[2024-01-24 13:58:11,201] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:11,203] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:11,203] [INFO] DQC Reference Directory: /var/lib/cwl/stgdebc70cd-c69b-488a-91e1-10f07a14cbe2/dqc_reference
[2024-01-24 13:58:12,522] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:12,523] [INFO] Task started: Prodigal
[2024-01-24 13:58:12,524] [INFO] Running command: gunzip -c /var/lib/cwl/stgdf9b11f9-23d4-477c-ae2b-5cdf682083cf/GCF_016495725.1_ASM1649572v1_genomic.fna.gz | prodigal -d GCF_016495725.1_ASM1649572v1_genomic.fna/cds.fna -a GCF_016495725.1_ASM1649572v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:25,075] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:25,075] [INFO] Task started: HMMsearch
[2024-01-24 13:58:25,076] [INFO] Running command: hmmsearch --tblout GCF_016495725.1_ASM1649572v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdebc70cd-c69b-488a-91e1-10f07a14cbe2/dqc_reference/reference_markers.hmm GCF_016495725.1_ASM1649572v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:25,448] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:25,449] [INFO] Found 6/6 markers.
[2024-01-24 13:58:25,489] [INFO] Query marker FASTA was written to GCF_016495725.1_ASM1649572v1_genomic.fna/markers.fasta
[2024-01-24 13:58:25,490] [INFO] Task started: Blastn
[2024-01-24 13:58:25,490] [INFO] Running command: blastn -query GCF_016495725.1_ASM1649572v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdebc70cd-c69b-488a-91e1-10f07a14cbe2/dqc_reference/reference_markers.fasta -out GCF_016495725.1_ASM1649572v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:26,086] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:26,091] [INFO] Selected 11 target genomes.
[2024-01-24 13:58:26,092] [INFO] Target genome list was writen to GCF_016495725.1_ASM1649572v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:26,097] [INFO] Task started: fastANI
[2024-01-24 13:58:26,098] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf9b11f9-23d4-477c-ae2b-5cdf682083cf/GCF_016495725.1_ASM1649572v1_genomic.fna.gz --refList GCF_016495725.1_ASM1649572v1_genomic.fna/target_genomes.txt --output GCF_016495725.1_ASM1649572v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:37,570] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:37,571] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdebc70cd-c69b-488a-91e1-10f07a14cbe2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:37,571] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdebc70cd-c69b-488a-91e1-10f07a14cbe2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:37,577] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:37,577] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:37,577] [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
Salicibibacter cibarius	strain=NKC5-3	GCA_016495725.1	2743000	2743000	type	True	100.0	1500	1504	95	conclusive
Salicibibacter cibi	strain=NKC21-4	GCA_016495865.1	2743001	2743001	type	True	88.76	987	1504	95	below_threshold
Salicibibacter halophilus	strain=NKC3-5	GCA_006740705.1	2502791	2502791	type	True	84.1561	844	1504	95	below_threshold
Salicibibacter kimchii	strain=NKC1-1	GCA_003336365.1	2099786	2099786	type	True	84.0959	838	1504	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:37,579] [INFO] DFAST Taxonomy check result was written to GCF_016495725.1_ASM1649572v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:37,579] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:37,580] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:37,580] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdebc70cd-c69b-488a-91e1-10f07a14cbe2/dqc_reference/checkm_data
[2024-01-24 13:58:37,581] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:37,630] [INFO] Task started: CheckM
[2024-01-24 13:58:37,630] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016495725.1_ASM1649572v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016495725.1_ASM1649572v1_genomic.fna/checkm_input GCF_016495725.1_ASM1649572v1_genomic.fna/checkm_result
[2024-01-24 13:59:20,510] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:20,512] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:20,534] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:20,535] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:20,535] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016495725.1_ASM1649572v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:20,536] [INFO] Task started: Blastn
[2024-01-24 13:59:20,536] [INFO] Running command: blastn -query GCF_016495725.1_ASM1649572v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdebc70cd-c69b-488a-91e1-10f07a14cbe2/dqc_reference/reference_markers_gtdb.fasta -out GCF_016495725.1_ASM1649572v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:21,314] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:21,319] [INFO] Selected 12 target genomes.
[2024-01-24 13:59:21,319] [INFO] Target genome list was writen to GCF_016495725.1_ASM1649572v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:21,336] [INFO] Task started: fastANI
[2024-01-24 13:59:21,337] [INFO] Running command: fastANI --query /var/lib/cwl/stgdf9b11f9-23d4-477c-ae2b-5cdf682083cf/GCF_016495725.1_ASM1649572v1_genomic.fna.gz --refList GCF_016495725.1_ASM1649572v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016495725.1_ASM1649572v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:31,788] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:31,801] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:31,801] [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_016495725.1	s__Salicibibacter cibarius	100.0	1500	1504	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Marinococcaceae;g__Salicibibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016495865.1	s__Salicibibacter cibi	88.7264	990	1504	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Marinococcaceae;g__Salicibibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006740705.1	s__Salicibibacter halophilus	84.1428	843	1504	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Marinococcaceae;g__Salicibibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003336365.1	s__Salicibibacter kimchii	84.1173	839	1504	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Marinococcaceae;g__Salicibibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100185.1	s__Natribacillus halophilus	80.8081	531	1504	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Marinococcaceae;g__Natribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207655.1	s__Geomicrobium halophilum	79.2366	219	1504	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Marinococcaceae;g__Geomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:31,803] [INFO] GTDB search result was written to GCF_016495725.1_ASM1649572v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:31,804] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:31,807] [INFO] DFAST_QC result json was written to GCF_016495725.1_ASM1649572v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:31,807] [INFO] DFAST_QC completed!
[2024-01-24 13:59:31,807] [INFO] Total running time: 0h1m21s