[2024-01-24 10:47:54,165] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:54,169] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:54,169] [INFO] DQC Reference Directory: /var/lib/cwl/stg1cde506c-5414-4d09-bcfa-b145d27f32f9/dqc_reference
[2024-01-24 10:48:03,340] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:03,343] [INFO] Task started: Prodigal
[2024-01-24 10:48:03,343] [INFO] Running command: gunzip -c /var/lib/cwl/stg060f3b7c-b8b7-4840-8abc-c8f78202f836/GCF_020164535.1_ASM2016453v1_genomic.fna.gz | prodigal -d GCF_020164535.1_ASM2016453v1_genomic.fna/cds.fna -a GCF_020164535.1_ASM2016453v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:14,910] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:14,911] [INFO] Task started: HMMsearch
[2024-01-24 10:48:14,911] [INFO] Running command: hmmsearch --tblout GCF_020164535.1_ASM2016453v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1cde506c-5414-4d09-bcfa-b145d27f32f9/dqc_reference/reference_markers.hmm GCF_020164535.1_ASM2016453v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:15,203] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:15,205] [INFO] Found 6/6 markers.
[2024-01-24 10:48:15,235] [INFO] Query marker FASTA was written to GCF_020164535.1_ASM2016453v1_genomic.fna/markers.fasta
[2024-01-24 10:48:15,235] [INFO] Task started: Blastn
[2024-01-24 10:48:15,236] [INFO] Running command: blastn -query GCF_020164535.1_ASM2016453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1cde506c-5414-4d09-bcfa-b145d27f32f9/dqc_reference/reference_markers.fasta -out GCF_020164535.1_ASM2016453v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:15,864] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:15,868] [INFO] Selected 16 target genomes.
[2024-01-24 10:48:15,869] [INFO] Target genome list was writen to GCF_020164535.1_ASM2016453v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:15,892] [INFO] Task started: fastANI
[2024-01-24 10:48:15,892] [INFO] Running command: fastANI --query /var/lib/cwl/stg060f3b7c-b8b7-4840-8abc-c8f78202f836/GCF_020164535.1_ASM2016453v1_genomic.fna.gz --refList GCF_020164535.1_ASM2016453v1_genomic.fna/target_genomes.txt --output GCF_020164535.1_ASM2016453v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:25,285] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:25,291] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1cde506c-5414-4d09-bcfa-b145d27f32f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:25,292] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1cde506c-5414-4d09-bcfa-b145d27f32f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:25,308] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:48:25,308] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:48:25,308] [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
Psychroflexus sediminis	strain=DSM 19803	GCA_900099815.1	470826	470826	type	True	79.8468	498	1008	95	below_threshold
Psychroflexus lacisalsi	strain=KACC 14089	GCA_020164495.1	503928	503928	type	True	79.4323	503	1008	95	below_threshold
Psychroflexus aurantiacus	strain=YR1-1	GCA_010820555.1	2709310	2709310	type	True	79.2918	434	1008	95	below_threshold
Psychroflexus tropicus	strain=DSM 15496	GCA_000378765.1	197345	197345	type	True	78.9356	453	1008	95	below_threshold
Psychroflexus gondwanensis	strain=ACAM 44	GCA_000355905.1	251	251	type	True	78.2912	368	1008	95	below_threshold
Psychroflexus torquis	strain=ATCC 700755	GCA_000153485.2	57029	57029	type	True	77.9994	334	1008	95	below_threshold
Zunongwangia atlantica	strain=22II14-10F7	GCA_002094855.1	1502297	1502297	type	True	76.4832	57	1008	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	76.4258	57	1008	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:25,312] [INFO] DFAST Taxonomy check result was written to GCF_020164535.1_ASM2016453v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:25,312] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:25,313] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:25,313] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1cde506c-5414-4d09-bcfa-b145d27f32f9/dqc_reference/checkm_data
[2024-01-24 10:48:25,314] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:25,349] [INFO] Task started: CheckM
[2024-01-24 10:48:25,350] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020164535.1_ASM2016453v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020164535.1_ASM2016453v1_genomic.fna/checkm_input GCF_020164535.1_ASM2016453v1_genomic.fna/checkm_result
[2024-01-24 10:49:03,387] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:03,388] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:03,410] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:03,410] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:03,411] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020164535.1_ASM2016453v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:03,412] [INFO] Task started: Blastn
[2024-01-24 10:49:03,412] [INFO] Running command: blastn -query GCF_020164535.1_ASM2016453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1cde506c-5414-4d09-bcfa-b145d27f32f9/dqc_reference/reference_markers_gtdb.fasta -out GCF_020164535.1_ASM2016453v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:04,304] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:04,311] [INFO] Selected 16 target genomes.
[2024-01-24 10:49:04,311] [INFO] Target genome list was writen to GCF_020164535.1_ASM2016453v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:04,324] [INFO] Task started: fastANI
[2024-01-24 10:49:04,324] [INFO] Running command: fastANI --query /var/lib/cwl/stg060f3b7c-b8b7-4840-8abc-c8f78202f836/GCF_020164535.1_ASM2016453v1_genomic.fna.gz --refList GCF_020164535.1_ASM2016453v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020164535.1_ASM2016453v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:13,798] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:13,818] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:49:13,818] [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_900099815.1	s__Psychroflexus sediminis	79.8661	495	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010820555.1	s__Psychroflexus sp010820555	79.3029	433	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003565575.1	s__Psychroflexus sp003565575	78.919	253	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378765.1	s__Psychroflexus tropicus	78.9149	455	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000355905.1	s__Psychroflexus gondwanensis	78.2897	369	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	98.53	98.53	0.91	0.91	2	-
GCF_002836055.1	s__Psychroflexus sp002836055	78.2651	290	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153485.2	s__Psychroflexus torquis	77.9977	334	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002094855.1	s__Zunongwangia atlantica	76.4832	57	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zunongwangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009741275.1	s__Winogradskyella endarachnes	76.4258	57	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015319355.1	s__Psychroserpens luteus	76.3943	51	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168045.1	s__Salegentibacter holothuriorum	76.3113	68	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168115.1	s__Salegentibacter salinarum	75.8518	78	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016469035.1	s__Gelidibacter salicanalis_A	75.5802	52	1008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gelidibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:13,821] [INFO] GTDB search result was written to GCF_020164535.1_ASM2016453v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:13,822] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:13,828] [INFO] DFAST_QC result json was written to GCF_020164535.1_ASM2016453v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:13,828] [INFO] DFAST_QC completed!
[2024-01-24 10:49:13,828] [INFO] Total running time: 0h1m20s