[2024-01-24 10:47:07,970] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:07,972] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:07,972] [INFO] DQC Reference Directory: /var/lib/cwl/stg6dc9efa1-05bb-452e-a44c-b042788679b9/dqc_reference
[2024-01-24 10:47:11,828] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:11,928] [INFO] Task started: Prodigal
[2024-01-24 10:47:11,929] [INFO] Running command: gunzip -c /var/lib/cwl/stg497cf0ab-ecb1-4146-9bfc-263c5eab3008/GCF_018598585.1_ASM1859858v1_genomic.fna.gz | prodigal -d GCF_018598585.1_ASM1859858v1_genomic.fna/cds.fna -a GCF_018598585.1_ASM1859858v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:33,505] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:33,506] [INFO] Task started: HMMsearch
[2024-01-24 10:47:33,506] [INFO] Running command: hmmsearch --tblout GCF_018598585.1_ASM1859858v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6dc9efa1-05bb-452e-a44c-b042788679b9/dqc_reference/reference_markers.hmm GCF_018598585.1_ASM1859858v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:33,830] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:33,831] [INFO] Found 6/6 markers.
[2024-01-24 10:47:33,883] [INFO] Query marker FASTA was written to GCF_018598585.1_ASM1859858v1_genomic.fna/markers.fasta
[2024-01-24 10:47:33,884] [INFO] Task started: Blastn
[2024-01-24 10:47:33,884] [INFO] Running command: blastn -query GCF_018598585.1_ASM1859858v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6dc9efa1-05bb-452e-a44c-b042788679b9/dqc_reference/reference_markers.fasta -out GCF_018598585.1_ASM1859858v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:34,547] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:34,552] [INFO] Selected 21 target genomes.
[2024-01-24 10:47:34,552] [INFO] Target genome list was writen to GCF_018598585.1_ASM1859858v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:35,140] [INFO] Task started: fastANI
[2024-01-24 10:47:35,141] [INFO] Running command: fastANI --query /var/lib/cwl/stg497cf0ab-ecb1-4146-9bfc-263c5eab3008/GCF_018598585.1_ASM1859858v1_genomic.fna.gz --refList GCF_018598585.1_ASM1859858v1_genomic.fna/target_genomes.txt --output GCF_018598585.1_ASM1859858v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:56,707] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:56,708] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6dc9efa1-05bb-452e-a44c-b042788679b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:56,708] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6dc9efa1-05bb-452e-a44c-b042788679b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:56,720] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:56,720] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:56,720] [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
Chryseosolibacter indicus	strain=PWU20	GCA_018598585.1	2782351	2782351	type	True	100.0	1842	1851	95	conclusive
Chryseosolibacter histidini	strain=PWU4	GCA_018598225.1	2782349	2782349	type	True	77.2122	120	1851	95	below_threshold
Pseudochryseolinea flava	strain=SDU1-6	GCA_003286915.1	2059302	2059302	type	True	76.7368	94	1851	95	below_threshold
Ohtaekwangia koreensis	strain=DSM 25262	GCA_900167975.1	688867	688867	type	True	76.6668	107	1851	95	below_threshold
Chryseotalea sanaruensis	strain=Ys	GCA_003990915.1	2482724	2482724	type	True	76.5095	53	1851	95	below_threshold
Chryseolinea soli	strain=KIS68-18	GCA_003589925.1	2321403	2321403	type	True	76.4259	59	1851	95	below_threshold
Chryseolinea serpens	strain=DSM 24574	GCA_900129725.1	947013	947013	type	True	76.3714	70	1851	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:56,722] [INFO] DFAST Taxonomy check result was written to GCF_018598585.1_ASM1859858v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:56,723] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:56,723] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:56,723] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6dc9efa1-05bb-452e-a44c-b042788679b9/dqc_reference/checkm_data
[2024-01-24 10:47:56,725] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:56,784] [INFO] Task started: CheckM
[2024-01-24 10:47:56,785] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018598585.1_ASM1859858v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018598585.1_ASM1859858v1_genomic.fna/checkm_input GCF_018598585.1_ASM1859858v1_genomic.fna/checkm_result
[2024-01-24 10:48:58,563] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:58,564] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:58,591] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:58,591] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:58,592] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018598585.1_ASM1859858v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:58,592] [INFO] Task started: Blastn
[2024-01-24 10:48:58,593] [INFO] Running command: blastn -query GCF_018598585.1_ASM1859858v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6dc9efa1-05bb-452e-a44c-b042788679b9/dqc_reference/reference_markers_gtdb.fasta -out GCF_018598585.1_ASM1859858v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:59,554] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:59,558] [INFO] Selected 26 target genomes.
[2024-01-24 10:48:59,559] [INFO] Target genome list was writen to GCF_018598585.1_ASM1859858v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:59,601] [INFO] Task started: fastANI
[2024-01-24 10:48:59,601] [INFO] Running command: fastANI --query /var/lib/cwl/stg497cf0ab-ecb1-4146-9bfc-263c5eab3008/GCF_018598585.1_ASM1859858v1_genomic.fna.gz --refList GCF_018598585.1_ASM1859858v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018598585.1_ASM1859858v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:21,676] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:21,687] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:21,687] [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
GCA_018598585.1	s__PWU20 sp018598585	100.0	1842	1851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__PWU20	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018598225.1	s__PWU20 sp018598225	77.2122	120	1851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__PWU20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902168185.1	s__Ohtaekwangia sp902168185	76.8083	108	1851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Ohtaekwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003286915.1	s__Ohtaekwangia flava	76.7368	93	1851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Ohtaekwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016787565.1	s__JAEUUG01 sp016787565	76.7269	57	1851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__JAEUUG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167975.1	s__Ohtaekwangia koreensis	76.6661	106	1851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Ohtaekwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902168205.1	s__Ohtaekwangia sp902168205	76.5334	115	1851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Ohtaekwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003589925.1	s__Chryseolinea soli	76.4259	59	1851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Chryseolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129725.1	s__Chryseolinea serpens	76.3714	70	1851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Chryseolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002432545.1	s__Ohtaekwangia sp002432545	75.9165	102	1851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Ohtaekwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303795.1	s__ELB16-189 sp017303795	75.727	50	1851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__ELB16-189	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:21,689] [INFO] GTDB search result was written to GCF_018598585.1_ASM1859858v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:21,690] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:21,693] [INFO] DFAST_QC result json was written to GCF_018598585.1_ASM1859858v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:21,693] [INFO] DFAST_QC completed!
[2024-01-24 10:49:21,693] [INFO] Total running time: 0h2m14s