[2024-01-24 13:36:43,922] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:43,923] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:43,923] [INFO] DQC Reference Directory: /var/lib/cwl/stg50ec395d-7b9b-4a58-8f70-8279d150cc2f/dqc_reference
[2024-01-24 13:36:45,183] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:45,184] [INFO] Task started: Prodigal
[2024-01-24 13:36:45,184] [INFO] Running command: gunzip -c /var/lib/cwl/stg9353ce3d-a7e9-444d-a73e-b3d53a79bdc2/GCF_013266735.1_LMG31463v1_genomic.fna.gz | prodigal -d GCF_013266735.1_LMG31463v1_genomic.fna/cds.fna -a GCF_013266735.1_LMG31463v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:08,513] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:08,513] [INFO] Task started: HMMsearch
[2024-01-24 13:37:08,513] [INFO] Running command: hmmsearch --tblout GCF_013266735.1_LMG31463v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50ec395d-7b9b-4a58-8f70-8279d150cc2f/dqc_reference/reference_markers.hmm GCF_013266735.1_LMG31463v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:08,879] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:08,881] [INFO] Found 6/6 markers.
[2024-01-24 13:37:08,950] [INFO] Query marker FASTA was written to GCF_013266735.1_LMG31463v1_genomic.fna/markers.fasta
[2024-01-24 13:37:08,951] [INFO] Task started: Blastn
[2024-01-24 13:37:08,951] [INFO] Running command: blastn -query GCF_013266735.1_LMG31463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50ec395d-7b9b-4a58-8f70-8279d150cc2f/dqc_reference/reference_markers.fasta -out GCF_013266735.1_LMG31463v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:09,646] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:09,649] [INFO] Selected 17 target genomes.
[2024-01-24 13:37:09,650] [INFO] Target genome list was writen to GCF_013266735.1_LMG31463v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:09,657] [INFO] Task started: fastANI
[2024-01-24 13:37:09,657] [INFO] Running command: fastANI --query /var/lib/cwl/stg9353ce3d-a7e9-444d-a73e-b3d53a79bdc2/GCF_013266735.1_LMG31463v1_genomic.fna.gz --refList GCF_013266735.1_LMG31463v1_genomic.fna/target_genomes.txt --output GCF_013266735.1_LMG31463v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:26,978] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:26,979] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50ec395d-7b9b-4a58-8f70-8279d150cc2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:26,979] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50ec395d-7b9b-4a58-8f70-8279d150cc2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:26,996] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:26,997] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:26,997] [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 foliorum	strain=LMG 31463	GCA_013266735.1	2739058	2739058	type	True	100.0	2007	2008	95	conclusive
Pedobacter panaciterrae	strain=LMG 23400	GCA_013204795.1	363849	363849	type	True	84.3306	1262	2008	95	below_threshold
Pedobacter frigoris	strain=RP-3-15	GCA_005116445.1	2571272	2571272	type	True	79.4941	464	2008	95	below_threshold
Pedobacter nyackensis	strain=DSM 19625	GCA_900176505.1	475255	475255	type	True	79.4689	492	2008	95	below_threshold
Pedobacter hiemivivus	strain=RP-3-8	GCA_004331685.1	2530454	2530454	type	True	79.3776	502	2008	95	below_threshold
Pedobacter psychroterrae	strain=RP-1-14	GCA_004331695.1	2530453	2530453	type	True	78.9711	394	2008	95	below_threshold
Pedobacter schmidteae	strain=eg	GCA_900564155.1	2201271	2201271	type	True	78.852	414	2008	95	below_threshold
Pedobacter gandavensis	strain=LMG 31462	GCA_014172405.1	2679963	2679963	type	True	78.8452	400	2008	95	below_threshold
Pedobacter polaris	strain=RP-3-22	GCA_005116505.1	2571273	2571273	type	True	78.4933	214	2008	95	below_threshold
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	77.6505	190	2008	95	below_threshold
Pedobacter borealis	strain=DSM 19626	GCA_000708285.2	475254	475254	type	True	77.6404	202	2008	95	below_threshold
Pedobacter xixiisoli	strain=S27	GCA_005925365.1	1476464	1476464	type	True	77.4811	177	2008	95	below_threshold
Pedobacter xixiisoli	strain=CGMCC 1.12803	GCA_900215335.1	1476464	1476464	type	True	77.4753	176	2008	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	77.2585	197	2008	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	76.4221	76	2008	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:26,999] [INFO] DFAST Taxonomy check result was written to GCF_013266735.1_LMG31463v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:27,000] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:27,000] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:27,000] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50ec395d-7b9b-4a58-8f70-8279d150cc2f/dqc_reference/checkm_data
[2024-01-24 13:37:27,002] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:27,065] [INFO] Task started: CheckM
[2024-01-24 13:37:27,066] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013266735.1_LMG31463v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013266735.1_LMG31463v1_genomic.fna/checkm_input GCF_013266735.1_LMG31463v1_genomic.fna/checkm_result
[2024-01-24 13:38:31,888] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:31,889] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:31,911] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:31,912] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:31,912] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013266735.1_LMG31463v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:31,912] [INFO] Task started: Blastn
[2024-01-24 13:38:31,913] [INFO] Running command: blastn -query GCF_013266735.1_LMG31463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50ec395d-7b9b-4a58-8f70-8279d150cc2f/dqc_reference/reference_markers_gtdb.fasta -out GCF_013266735.1_LMG31463v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:32,715] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:32,718] [INFO] Selected 8 target genomes.
[2024-01-24 13:38:32,719] [INFO] Target genome list was writen to GCF_013266735.1_LMG31463v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:32,730] [INFO] Task started: fastANI
[2024-01-24 13:38:32,730] [INFO] Running command: fastANI --query /var/lib/cwl/stg9353ce3d-a7e9-444d-a73e-b3d53a79bdc2/GCF_013266735.1_LMG31463v1_genomic.fna.gz --refList GCF_013266735.1_LMG31463v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013266735.1_LMG31463v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:43,759] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:43,774] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:43,775] [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_013266735.1	s__Pedobacter foliorum	100.0	2007	2008	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_018492665.1	s__Pedobacter sp018492665	93.7884	1511	2008	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	88.1936	1334	2008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000523515.1	s__Pedobacter sp000523515	84.3839	1257	2008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013204795.1	s__Pedobacter panaciterrae	84.3185	1264	2008	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	84.2517	1158	2008	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	83.2966	1148	2008	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176505.1	s__Pedobacter nyackensis	79.4842	491	2008	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 13:38:43,785] [INFO] GTDB search result was written to GCF_013266735.1_LMG31463v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:43,785] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:43,789] [INFO] DFAST_QC result json was written to GCF_013266735.1_LMG31463v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:43,789] [INFO] DFAST_QC completed!
[2024-01-24 13:38:43,789] [INFO] Total running time: 0h1m60s