[2024-01-24 13:09:33,445] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:33,448] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:33,448] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a877e8d-6c90-4e20-a0ca-c89ae7cd0208/dqc_reference
[2024-01-24 13:09:34,794] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:34,795] [INFO] Task started: Prodigal
[2024-01-24 13:09:34,795] [INFO] Running command: gunzip -c /var/lib/cwl/stg4513adeb-0979-4d7e-8795-32c59ba9a903/GCF_003313505.1_ASM331350v1_genomic.fna.gz | prodigal -d GCF_003313505.1_ASM331350v1_genomic.fna/cds.fna -a GCF_003313505.1_ASM331350v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:56,539] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:56,540] [INFO] Task started: HMMsearch
[2024-01-24 13:09:56,540] [INFO] Running command: hmmsearch --tblout GCF_003313505.1_ASM331350v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a877e8d-6c90-4e20-a0ca-c89ae7cd0208/dqc_reference/reference_markers.hmm GCF_003313505.1_ASM331350v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:56,791] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:56,792] [INFO] Found 6/6 markers.
[2024-01-24 13:09:56,831] [INFO] Query marker FASTA was written to GCF_003313505.1_ASM331350v1_genomic.fna/markers.fasta
[2024-01-24 13:09:56,832] [INFO] Task started: Blastn
[2024-01-24 13:09:56,832] [INFO] Running command: blastn -query GCF_003313505.1_ASM331350v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a877e8d-6c90-4e20-a0ca-c89ae7cd0208/dqc_reference/reference_markers.fasta -out GCF_003313505.1_ASM331350v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:57,427] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:57,430] [INFO] Selected 12 target genomes.
[2024-01-24 13:09:57,430] [INFO] Target genome list was writen to GCF_003313505.1_ASM331350v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:57,434] [INFO] Task started: fastANI
[2024-01-24 13:09:57,434] [INFO] Running command: fastANI --query /var/lib/cwl/stg4513adeb-0979-4d7e-8795-32c59ba9a903/GCF_003313505.1_ASM331350v1_genomic.fna.gz --refList GCF_003313505.1_ASM331350v1_genomic.fna/target_genomes.txt --output GCF_003313505.1_ASM331350v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:08,212] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:08,212] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a877e8d-6c90-4e20-a0ca-c89ae7cd0208/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:08,213] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a877e8d-6c90-4e20-a0ca-c89ae7cd0208/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:08,221] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:08,221] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:08,222] [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 nanyangensis	strain=Q-4	GCA_003313505.1	1562389	1562389	type	True	100.0	1566	1567	95	conclusive
Pedobacter chitinilyticus	strain=CM134L-2	GCA_004025525.1	2233776	2233776	type	True	84.1023	1095	1567	95	below_threshold
Pedobacter chitinilyticus	strain=CM134L-2	GCA_003313385.1	2233776	2233776	type	True	84.0617	1096	1567	95	below_threshold
Pedobacter ureilyticus	strain=THG-T11	GCA_005925345.1	1393051	1393051	type	True	79.9043	609	1567	95	below_threshold
Pedobacter xixiisoli	strain=S27	GCA_005925365.1	1476464	1476464	type	True	79.4904	598	1567	95	below_threshold
Pedobacter xixiisoli	strain=CGMCC 1.12803	GCA_900215335.1	1476464	1476464	type	True	79.4653	599	1567	95	below_threshold
Pedobacter helvus	strain=P-25	GCA_005925325.1	2563444	2563444	type	True	79.3701	595	1567	95	below_threshold
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	76.6536	162	1567	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	76.3989	55	1567	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	76.1037	59	1567	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:08,224] [INFO] DFAST Taxonomy check result was written to GCF_003313505.1_ASM331350v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:08,224] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:08,224] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:08,225] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a877e8d-6c90-4e20-a0ca-c89ae7cd0208/dqc_reference/checkm_data
[2024-01-24 13:10:08,226] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:08,269] [INFO] Task started: CheckM
[2024-01-24 13:10:08,269] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003313505.1_ASM331350v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003313505.1_ASM331350v1_genomic.fna/checkm_input GCF_003313505.1_ASM331350v1_genomic.fna/checkm_result
[2024-01-24 13:11:05,837] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:05,838] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:05,856] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:05,856] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:05,857] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003313505.1_ASM331350v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:05,857] [INFO] Task started: Blastn
[2024-01-24 13:11:05,857] [INFO] Running command: blastn -query GCF_003313505.1_ASM331350v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a877e8d-6c90-4e20-a0ca-c89ae7cd0208/dqc_reference/reference_markers_gtdb.fasta -out GCF_003313505.1_ASM331350v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:06,623] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:06,626] [INFO] Selected 9 target genomes.
[2024-01-24 13:11:06,626] [INFO] Target genome list was writen to GCF_003313505.1_ASM331350v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:06,632] [INFO] Task started: fastANI
[2024-01-24 13:11:06,632] [INFO] Running command: fastANI --query /var/lib/cwl/stg4513adeb-0979-4d7e-8795-32c59ba9a903/GCF_003313505.1_ASM331350v1_genomic.fna.gz --refList GCF_003313505.1_ASM331350v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003313505.1_ASM331350v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:16,595] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:16,603] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:16,603] [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_003313505.1	s__Pedobacter nanyangensis	100.0	1566	1567	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_003313385.1	s__Pedobacter chitinilyticus	84.0617	1096	1567	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	97.94	95.89	0.93	0.87	3	-
GCF_005925345.1	s__Pedobacter ureilyticus	79.8941	610	1567	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	79.4614	599	1567	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005925325.1	s__Pedobacter helvus	79.3619	596	1567	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	79.2554	538	1567	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	79.1977	507	1567	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000633455.1	s__Pedobacter jeongneungensis	77.1728	197	1567	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	76.9604	107	1567	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.76	98.76	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:16,605] [INFO] GTDB search result was written to GCF_003313505.1_ASM331350v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:16,606] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:16,608] [INFO] DFAST_QC result json was written to GCF_003313505.1_ASM331350v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:16,608] [INFO] DFAST_QC completed!
[2024-01-24 13:11:16,608] [INFO] Total running time: 0h1m43s