[2024-01-24 14:55:36,852] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:36,853] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:36,854] [INFO] DQC Reference Directory: /var/lib/cwl/stg22776f25-aefb-45a5-8923-be147f99bb43/dqc_reference
[2024-01-24 14:55:38,064] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:38,065] [INFO] Task started: Prodigal
[2024-01-24 14:55:38,065] [INFO] Running command: gunzip -c /var/lib/cwl/stged0e0e06-a481-442e-adff-1d4415d1af45/GCF_004310665.1_ASM431066v1_genomic.fna.gz | prodigal -d GCF_004310665.1_ASM431066v1_genomic.fna/cds.fna -a GCF_004310665.1_ASM431066v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:00,856] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:00,857] [INFO] Task started: HMMsearch
[2024-01-24 14:56:00,857] [INFO] Running command: hmmsearch --tblout GCF_004310665.1_ASM431066v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22776f25-aefb-45a5-8923-be147f99bb43/dqc_reference/reference_markers.hmm GCF_004310665.1_ASM431066v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:01,246] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:01,247] [INFO] Found 6/6 markers.
[2024-01-24 14:56:01,316] [INFO] Query marker FASTA was written to GCF_004310665.1_ASM431066v1_genomic.fna/markers.fasta
[2024-01-24 14:56:01,316] [INFO] Task started: Blastn
[2024-01-24 14:56:01,316] [INFO] Running command: blastn -query GCF_004310665.1_ASM431066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22776f25-aefb-45a5-8923-be147f99bb43/dqc_reference/reference_markers.fasta -out GCF_004310665.1_ASM431066v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:01,964] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:01,968] [INFO] Selected 13 target genomes.
[2024-01-24 14:56:01,968] [INFO] Target genome list was writen to GCF_004310665.1_ASM431066v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:01,974] [INFO] Task started: fastANI
[2024-01-24 14:56:01,974] [INFO] Running command: fastANI --query /var/lib/cwl/stged0e0e06-a481-442e-adff-1d4415d1af45/GCF_004310665.1_ASM431066v1_genomic.fna.gz --refList GCF_004310665.1_ASM431066v1_genomic.fna/target_genomes.txt --output GCF_004310665.1_ASM431066v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:18,381] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:18,381] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22776f25-aefb-45a5-8923-be147f99bb43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:18,382] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22776f25-aefb-45a5-8923-be147f99bb43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:18,398] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:56:18,398] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:18,398] [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 kyonggii	strain=K-4-11-1	GCA_004310665.1	1926871	1926871	type	True	100.0	2025	2027	95	conclusive
Pedobacter borealis	strain=DSM 19626	GCA_000708285.2	475254	475254	type	True	92.0654	1235	2027	95	below_threshold
Pedobacter ginsenosidimutans	strain=KACC 14530	GCA_001442625.1	687842	687842	type	True	91.897	1529	2027	95	below_threshold
Pedobacter psychrodurus	strain=RP-3-21	GCA_004331735.1	2530456	2530456	type	True	89.1435	1396	2027	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_003664035.1	475253	475253	type	True	86.3588	1294	2027	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_004402005.1	475253	475253	type	True	86.3469	1310	2027	95	below_threshold
Pedobacter terrae	strain=DSM 17933	GCA_900100705.1	405671	405671	type	True	84.0713	1164	2027	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	81.7001	1046	2027	95	below_threshold
Pedobacter agri	strain=PB92	GCA_000258495.1	454586	454586	type	True	80.3307	667	2027	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	76.4864	88	2027	95	below_threshold
Sphingobacterium faecale	strain=C459-1	GCA_016746095.1	2803775	2803775	type	True	76.4508	53	2027	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:18,400] [INFO] DFAST Taxonomy check result was written to GCF_004310665.1_ASM431066v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:18,400] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:18,400] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:18,401] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22776f25-aefb-45a5-8923-be147f99bb43/dqc_reference/checkm_data
[2024-01-24 14:56:18,402] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:18,469] [INFO] Task started: CheckM
[2024-01-24 14:56:18,469] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004310665.1_ASM431066v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004310665.1_ASM431066v1_genomic.fna/checkm_input GCF_004310665.1_ASM431066v1_genomic.fna/checkm_result
[2024-01-24 14:57:23,272] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:23,273] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:23,300] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:23,301] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:23,301] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004310665.1_ASM431066v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:23,301] [INFO] Task started: Blastn
[2024-01-24 14:57:23,302] [INFO] Running command: blastn -query GCF_004310665.1_ASM431066v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg22776f25-aefb-45a5-8923-be147f99bb43/dqc_reference/reference_markers_gtdb.fasta -out GCF_004310665.1_ASM431066v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:24,184] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:24,187] [INFO] Selected 10 target genomes.
[2024-01-24 14:57:24,187] [INFO] Target genome list was writen to GCF_004310665.1_ASM431066v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:24,198] [INFO] Task started: fastANI
[2024-01-24 14:57:24,198] [INFO] Running command: fastANI --query /var/lib/cwl/stged0e0e06-a481-442e-adff-1d4415d1af45/GCF_004310665.1_ASM431066v1_genomic.fna.gz --refList GCF_004310665.1_ASM431066v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004310665.1_ASM431066v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:39,347] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:39,360] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:39,360] [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_004310665.1	s__Pedobacter kyonggii	100.0	2025	2027	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_000708285.2	s__Pedobacter borealis	92.0936	1233	2027	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613605.1	s__Pedobacter sp018613605	92.0474	1520	2027	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	0.95	0.95	2	-
GCF_001442625.1	s__Pedobacter ginsenosidimutans	91.9119	1528	2027	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387415.1	s__Pedobacter sp003387415	90.9786	1416	2027	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054145.1	s__Pedobacter sp003054145	88.9724	1357	2027	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014692875.1	s__Pedobacter sp011759615	88.3573	1399	2027	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.16	98.15	0.91	0.91	3	-
GCA_002151545.1	s__Pedobacter sp002151545	87.9366	1382	2027	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342125.1	s__Pedobacter sp004342125	86.1832	1311	2027	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	95.29	95.29	0.84	0.84	2	-
GCF_001421515.1	s__Pedobacter sp001421515	83.6314	1193	2027	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 14:57:39,362] [INFO] GTDB search result was written to GCF_004310665.1_ASM431066v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:39,362] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:39,365] [INFO] DFAST_QC result json was written to GCF_004310665.1_ASM431066v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:39,365] [INFO] DFAST_QC completed!
[2024-01-24 14:57:39,365] [INFO] Total running time: 0h2m3s