[2024-01-24 14:05:34,207] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:34,209] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:34,209] [INFO] DQC Reference Directory: /var/lib/cwl/stg40c34dc4-8ac9-44c1-8e16-8d7805debceb/dqc_reference
[2024-01-24 14:05:35,490] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:35,491] [INFO] Task started: Prodigal
[2024-01-24 14:05:35,492] [INFO] Running command: gunzip -c /var/lib/cwl/stg001e63f1-6e77-4bd8-95d2-dc036f7c32fa/GCF_000832545.1_ASM83254v1_genomic.fna.gz | prodigal -d GCF_000832545.1_ASM83254v1_genomic.fna/cds.fna -a GCF_000832545.1_ASM83254v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:55,650] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:55,650] [INFO] Task started: HMMsearch
[2024-01-24 14:05:55,650] [INFO] Running command: hmmsearch --tblout GCF_000832545.1_ASM83254v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40c34dc4-8ac9-44c1-8e16-8d7805debceb/dqc_reference/reference_markers.hmm GCF_000832545.1_ASM83254v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:56,017] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:56,019] [INFO] Found 6/6 markers.
[2024-01-24 14:05:56,072] [INFO] Query marker FASTA was written to GCF_000832545.1_ASM83254v1_genomic.fna/markers.fasta
[2024-01-24 14:05:56,072] [INFO] Task started: Blastn
[2024-01-24 14:05:56,073] [INFO] Running command: blastn -query GCF_000832545.1_ASM83254v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40c34dc4-8ac9-44c1-8e16-8d7805debceb/dqc_reference/reference_markers.fasta -out GCF_000832545.1_ASM83254v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:56,775] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:56,779] [INFO] Selected 15 target genomes.
[2024-01-24 14:05:56,779] [INFO] Target genome list was writen to GCF_000832545.1_ASM83254v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:56,786] [INFO] Task started: fastANI
[2024-01-24 14:05:56,786] [INFO] Running command: fastANI --query /var/lib/cwl/stg001e63f1-6e77-4bd8-95d2-dc036f7c32fa/GCF_000832545.1_ASM83254v1_genomic.fna.gz --refList GCF_000832545.1_ASM83254v1_genomic.fna/target_genomes.txt --output GCF_000832545.1_ASM83254v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:10,486] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:10,487] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40c34dc4-8ac9-44c1-8e16-8d7805debceb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:10,487] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40c34dc4-8ac9-44c1-8e16-8d7805debceb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:10,497] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:10,498] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:10,498] [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
Pedobacter lusitanus	strain=NL19	GCA_000832545.1	1503925	1503925	type	True	100.0	1895	1908	95	conclusive
Pedobacter cryoconitis	strain=DSM 14825	GCA_003259615.1	188932	188932	suspected-type	True	82.7682	1106	1908	95	below_threshold
Pedobacter hartonius	strain=DSM 19033	GCA_900107535.1	425514	425514	type	True	79.746	456	1908	95	below_threshold
Pedobacter westerhofensis	strain=DSM 19036	GCA_900182595.1	425512	425512	type	True	79.5297	445	1908	95	below_threshold
Pedobacter antarcticus	strain=ATCC 51969	GCA_900112985.1	34086	34086	type	True	79.1677	357	1908	95	below_threshold
Pedobacter antarcticus	strain=4BY	GCA_000722885.1	34086	34086	type	True	79.111	351	1908	95	below_threshold
Pedobacter metabolipauper	strain=DSM 19035	GCA_004362715.1	425513	425513	type	True	78.2373	257	1908	95	below_threshold
Pedobacter foliorum	strain=LMG 31463	GCA_013266735.1	2739058	2739058	type	True	78.1834	257	1908	95	below_threshold
Pedobacter steynii	strain=DSM 19110	GCA_900103665.1	430522	430522	type	True	78.1304	360	1908	95	below_threshold
Pedobacter nanyangensis	strain=Q-4	GCA_003313505.1	1562389	1562389	type	True	77.3069	99	1908	95	below_threshold
Pedobacter aquae	strain=CJ43	GCA_008195825.1	2605747	2605747	type	True	76.9525	76	1908	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:10,500] [INFO] DFAST Taxonomy check result was written to GCF_000832545.1_ASM83254v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:10,501] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:10,501] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:10,501] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40c34dc4-8ac9-44c1-8e16-8d7805debceb/dqc_reference/checkm_data
[2024-01-24 14:06:10,503] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:10,559] [INFO] Task started: CheckM
[2024-01-24 14:06:10,560] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000832545.1_ASM83254v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000832545.1_ASM83254v1_genomic.fna/checkm_input GCF_000832545.1_ASM83254v1_genomic.fna/checkm_result
[2024-01-24 14:07:09,713] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:09,715] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:09,732] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:09,732] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:09,733] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000832545.1_ASM83254v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:09,733] [INFO] Task started: Blastn
[2024-01-24 14:07:09,733] [INFO] Running command: blastn -query GCF_000832545.1_ASM83254v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40c34dc4-8ac9-44c1-8e16-8d7805debceb/dqc_reference/reference_markers_gtdb.fasta -out GCF_000832545.1_ASM83254v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:10,562] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:10,566] [INFO] Selected 7 target genomes.
[2024-01-24 14:07:10,566] [INFO] Target genome list was writen to GCF_000832545.1_ASM83254v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:10,574] [INFO] Task started: fastANI
[2024-01-24 14:07:10,575] [INFO] Running command: fastANI --query /var/lib/cwl/stg001e63f1-6e77-4bd8-95d2-dc036f7c32fa/GCF_000832545.1_ASM83254v1_genomic.fna.gz --refList GCF_000832545.1_ASM83254v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000832545.1_ASM83254v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:19,349] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:19,356] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:19,356] [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_000832545.1	s__Pedobacter lusitanus	100.0	1895	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014200605.1	s__Pedobacter cryoconitis_B	83.5552	1212	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.88	98.88	0.94	0.94	2	-
GCA_014302835.1	s__Pedobacter sp014302835	82.8511	926	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259615.1	s__Pedobacter cryoconitis	82.7661	1105	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200595.1	s__Pedobacter cryoconitis_C	82.6673	1164	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.76	98.76	0.93	0.93	2	-
GCF_001590605.1	s__Pedobacter cryoconitis_A	82.6547	1042	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207135.1	s__Pedobacter cryoconitis_D	81.5553	929	1908	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:19,358] [INFO] GTDB search result was written to GCF_000832545.1_ASM83254v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:19,359] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:19,362] [INFO] DFAST_QC result json was written to GCF_000832545.1_ASM83254v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:19,362] [INFO] DFAST_QC completed!
[2024-01-24 14:07:19,362] [INFO] Total running time: 0h1m45s