469v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024494695.1_ASM2449469v1_genomic.fna/checkm_input GCF_024494695.1_ASM2449469v1_genomic.fna/checkm_result
[2024-01-24 10:58:29,069] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:29,070] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 17.05%
Strain heterogeneity: 85.71%
--------------------------------------------------------------------------------
[2024-01-24 10:58:29,093] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:29,094] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:29,094] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024494695.1_ASM2449469v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:29,095] [INFO] Task started: Blastn
[2024-01-24 10:58:29,095] [INFO] Running command: blastn -query GCF_024494695.1_ASM2449469v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f2cc0f8-8b49-4d3a-ad8b-bb1234498889/dqc_reference/reference_markers_gtdb.fasta -out GCF_024494695.1_ASM2449469v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:30,293] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:30,296] [INFO] Selected 10 target genomes.
[2024-01-24 10:58:30,296] [INFO] Target genome list was writen to GCF_024494695.1_ASM2449469v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:30,303] [INFO] Task started: fastANI
[2024-01-24 10:58:30,303] [INFO] Running command: fastANI --query /var/lib/cwl/stg91716263-a137-47ed-b415-a6bd32379058/GCF_024494695.1_ASM2449469v1_genomic.fna.gz --refList GCF_024494695.1_ASM2449469v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024494695.1_ASM2449469v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:39,614] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:39,631] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:58:39,631] [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_900215575.1	s__Natronoarchaeum philippinense	85.9334	839	1337	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natronoarchaeaceae;g__Natronoarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003675855.1	s__Halostella salina	79.8233	577	1337	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003675875.1	s__Halostella sp003675875	79.7014	604	1337	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004785955.1	s__Halostella litorea	79.6901	597	1337	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003023565.1	s__Halostella sp003023565	79.2723	478	1337	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017094485.1	s__Natronoarchaeum sp017094485	79.1393	436	1337	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natronoarchaeaceae;g__Natronoarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003369835.1	s__Halorussus rarus	78.5153	558	1337	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004765795.1	s__Halorussus sp004765795	78.4587	491	1337	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	98.88	98.88	0.88	0.88	2	-
GCF_900110865.1	s__Natrinema salaciae	78.1906	511	1337	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004765805.1	s__Halorussus sp004765805	78.0852	461	1337	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:39,633] [INFO] GTDB search result was written to GCF_024494695.1_ASM2449469v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:39,633] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:39,636] [INFO] DFAST_QC result json was written to GCF_024494695.1_ASM2449469v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:39,637] [INFO] DFAST_QC completed!
[2024-01-24 10:58:39,637] [INFO] Total running time: 0h1m31s