[2024-01-25 18:03:50,488] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:03:50,491] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:03:50,491] [INFO] DQC Reference Directory: /var/lib/cwl/stg5052bf89-beeb-402a-9f1a-2923a24ae67b/dqc_reference
[2024-01-25 18:03:51,636] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:03:51,637] [INFO] Task started: Prodigal
[2024-01-25 18:03:51,637] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ccb74ac-8f4c-4e1b-a748-76dbb549a02f/GCF_003208655.1_ASM320865v1_genomic.fna.gz | prodigal -d GCF_003208655.1_ASM320865v1_genomic.fna/cds.fna -a GCF_003208655.1_ASM320865v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:04:12,659] [INFO] Task succeeded: Prodigal
[2024-01-25 18:04:12,660] [INFO] Task started: HMMsearch
[2024-01-25 18:04:12,660] [INFO] Running command: hmmsearch --tblout GCF_003208655.1_ASM320865v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5052bf89-beeb-402a-9f1a-2923a24ae67b/dqc_reference/reference_markers.hmm GCF_003208655.1_ASM320865v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:04:12,939] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:04:12,939] [INFO] Found 6/6 markers.
[2024-01-25 18:04:12,982] [INFO] Query marker FASTA was written to GCF_003208655.1_ASM320865v1_genomic.fna/markers.fasta
[2024-01-25 18:04:12,982] [INFO] Task started: Blastn
[2024-01-25 18:04:12,982] [INFO] Running command: blastn -query GCF_003208655.1_ASM320865v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5052bf89-beeb-402a-9f1a-2923a24ae67b/dqc_reference/reference_markers.fasta -out GCF_003208655.1_ASM320865v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:04:13,532] [INFO] Task succeeded: Blastn
[2024-01-25 18:04:13,535] [INFO] Selected 20 target genomes.
[2024-01-25 18:04:13,535] [INFO] Target genome list was writen to GCF_003208655.1_ASM320865v1_genomic.fna/target_genomes.txt
[2024-01-25 18:04:13,564] [INFO] Task started: fastANI
[2024-01-25 18:04:13,564] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ccb74ac-8f4c-4e1b-a748-76dbb549a02f/GCF_003208655.1_ASM320865v1_genomic.fna.gz --refList GCF_003208655.1_ASM320865v1_genomic.fna/target_genomes.txt --output GCF_003208655.1_ASM320865v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:04:32,451] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:32,451] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5052bf89-beeb-402a-9f1a-2923a24ae67b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:04:32,452] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5052bf89-beeb-402a-9f1a-2923a24ae67b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:04:32,465] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:04:32,465] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:04:32,466] [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 nutrimenti	strain=DSM 27372	GCA_003208655.1	1241337	1241337	type	True	100.0	1894	1894	95	conclusive
Pedobacter caeni	strain=DSM 16990	GCA_900129215.1	288992	288992	type	True	78.9613	378	1894	95	below_threshold
Pedobacter frigoris	strain=RP-3-15	GCA_005116445.1	2571272	2571272	type	True	78.8054	248	1894	95	below_threshold
Pedobacter duraquae	strain=DSM 19034	GCA_004362245.1	425511	425511	type	True	78.3204	226	1894	95	below_threshold
Pedobacter heparinus	strain=DSM 2366	GCA_000023825.1	984	984	type	True	78.1077	321	1894	95	below_threshold
Pedobacter lusitanus	strain=NL19	GCA_000832545.1	1503925	1503925	type	True	78.0077	265	1894	95	below_threshold
Pedobacter schmidteae	strain=eg	GCA_900564155.1	2201271	2201271	type	True	77.9662	300	1894	95	below_threshold
Pedobacter westerhofensis	strain=DSM 19036	GCA_900182595.1	425512	425512	type	True	77.9625	251	1894	95	below_threshold
Pedobacter antarcticus	strain=ATCC 51969	GCA_900112985.1	34086	34086	type	True	77.8858	213	1894	95	below_threshold
Pedobacter antarcticus	strain=4BY	GCA_000722885.1	34086	34086	type	True	77.8761	209	1894	95	below_threshold
Pedobacter hiemivivus	strain=RP-3-8	GCA_004331685.1	2530454	2530454	type	True	77.7792	272	1894	95	below_threshold
Pedobacter gandavensis	strain=LMG 31462	GCA_014172405.1	2679963	2679963	type	True	77.6547	289	1894	95	below_threshold
Pedobacter steynii	strain=DSM 19110	GCA_900103665.1	430522	430522	type	True	77.6103	355	1894	95	below_threshold
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	77.1303	143	1894	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	76.9591	173	1894	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	76.0974	51	1894	95	below_threshold
Mucilaginibacter phyllosphaerae	strain=PP-F2FG21	GCA_004378255.1	1812349	1812349	type	True	76.0956	57	1894	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	75.8277	68	1894	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:04:32,467] [INFO] DFAST Taxonomy check result was written to GCF_003208655.1_ASM320865v1_genomic.fna/tc_result.tsv
[2024-01-25 18:04:32,468] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:04:32,468] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:04:32,468] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5052bf89-beeb-402a-9f1a-2923a24ae67b/dqc_reference/checkm_data
[2024-01-25 18:04:32,469] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:04:32,522] [INFO] Task started: CheckM
[2024-01-25 18:04:32,522] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003208655.1_ASM320865v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003208655.1_ASM320865v1_genomic.fna/checkm_input GCF_003208655.1_ASM320865v1_genomic.fna/checkm_result
[2024-01-25 18:05:30,389] [INFO] Task succeeded: CheckM
[2024-01-25 18:05:30,390] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:05:30,416] [INFO] ===== Completeness check finished =====
[2024-01-25 18:05:30,416] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:05:30,417] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003208655.1_ASM320865v1_genomic.fna/markers.fasta)
[2024-01-25 18:05:30,418] [INFO] Task started: Blastn
[2024-01-25 18:05:30,418] [INFO] Running command: blastn -query GCF_003208655.1_ASM320865v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5052bf89-beeb-402a-9f1a-2923a24ae67b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003208655.1_ASM320865v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:05:31,205] [INFO] Task succeeded: Blastn
[2024-01-25 18:05:31,208] [INFO] Selected 18 target genomes.
[2024-01-25 18:05:31,208] [INFO] Target genome list was writen to GCF_003208655.1_ASM320865v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:05:31,227] [INFO] Task started: fastANI
[2024-01-25 18:05:31,228] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ccb74ac-8f4c-4e1b-a748-76dbb549a02f/GCF_003208655.1_ASM320865v1_genomic.fna.gz --refList GCF_003208655.1_ASM320865v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003208655.1_ASM320865v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:05:51,724] [INFO] Task succeeded: fastANI
[2024-01-25 18:05:51,736] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:05:51,737] [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_003208655.1	s__Pedobacter nutrimenti	100.0	1894	1894	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_004364225.1	s__Pedobacter sp004364225	79.4833	586	1894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590605.1	s__Pedobacter cryoconitis_A	79.1873	288	1894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003061025.1	s__Pedobacter sp003061025	79.102	506	1894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129215.1	s__Pedobacter caeni	78.9548	378	1894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015752175.1	s__Pedobacter sp015752175	78.8064	288	1894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116445.1	s__Pedobacter sp005116445	78.8054	248	1894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002736205.1	s__Pedobacter ginsengisoli	78.3043	258	1894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362245.1	s__Pedobacter duraquae	78.3032	227	1894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223055.1	s__Pedobacter sp015223055	78.0666	293	1894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003852525.1	s__Pedobacter sp003852525	77.986	368	1894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014472395.1	s__Pedobacter sp014472395	77.9524	278	1894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001721645.1	s__Pedobacter steynii_A	77.9079	343	1894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112985.1	s__Pedobacter antarcticus	77.8881	216	1894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	99.39	98.80	0.96	0.91	3	-
GCF_000170795.1	s__Pedobacter sp000170795	77.8719	256	1894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014172405.1	s__Pedobacter gandavensis	77.6486	289	1894	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	77.3261	110	1894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655115.1	s__Pedobacter sp015655115	76.9053	166	1894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:05:51,738] [INFO] GTDB search result was written to GCF_003208655.1_ASM320865v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:05:51,739] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:05:51,742] [INFO] DFAST_QC result json was written to GCF_003208655.1_ASM320865v1_genomic.fna/dqc_result.json
[2024-01-25 18:05:51,742] [INFO] DFAST_QC completed!
[2024-01-25 18:05:51,743] [INFO] Total running time: 0h2m1s