[2024-01-24 12:54:39,511] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:39,514] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:39,514] [INFO] DQC Reference Directory: /var/lib/cwl/stg9556bb62-2ac9-4596-8eee-e9996dccb192/dqc_reference
[2024-01-24 12:54:40,975] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:40,978] [INFO] Task started: Prodigal
[2024-01-24 12:54:40,978] [INFO] Running command: gunzip -c /var/lib/cwl/stgb04929f9-9c8c-496f-8048-07a76bd830a5/GCF_005925325.1_ASM592532v1_genomic.fna.gz | prodigal -d GCF_005925325.1_ASM592532v1_genomic.fna/cds.fna -a GCF_005925325.1_ASM592532v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:55:00,098] [INFO] Task succeeded: Prodigal
[2024-01-24 12:55:00,099] [INFO] Task started: HMMsearch
[2024-01-24 12:55:00,099] [INFO] Running command: hmmsearch --tblout GCF_005925325.1_ASM592532v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9556bb62-2ac9-4596-8eee-e9996dccb192/dqc_reference/reference_markers.hmm GCF_005925325.1_ASM592532v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:55:00,429] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:55:00,431] [INFO] Found 6/6 markers.
[2024-01-24 12:55:00,473] [INFO] Query marker FASTA was written to GCF_005925325.1_ASM592532v1_genomic.fna/markers.fasta
[2024-01-24 12:55:00,473] [INFO] Task started: Blastn
[2024-01-24 12:55:00,474] [INFO] Running command: blastn -query GCF_005925325.1_ASM592532v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9556bb62-2ac9-4596-8eee-e9996dccb192/dqc_reference/reference_markers.fasta -out GCF_005925325.1_ASM592532v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:01,081] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:01,085] [INFO] Selected 13 target genomes.
[2024-01-24 12:55:01,086] [INFO] Target genome list was writen to GCF_005925325.1_ASM592532v1_genomic.fna/target_genomes.txt
[2024-01-24 12:55:01,094] [INFO] Task started: fastANI
[2024-01-24 12:55:01,094] [INFO] Running command: fastANI --query /var/lib/cwl/stgb04929f9-9c8c-496f-8048-07a76bd830a5/GCF_005925325.1_ASM592532v1_genomic.fna.gz --refList GCF_005925325.1_ASM592532v1_genomic.fna/target_genomes.txt --output GCF_005925325.1_ASM592532v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:55:14,043] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:14,043] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9556bb62-2ac9-4596-8eee-e9996dccb192/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:55:14,044] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9556bb62-2ac9-4596-8eee-e9996dccb192/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:55:14,054] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:55:14,054] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:55:14,055] [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 helvus	strain=P-25	GCA_005925325.1	2563444	2563444	type	True	100.0	1533	1533	95	conclusive
Pedobacter xixiisoli	strain=S27	GCA_005925365.1	1476464	1476464	type	True	82.9268	1001	1533	95	below_threshold
Pedobacter xixiisoli	strain=CGMCC 1.12803	GCA_900215335.1	1476464	1476464	type	True	82.9258	1014	1533	95	below_threshold
Pedobacter ureilyticus	strain=THG-T11	GCA_005925345.1	1393051	1393051	type	True	82.4772	912	1533	95	below_threshold
Pedobacter chitinilyticus	strain=CM134L-2	GCA_004025525.1	2233776	2233776	type	True	79.9396	715	1533	95	below_threshold
Pedobacter nanyangensis	strain=Q-4	GCA_003313505.1	1562389	1562389	type	True	79.5012	580	1533	95	below_threshold
Pedobacter frigiditerrae	strain=RP-1-13	GCA_004331645.1	2530452	2530452	type	True	77.8627	340	1533	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	77.8375	218	1533	95	below_threshold
Pedobacter zeae	strain=DSM 100774	GCA_014196715.1	1737356	1737356	type	True	77.479	198	1533	95	below_threshold
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	77.3895	230	1533	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	77.2802	70	1533	95	below_threshold
Pedobacter mucosus	strain=Q8-18	GCA_022200785.1	2895286	2895286	type	True	77.2521	187	1533	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:55:14,056] [INFO] DFAST Taxonomy check result was written to GCF_005925325.1_ASM592532v1_genomic.fna/tc_result.tsv
[2024-01-24 12:55:14,057] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:55:14,057] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:55:14,057] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9556bb62-2ac9-4596-8eee-e9996dccb192/dqc_reference/checkm_data
[2024-01-24 12:55:14,059] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:55:14,103] [INFO] Task started: CheckM
[2024-01-24 12:55:14,103] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005925325.1_ASM592532v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005925325.1_ASM592532v1_genomic.fna/checkm_input GCF_005925325.1_ASM592532v1_genomic.fna/checkm_result
[2024-01-24 12:56:05,399] [INFO] Task succeeded: CheckM
[2024-01-24 12:56:05,401] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:56:05,426] [INFO] ===== Completeness check finished =====
[2024-01-24 12:56:05,426] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:56:05,426] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005925325.1_ASM592532v1_genomic.fna/markers.fasta)
[2024-01-24 12:56:05,427] [INFO] Task started: Blastn
[2024-01-24 12:56:05,427] [INFO] Running command: blastn -query GCF_005925325.1_ASM592532v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9556bb62-2ac9-4596-8eee-e9996dccb192/dqc_reference/reference_markers_gtdb.fasta -out GCF_005925325.1_ASM592532v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:56:06,275] [INFO] Task succeeded: Blastn
[2024-01-24 12:56:06,279] [INFO] Selected 7 target genomes.
[2024-01-24 12:56:06,279] [INFO] Target genome list was writen to GCF_005925325.1_ASM592532v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:56:06,310] [INFO] Task started: fastANI
[2024-01-24 12:56:06,311] [INFO] Running command: fastANI --query /var/lib/cwl/stgb04929f9-9c8c-496f-8048-07a76bd830a5/GCF_005925325.1_ASM592532v1_genomic.fna.gz --refList GCF_005925325.1_ASM592532v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005925325.1_ASM592532v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:56:13,534] [INFO] Task succeeded: fastANI
[2024-01-24 12:56:13,546] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:56:13,546] [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_005925325.1	s__Pedobacter helvus	100.0	1532	1533	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_900215335.1	s__Pedobacter xixiisoli	82.9341	1013	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005925345.1	s__Pedobacter ureilyticus	82.4657	913	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002399615.1	s__Pedobacter sp002399615	80.962	615	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003313385.1	s__Pedobacter chitinilyticus	79.9815	700	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	97.94	95.89	0.93	0.87	3	-
GCF_003313335.1	s__Pedobacter zeaxanthinifaciens	79.7577	589	1533	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003313505.1	s__Pedobacter nanyangensis	79.5012	580	1533	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 12:56:13,548] [INFO] GTDB search result was written to GCF_005925325.1_ASM592532v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:56:13,549] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:56:13,552] [INFO] DFAST_QC result json was written to GCF_005925325.1_ASM592532v1_genomic.fna/dqc_result.json
[2024-01-24 12:56:13,552] [INFO] DFAST_QC completed!
[2024-01-24 12:56:13,553] [INFO] Total running time: 0h1m34s