[2024-01-25 20:00:05,421] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:00:05,422] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:00:05,422] [INFO] DQC Reference Directory: /var/lib/cwl/stgdec9aa17-0972-4f7b-8db3-5afe80dd18ef/dqc_reference
[2024-01-25 20:00:06,525] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:00:06,526] [INFO] Task started: Prodigal
[2024-01-25 20:00:06,526] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f36cdda-ec2a-425a-8393-b7dfb7bf72ad/GCF_900564155.1_PRJEB26455_genomic.fna.gz | prodigal -d GCF_900564155.1_PRJEB26455_genomic.fna/cds.fna -a GCF_900564155.1_PRJEB26455_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:00:29,930] [INFO] Task succeeded: Prodigal
[2024-01-25 20:00:29,931] [INFO] Task started: HMMsearch
[2024-01-25 20:00:29,931] [INFO] Running command: hmmsearch --tblout GCF_900564155.1_PRJEB26455_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdec9aa17-0972-4f7b-8db3-5afe80dd18ef/dqc_reference/reference_markers.hmm GCF_900564155.1_PRJEB26455_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:00:30,222] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:00:30,223] [INFO] Found 6/6 markers.
[2024-01-25 20:00:30,269] [INFO] Query marker FASTA was written to GCF_900564155.1_PRJEB26455_genomic.fna/markers.fasta
[2024-01-25 20:00:30,269] [INFO] Task started: Blastn
[2024-01-25 20:00:30,269] [INFO] Running command: blastn -query GCF_900564155.1_PRJEB26455_genomic.fna/markers.fasta -db /var/lib/cwl/stgdec9aa17-0972-4f7b-8db3-5afe80dd18ef/dqc_reference/reference_markers.fasta -out GCF_900564155.1_PRJEB26455_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:00:30,831] [INFO] Task succeeded: Blastn
[2024-01-25 20:00:30,836] [INFO] Selected 15 target genomes.
[2024-01-25 20:00:30,836] [INFO] Target genome list was writen to GCF_900564155.1_PRJEB26455_genomic.fna/target_genomes.txt
[2024-01-25 20:00:30,860] [INFO] Task started: fastANI
[2024-01-25 20:00:30,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f36cdda-ec2a-425a-8393-b7dfb7bf72ad/GCF_900564155.1_PRJEB26455_genomic.fna.gz --refList GCF_900564155.1_PRJEB26455_genomic.fna/target_genomes.txt --output GCF_900564155.1_PRJEB26455_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:00:45,792] [INFO] Task succeeded: fastANI
[2024-01-25 20:00:45,793] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdec9aa17-0972-4f7b-8db3-5afe80dd18ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:00:45,793] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdec9aa17-0972-4f7b-8db3-5afe80dd18ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:00:45,801] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:00:45,801] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:00:45,801] [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 schmidteae	strain=eg	GCA_900564155.1	2201271	2201271	type	True	100.0	2065	2066	95	conclusive
Pedobacter hiemivivus	strain=RP-3-8	GCA_004331685.1	2530454	2530454	type	True	80.1944	795	2066	95	below_threshold
Pedobacter nyackensis	strain=DSM 19625	GCA_900176505.1	475255	475255	type	True	80.1155	812	2066	95	below_threshold
Pedobacter heparinus	strain=DSM 2366	GCA_000023825.1	984	984	type	True	80.0466	697	2066	95	below_threshold
Pedobacter heparinus	strain=DSM 2366	GCA_000410815.1	984	984	type	True	79.9865	704	2066	95	below_threshold
Pedobacter africanus	strain=DSM 12126	GCA_900176535.1	151894	151894	type	True	79.6681	739	2066	95	below_threshold
Pedobacter foliorum	strain=LMG 31463	GCA_013266735.1	2739058	2739058	type	True	78.7349	423	2066	95	below_threshold
Pedobacter steynii	strain=DSM 19110	GCA_900103665.1	430522	430522	type	True	78.7266	399	2066	95	below_threshold
Pedobacter psychroterrae	strain=RP-1-14	GCA_004331695.1	2530453	2530453	type	True	78.4799	335	2066	95	below_threshold
Pedobacter mucosus	strain=Q8-18	GCA_022200785.1	2895286	2895286	type	True	78.0191	124	2066	95	below_threshold
Pedobacter kyonggii	strain=K-4-11-1	GCA_004310665.1	1926871	1926871	type	True	77.6041	187	2066	95	below_threshold
Pedobacter psychrophilus	strain=CCM 8644	GCA_001652725.1	1826909	1826909	type	True	76.5714	69	2066	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:00:45,803] [INFO] DFAST Taxonomy check result was written to GCF_900564155.1_PRJEB26455_genomic.fna/tc_result.tsv
[2024-01-25 20:00:45,803] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:00:45,803] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:00:45,803] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdec9aa17-0972-4f7b-8db3-5afe80dd18ef/dqc_reference/checkm_data
[2024-01-25 20:00:45,804] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:00:45,865] [INFO] Task started: CheckM
[2024-01-25 20:00:45,865] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900564155.1_PRJEB26455_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900564155.1_PRJEB26455_genomic.fna/checkm_input GCF_900564155.1_PRJEB26455_genomic.fna/checkm_result
[2024-01-25 20:01:50,335] [INFO] Task succeeded: CheckM
[2024-01-25 20:01:50,339] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:01:50,366] [INFO] ===== Completeness check finished =====
[2024-01-25 20:01:50,366] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:01:50,370] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900564155.1_PRJEB26455_genomic.fna/markers.fasta)
[2024-01-25 20:01:50,370] [INFO] Task started: Blastn
[2024-01-25 20:01:50,370] [INFO] Running command: blastn -query GCF_900564155.1_PRJEB26455_genomic.fna/markers.fasta -db /var/lib/cwl/stgdec9aa17-0972-4f7b-8db3-5afe80dd18ef/dqc_reference/reference_markers_gtdb.fasta -out GCF_900564155.1_PRJEB26455_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:51,222] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:51,227] [INFO] Selected 12 target genomes.
[2024-01-25 20:01:51,228] [INFO] Target genome list was writen to GCF_900564155.1_PRJEB26455_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:01:51,244] [INFO] Task started: fastANI
[2024-01-25 20:01:51,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f36cdda-ec2a-425a-8393-b7dfb7bf72ad/GCF_900564155.1_PRJEB26455_genomic.fna.gz --refList GCF_900564155.1_PRJEB26455_genomic.fna/target_genomes_gtdb.txt --output GCF_900564155.1_PRJEB26455_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:02:06,397] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:06,405] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:02:06,405] [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_900564155.1	s__Pedobacter sp900564155	100.0	2064	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_004331685.1	s__Pedobacter sp004331685	80.1953	793	2066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	97.88	97.88	0.86	0.86	2	-
GCF_900100435.1	s__Pedobacter sp900100435	80.1723	829	2066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900176505.1	s__Pedobacter nyackensis	80.1277	810	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_000023825.1	s__Pedobacter heparinus	80.0528	697	2066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	99.29	98.59	0.94	0.88	3	-
GCF_900176535.1	s__Pedobacter africanus	79.6711	738	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_015223055.1	s__Pedobacter sp015223055	79.2297	531	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_002736205.1	s__Pedobacter ginsengisoli	79.0482	427	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_003852525.1	s__Pedobacter sp003852525	78.7108	421	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_004364225.1	s__Pedobacter sp004364225	77.8621	358	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_014395225.1	s__Pedobacter roseus	77.5712	237	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_000633455.1	s__Pedobacter jeongneungensis	77.3481	197	2066	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:02:06,406] [INFO] GTDB search result was written to GCF_900564155.1_PRJEB26455_genomic.fna/result_gtdb.tsv
[2024-01-25 20:02:06,407] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:02:06,410] [INFO] DFAST_QC result json was written to GCF_900564155.1_PRJEB26455_genomic.fna/dqc_result.json
[2024-01-25 20:02:06,410] [INFO] DFAST_QC completed!
[2024-01-25 20:02:06,410] [INFO] Total running time: 0h2m1s