[2024-01-24 10:48:09,191] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:48:09,193] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:48:09,193] [INFO] DQC Reference Directory: /var/lib/cwl/stg45714c01-9981-4f12-a9ec-ff1835b806d3/dqc_reference
[2024-01-24 10:48:23,955] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:23,957] [INFO] Task started: Prodigal
[2024-01-24 10:48:23,957] [INFO] Running command: gunzip -c /var/lib/cwl/stg839fe1ba-c62f-4459-8746-abeb43cd5a74/GCF_004025525.1_ASM402552v1_genomic.fna.gz | prodigal -d GCF_004025525.1_ASM402552v1_genomic.fna/cds.fna -a GCF_004025525.1_ASM402552v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:45,661] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:45,662] [INFO] Task started: HMMsearch
[2024-01-24 10:48:45,662] [INFO] Running command: hmmsearch --tblout GCF_004025525.1_ASM402552v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45714c01-9981-4f12-a9ec-ff1835b806d3/dqc_reference/reference_markers.hmm GCF_004025525.1_ASM402552v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:45,968] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:45,969] [INFO] Found 6/6 markers.
[2024-01-24 10:48:46,028] [INFO] Query marker FASTA was written to GCF_004025525.1_ASM402552v1_genomic.fna/markers.fasta
[2024-01-24 10:48:46,029] [INFO] Task started: Blastn
[2024-01-24 10:48:46,029] [INFO] Running command: blastn -query GCF_004025525.1_ASM402552v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45714c01-9981-4f12-a9ec-ff1835b806d3/dqc_reference/reference_markers.fasta -out GCF_004025525.1_ASM402552v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:46,635] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:46,640] [INFO] Selected 14 target genomes.
[2024-01-24 10:48:46,640] [INFO] Target genome list was writen to GCF_004025525.1_ASM402552v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:46,665] [INFO] Task started: fastANI
[2024-01-24 10:48:46,665] [INFO] Running command: fastANI --query /var/lib/cwl/stg839fe1ba-c62f-4459-8746-abeb43cd5a74/GCF_004025525.1_ASM402552v1_genomic.fna.gz --refList GCF_004025525.1_ASM402552v1_genomic.fna/target_genomes.txt --output GCF_004025525.1_ASM402552v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:49:02,558] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:02,559] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45714c01-9981-4f12-a9ec-ff1835b806d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:49:02,559] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45714c01-9981-4f12-a9ec-ff1835b806d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:49:02,576] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:49:02,577] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:49:02,577] [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
Pedobacter chitinilyticus	strain=CM134L-2	GCA_004025525.1	2233776	2233776	type	True	100.0	1679	1680	95	conclusive
Pedobacter chitinilyticus	strain=CM134L-2	GCA_003313385.1	2233776	2233776	type	True	99.9983	1679	1680	95	conclusive
Pedobacter nanyangensis	strain=Q-4	GCA_003313505.1	1562389	1562389	type	True	84.0575	1066	1680	95	below_threshold
Pedobacter helvus	strain=P-25	GCA_005925325.1	2563444	2563444	type	True	80.1167	696	1680	95	below_threshold
Pedobacter xixiisoli	strain=S27	GCA_005925365.1	1476464	1476464	type	True	80.0177	718	1680	95	below_threshold
Pedobacter xixiisoli	strain=CGMCC 1.12803	GCA_900215335.1	1476464	1476464	type	True	79.9795	721	1680	95	below_threshold
Pedobacter planticolens	strain=LMG 31464	GCA_014172375.1	2679964	2679964	type	True	78.0442	287	1680	95	below_threshold
Pedobacter polaris	strain=RP-3-22	GCA_005116505.1	2571273	2571273	type	True	77.8908	293	1680	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_003664035.1	475253	475253	type	True	77.6528	210	1680	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	77.5127	203	1680	95	below_threshold
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	77.3	199	1680	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	76.56	60	1680	95	below_threshold
Mucilaginibacter robiniae	strain=F39-2	GCA_012849215.1	2728022	2728022	type	True	76.4259	71	1680	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:49:02,596] [INFO] DFAST Taxonomy check result was written to GCF_004025525.1_ASM402552v1_genomic.fna/tc_result.tsv
[2024-01-24 10:49:02,597] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:49:02,597] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:49:02,598] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45714c01-9981-4f12-a9ec-ff1835b806d3/dqc_reference/checkm_data
[2024-01-24 10:49:02,599] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:49:02,696] [INFO] Task started: CheckM
[2024-01-24 10:49:02,696] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004025525.1_ASM402552v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004025525.1_ASM402552v1_genomic.fna/checkm_input GCF_004025525.1_ASM402552v1_genomic.fna/checkm_result
[2024-01-24 10:50:06,147] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:06,148] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:06,171] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:06,172] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:06,172] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004025525.1_ASM402552v1_genomic.fna/markers.fasta)
[2024-01-24 10:50:06,173] [INFO] Task started: Blastn
[2024-01-24 10:50:06,173] [INFO] Running command: blastn -query GCF_004025525.1_ASM402552v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45714c01-9981-4f12-a9ec-ff1835b806d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_004025525.1_ASM402552v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:07,011] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:07,019] [INFO] Selected 12 target genomes.
[2024-01-24 10:50:07,019] [INFO] Target genome list was writen to GCF_004025525.1_ASM402552v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:07,029] [INFO] Task started: fastANI
[2024-01-24 10:50:07,029] [INFO] Running command: fastANI --query /var/lib/cwl/stg839fe1ba-c62f-4459-8746-abeb43cd5a74/GCF_004025525.1_ASM402552v1_genomic.fna.gz --refList GCF_004025525.1_ASM402552v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004025525.1_ASM402552v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:18,108] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:18,125] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:50:18,125] [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_003313385.1	s__Pedobacter chitinilyticus	99.9983	1679	1680	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	97.94	95.89	0.93	0.87	3	conclusive
GCF_003313505.1	s__Pedobacter nanyangensis	84.0526	1067	1680	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005925325.1	s__Pedobacter helvus	80.1028	699	1680	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215335.1	s__Pedobacter xixiisoli	79.9678	723	1680	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002399615.1	s__Pedobacter sp002399615	79.6295	523	1680	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005925345.1	s__Pedobacter ureilyticus	79.6268	655	1680	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003313335.1	s__Pedobacter zeaxanthinifaciens	79.4035	556	1680	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428855.1	s__Pedobacter sp016428855	79.176	504	1680	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014172375.1	s__Pedobacter planticolens	78.0442	287	1680	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116505.1	s__Pedobacter sp005116505	77.8908	293	1680	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903166585.1	s__Pedobacter sp903166585	77.5111	203	1680	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002333205.1	s__Pedobacter sp002333205	77.1875	80	1680	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 10:50:18,127] [INFO] GTDB search result was written to GCF_004025525.1_ASM402552v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:18,128] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:18,132] [INFO] DFAST_QC result json was written to GCF_004025525.1_ASM402552v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:18,132] [INFO] DFAST_QC completed!
[2024-01-24 10:50:18,132] [INFO] Total running time: 0h2m9s