[2024-01-24 13:28:01,407] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:01,410] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:01,410] [INFO] DQC Reference Directory: /var/lib/cwl/stgb1e5f0be-88ca-4c2c-8a53-164c4fd9e609/dqc_reference
[2024-01-24 13:28:02,789] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:02,790] [INFO] Task started: Prodigal
[2024-01-24 13:28:02,790] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b2ae7fd-a5a1-4a08-8ba4-41551c2b4938/GCF_013204795.1_ASM1320479v1_genomic.fna.gz | prodigal -d GCF_013204795.1_ASM1320479v1_genomic.fna/cds.fna -a GCF_013204795.1_ASM1320479v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:27,416] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:27,417] [INFO] Task started: HMMsearch
[2024-01-24 13:28:27,417] [INFO] Running command: hmmsearch --tblout GCF_013204795.1_ASM1320479v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb1e5f0be-88ca-4c2c-8a53-164c4fd9e609/dqc_reference/reference_markers.hmm GCF_013204795.1_ASM1320479v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:27,748] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:27,749] [INFO] Found 6/6 markers.
[2024-01-24 13:28:27,801] [INFO] Query marker FASTA was written to GCF_013204795.1_ASM1320479v1_genomic.fna/markers.fasta
[2024-01-24 13:28:27,801] [INFO] Task started: Blastn
[2024-01-24 13:28:27,801] [INFO] Running command: blastn -query GCF_013204795.1_ASM1320479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1e5f0be-88ca-4c2c-8a53-164c4fd9e609/dqc_reference/reference_markers.fasta -out GCF_013204795.1_ASM1320479v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:28,447] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:28,451] [INFO] Selected 18 target genomes.
[2024-01-24 13:28:28,451] [INFO] Target genome list was writen to GCF_013204795.1_ASM1320479v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:28,469] [INFO] Task started: fastANI
[2024-01-24 13:28:28,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b2ae7fd-a5a1-4a08-8ba4-41551c2b4938/GCF_013204795.1_ASM1320479v1_genomic.fna.gz --refList GCF_013204795.1_ASM1320479v1_genomic.fna/target_genomes.txt --output GCF_013204795.1_ASM1320479v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:46,833] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:46,834] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb1e5f0be-88ca-4c2c-8a53-164c4fd9e609/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:46,834] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb1e5f0be-88ca-4c2c-8a53-164c4fd9e609/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:46,849] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:46,849] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:46,849] [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 panaciterrae	strain=LMG 23400	GCA_013204795.1	363849	363849	type	True	100.0	2065	2066	95	conclusive
Pedobacter foliorum	strain=LMG 31463	GCA_013266735.1	2739058	2739058	type	True	84.2813	1292	2066	95	below_threshold
Pedobacter frigoris	strain=RP-3-15	GCA_005116445.1	2571272	2571272	type	True	79.4119	460	2066	95	below_threshold
Pedobacter hiemivivus	strain=RP-3-8	GCA_004331685.1	2530454	2530454	type	True	79.1689	477	2066	95	below_threshold
Pedobacter heparinus	strain=DSM 2366	GCA_000410815.1	984	984	type	True	79.055	425	2066	95	below_threshold
Pedobacter heparinus	strain=DSM 2366	GCA_000023825.1	984	984	type	True	79.0104	424	2066	95	below_threshold
Pedobacter schmidteae	strain=eg	GCA_900564155.1	2201271	2201271	type	True	78.9928	414	2066	95	below_threshold
Pedobacter nyackensis	strain=DSM 19625	GCA_900176505.1	475255	475255	type	True	78.9301	486	2066	95	below_threshold
Pedobacter gandavensis	strain=LMG 31462	GCA_014172405.1	2679963	2679963	type	True	78.762	382	2066	95	below_threshold
Pedobacter caeni	strain=DSM 16990	GCA_900129215.1	288992	288992	type	True	78.7576	462	2066	95	below_threshold
Pedobacter steynii	strain=DSM 19110	GCA_900103665.1	430522	430522	type	True	78.6257	449	2066	95	below_threshold
Pedobacter africanus	strain=DSM 12126	GCA_900176535.1	151894	151894	type	True	78.5348	385	2066	95	below_threshold
Pedobacter hartonius	strain=DSM 19033	GCA_900107535.1	425514	425514	type	True	78.463	207	2066	95	below_threshold
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	77.7078	186	2066	95	below_threshold
Pedobacter psychrotolerans	strain=CGMCC 1.15644	GCA_014643495.1	1843235	1843235	type	True	77.3969	192	2066	95	below_threshold
Pedobacter aquae	strain=CJ43	GCA_008195825.1	2605747	2605747	type	True	76.9024	93	2066	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	76.3958	70	2066	95	below_threshold
Mucilaginibacter achroorhodeus	strain=MJ1a	GCA_007846095.1	2599294	2599294	type	True	76.3494	63	2066	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:46,851] [INFO] DFAST Taxonomy check result was written to GCF_013204795.1_ASM1320479v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:46,852] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:46,852] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:46,852] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb1e5f0be-88ca-4c2c-8a53-164c4fd9e609/dqc_reference/checkm_data
[2024-01-24 13:28:46,853] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:46,911] [INFO] Task started: CheckM
[2024-01-24 13:28:46,911] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013204795.1_ASM1320479v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013204795.1_ASM1320479v1_genomic.fna/checkm_input GCF_013204795.1_ASM1320479v1_genomic.fna/checkm_result
[2024-01-24 13:29:51,968] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:51,969] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:51,991] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:51,991] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:51,992] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013204795.1_ASM1320479v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:51,992] [INFO] Task started: Blastn
[2024-01-24 13:29:51,992] [INFO] Running command: blastn -query GCF_013204795.1_ASM1320479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb1e5f0be-88ca-4c2c-8a53-164c4fd9e609/dqc_reference/reference_markers_gtdb.fasta -out GCF_013204795.1_ASM1320479v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:52,790] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:52,794] [INFO] Selected 6 target genomes.
[2024-01-24 13:29:52,794] [INFO] Target genome list was writen to GCF_013204795.1_ASM1320479v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:52,801] [INFO] Task started: fastANI
[2024-01-24 13:29:52,802] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b2ae7fd-a5a1-4a08-8ba4-41551c2b4938/GCF_013204795.1_ASM1320479v1_genomic.fna.gz --refList GCF_013204795.1_ASM1320479v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013204795.1_ASM1320479v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:01,375] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:01,382] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:01,382] [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_013204795.1	s__Pedobacter panaciterrae	100.0	2065	2066	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_000523515.1	s__Pedobacter sp000523515	92.4972	1713	2066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001636695.1	s__Pedobacter panaciterrae_A	86.3201	1357	2066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054115.1	s__Pedobacter sp003054115	84.7469	1182	2066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018492665.1	s__Pedobacter sp018492665	84.4228	1183	2066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013266735.1	s__Pedobacter foliorum	84.2665	1294	2066	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 13:30:01,384] [INFO] GTDB search result was written to GCF_013204795.1_ASM1320479v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:01,384] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:01,387] [INFO] DFAST_QC result json was written to GCF_013204795.1_ASM1320479v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:01,388] [INFO] DFAST_QC completed!
[2024-01-24 13:30:01,388] [INFO] Total running time: 0h1m60s