[2024-01-24 14:05:31,704] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:31,706] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:31,706] [INFO] DQC Reference Directory: /var/lib/cwl/stg768ef0c3-6abb-49ed-9257-86ea29fb3509/dqc_reference
[2024-01-24 14:05:32,908] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:32,908] [INFO] Task started: Prodigal
[2024-01-24 14:05:32,909] [INFO] Running command: gunzip -c /var/lib/cwl/stgeca56404-368e-46f4-89a5-da2185320575/GCF_003313325.1_ASM331332v1_genomic.fna.gz | prodigal -d GCF_003313325.1_ASM331332v1_genomic.fna/cds.fna -a GCF_003313325.1_ASM331332v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:48,534] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:48,534] [INFO] Task started: HMMsearch
[2024-01-24 14:05:48,534] [INFO] Running command: hmmsearch --tblout GCF_003313325.1_ASM331332v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg768ef0c3-6abb-49ed-9257-86ea29fb3509/dqc_reference/reference_markers.hmm GCF_003313325.1_ASM331332v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:48,862] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:48,863] [INFO] Found 6/6 markers.
[2024-01-24 14:05:48,910] [INFO] Query marker FASTA was written to GCF_003313325.1_ASM331332v1_genomic.fna/markers.fasta
[2024-01-24 14:05:48,911] [INFO] Task started: Blastn
[2024-01-24 14:05:48,911] [INFO] Running command: blastn -query GCF_003313325.1_ASM331332v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg768ef0c3-6abb-49ed-9257-86ea29fb3509/dqc_reference/reference_markers.fasta -out GCF_003313325.1_ASM331332v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:49,586] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:49,601] [INFO] Selected 15 target genomes.
[2024-01-24 14:05:49,602] [INFO] Target genome list was writen to GCF_003313325.1_ASM331332v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:49,608] [INFO] Task started: fastANI
[2024-01-24 14:05:49,608] [INFO] Running command: fastANI --query /var/lib/cwl/stgeca56404-368e-46f4-89a5-da2185320575/GCF_003313325.1_ASM331332v1_genomic.fna.gz --refList GCF_003313325.1_ASM331332v1_genomic.fna/target_genomes.txt --output GCF_003313325.1_ASM331332v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:05,400] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:05,401] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg768ef0c3-6abb-49ed-9257-86ea29fb3509/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:05,402] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg768ef0c3-6abb-49ed-9257-86ea29fb3509/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:05,418] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:05,418] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:05,418] [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 namyangjuensis	strain=5G38	GCA_003313325.1	600626	600626	type	True	100.0	1432	1432	95	conclusive
Pedobacter cryotolerans	strain=AR-2-6	GCA_005116475.1	2571270	2571270	type	True	79.5625	585	1432	95	below_threshold
Pedobacter planticolens	strain=LMG 31464	GCA_014172375.1	2679964	2679964	type	True	79.4473	508	1432	95	below_threshold
Pedobacter polaris	strain=RP-3-22	GCA_005116505.1	2571273	2571273	type	True	79.3822	519	1432	95	below_threshold
Pedobacter frigiditerrae	strain=RP-1-13	GCA_004331645.1	2530452	2530452	type	True	79.2198	507	1432	95	below_threshold
Pedobacter helvus	strain=P-25	GCA_005925325.1	2563444	2563444	type	True	78.1903	339	1432	95	below_threshold
Pedobacter ureilyticus	strain=THG-T11	GCA_005925345.1	1393051	1393051	type	True	78.1897	344	1432	95	below_threshold
Pedobacter hartonius	strain=DSM 19033	GCA_900107535.1	425514	425514	type	True	78.0875	110	1432	95	below_threshold
Pedobacter psychrodurus	strain=RP-3-21	GCA_004331735.1	2530456	2530456	type	True	77.9544	261	1432	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	77.8527	242	1432	95	below_threshold
Pedobacter panaciterrae	strain=LMG 23400	GCA_013204795.1	363849	363849	type	True	77.8507	206	1432	95	below_threshold
Mucilaginibacter celer	strain=HYN0043	GCA_003576455.2	2305508	2305508	type	True	77.2567	63	1432	95	below_threshold
Mucilaginibacter oryzae	strain=DSM 19975	GCA_003148845.1	468058	468058	type	True	76.6863	61	1432	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:05,423] [INFO] DFAST Taxonomy check result was written to GCF_003313325.1_ASM331332v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:05,424] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:05,424] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:05,425] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg768ef0c3-6abb-49ed-9257-86ea29fb3509/dqc_reference/checkm_data
[2024-01-24 14:06:05,428] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:05,476] [INFO] Task started: CheckM
[2024-01-24 14:06:05,476] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003313325.1_ASM331332v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003313325.1_ASM331332v1_genomic.fna/checkm_input GCF_003313325.1_ASM331332v1_genomic.fna/checkm_result
[2024-01-24 14:06:53,551] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:53,553] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:53,571] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:53,571] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:53,572] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003313325.1_ASM331332v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:53,572] [INFO] Task started: Blastn
[2024-01-24 14:06:53,572] [INFO] Running command: blastn -query GCF_003313325.1_ASM331332v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg768ef0c3-6abb-49ed-9257-86ea29fb3509/dqc_reference/reference_markers_gtdb.fasta -out GCF_003313325.1_ASM331332v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:54,429] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:54,433] [INFO] Selected 13 target genomes.
[2024-01-24 14:06:54,434] [INFO] Target genome list was writen to GCF_003313325.1_ASM331332v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:54,443] [INFO] Task started: fastANI
[2024-01-24 14:06:54,444] [INFO] Running command: fastANI --query /var/lib/cwl/stgeca56404-368e-46f4-89a5-da2185320575/GCF_003313325.1_ASM331332v1_genomic.fna.gz --refList GCF_003313325.1_ASM331332v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003313325.1_ASM331332v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:05,272] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:05,288] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:05,288] [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_003313325.1	s__Pedobacter namyangjuensis	100.0	1432	1432	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_005116475.1	s__Pedobacter sp005116475	79.575	584	1432	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	79.4569	507	1432	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116505.1	s__Pedobacter sp005116505	79.3915	518	1432	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001412215.1	s__Pedobacter sp001412215	79.3222	453	1432	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	79.284	494	1432	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	79.2026	510	1432	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005925345.1	s__Pedobacter ureilyticus	78.2111	342	1432	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005925325.1	s__Pedobacter helvus	78.1907	339	1432	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002399615.1	s__Pedobacter sp002399615	78.0605	296	1432	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331735.1	s__Pedobacter sp004331735	77.9473	260	1432	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003313335.1	s__Pedobacter zeaxanthinifaciens	77.9248	281	1432	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423945.1	s__Pedobacter sp001423945	77.7771	214	1432	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 14:07:05,291] [INFO] GTDB search result was written to GCF_003313325.1_ASM331332v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:05,292] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:05,295] [INFO] DFAST_QC result json was written to GCF_003313325.1_ASM331332v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:05,295] [INFO] DFAST_QC completed!
[2024-01-24 14:07:05,296] [INFO] Total running time: 0h1m34s