[2024-01-24 12:31:03,566] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:03,568] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:03,569] [INFO] DQC Reference Directory: /var/lib/cwl/stgaae21017-2f19-4bb3-9916-649d4262f943/dqc_reference
[2024-01-24 12:31:04,769] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:04,770] [INFO] Task started: Prodigal
[2024-01-24 12:31:04,770] [INFO] Running command: gunzip -c /var/lib/cwl/stgff5fd6c6-0eaa-421a-b465-ef11561bc7a6/GCF_005116475.1_ASM511647v1_genomic.fna.gz | prodigal -d GCF_005116475.1_ASM511647v1_genomic.fna/cds.fna -a GCF_005116475.1_ASM511647v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:19,358] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:19,358] [INFO] Task started: HMMsearch
[2024-01-24 12:31:19,358] [INFO] Running command: hmmsearch --tblout GCF_005116475.1_ASM511647v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaae21017-2f19-4bb3-9916-649d4262f943/dqc_reference/reference_markers.hmm GCF_005116475.1_ASM511647v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:19,688] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:19,690] [INFO] Found 6/6 markers.
[2024-01-24 12:31:19,725] [INFO] Query marker FASTA was written to GCF_005116475.1_ASM511647v1_genomic.fna/markers.fasta
[2024-01-24 12:31:19,725] [INFO] Task started: Blastn
[2024-01-24 12:31:19,725] [INFO] Running command: blastn -query GCF_005116475.1_ASM511647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaae21017-2f19-4bb3-9916-649d4262f943/dqc_reference/reference_markers.fasta -out GCF_005116475.1_ASM511647v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:20,380] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:20,384] [INFO] Selected 12 target genomes.
[2024-01-24 12:31:20,385] [INFO] Target genome list was writen to GCF_005116475.1_ASM511647v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:20,390] [INFO] Task started: fastANI
[2024-01-24 12:31:20,390] [INFO] Running command: fastANI --query /var/lib/cwl/stgff5fd6c6-0eaa-421a-b465-ef11561bc7a6/GCF_005116475.1_ASM511647v1_genomic.fna.gz --refList GCF_005116475.1_ASM511647v1_genomic.fna/target_genomes.txt --output GCF_005116475.1_ASM511647v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:30,663] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:30,664] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaae21017-2f19-4bb3-9916-649d4262f943/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:30,664] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaae21017-2f19-4bb3-9916-649d4262f943/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:30,673] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:30,674] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:30,674] [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 cryotolerans	strain=AR-2-6	GCA_005116475.1	2571270	2571270	type	True	100.0	1400	1401	95	conclusive
Pedobacter polaris	strain=RP-3-22	GCA_005116505.1	2571273	2571273	type	True	80.7548	749	1401	95	below_threshold
Pedobacter planticolens	strain=LMG 31464	GCA_014172375.1	2679964	2679964	type	True	80.3609	658	1401	95	below_threshold
Pedobacter frigiditerrae	strain=RP-1-13	GCA_004331645.1	2530452	2530452	type	True	80.3088	723	1401	95	below_threshold
Pedobacter namyangjuensis	strain=5G38	GCA_003313325.1	600626	600626	type	True	79.3569	617	1401	95	below_threshold
Pedobacter xixiisoli	strain=S27	GCA_005925365.1	1476464	1476464	type	True	78.1278	384	1401	95	below_threshold
Pedobacter xixiisoli	strain=CGMCC 1.12803	GCA_900215335.1	1476464	1476464	type	True	78.0643	388	1401	95	below_threshold
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	77.863	386	1401	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	77.8503	263	1401	95	below_threshold
Pedobacter segetis	strain=SD-b	GCA_016623585.1	2793069	2793069	type	True	76.262	108	1401	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:30,676] [INFO] DFAST Taxonomy check result was written to GCF_005116475.1_ASM511647v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:30,676] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:30,676] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:30,677] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaae21017-2f19-4bb3-9916-649d4262f943/dqc_reference/checkm_data
[2024-01-24 12:31:30,678] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:30,719] [INFO] Task started: CheckM
[2024-01-24 12:31:30,720] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005116475.1_ASM511647v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005116475.1_ASM511647v1_genomic.fna/checkm_input GCF_005116475.1_ASM511647v1_genomic.fna/checkm_result
[2024-01-24 12:32:14,190] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:14,191] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:14,212] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:14,213] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:14,213] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005116475.1_ASM511647v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:14,214] [INFO] Task started: Blastn
[2024-01-24 12:32:14,214] [INFO] Running command: blastn -query GCF_005116475.1_ASM511647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaae21017-2f19-4bb3-9916-649d4262f943/dqc_reference/reference_markers_gtdb.fasta -out GCF_005116475.1_ASM511647v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:15,063] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:15,067] [INFO] Selected 7 target genomes.
[2024-01-24 12:32:15,067] [INFO] Target genome list was writen to GCF_005116475.1_ASM511647v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:15,073] [INFO] Task started: fastANI
[2024-01-24 12:32:15,073] [INFO] Running command: fastANI --query /var/lib/cwl/stgff5fd6c6-0eaa-421a-b465-ef11561bc7a6/GCF_005116475.1_ASM511647v1_genomic.fna.gz --refList GCF_005116475.1_ASM511647v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005116475.1_ASM511647v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:21,890] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:21,901] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:21,901] [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_005116475.1	s__Pedobacter sp005116475	100.0	1400	1401	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_005116505.1	s__Pedobacter sp005116505	80.7443	750	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014172375.1	s__Pedobacter planticolens	80.37	657	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331645.1	s__Pedobacter sp004331645	80.3084	723	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013204825.1	s__Pedobacter boryungensis	80.0622	589	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004295885.1	s__Pedobacter sp004295885	79.6624	423	1401	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	78.0728	387	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:21,903] [INFO] GTDB search result was written to GCF_005116475.1_ASM511647v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:21,903] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:21,906] [INFO] DFAST_QC result json was written to GCF_005116475.1_ASM511647v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:21,906] [INFO] DFAST_QC completed!
[2024-01-24 12:32:21,907] [INFO] Total running time: 0h1m18s