[2024-01-25 18:50:05,577] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:50:05,578] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:50:05,578] [INFO] DQC Reference Directory: /var/lib/cwl/stg61755243-e65a-4ff5-b745-cf928a0508ed/dqc_reference
[2024-01-25 18:50:06,721] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:50:06,722] [INFO] Task started: Prodigal
[2024-01-25 18:50:06,722] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb1bded5-5179-4cad-ba01-599d70bdbe87/GCF_025460835.1_ASM2546083v1_genomic.fna.gz | prodigal -d GCF_025460835.1_ASM2546083v1_genomic.fna/cds.fna -a GCF_025460835.1_ASM2546083v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:50:31,133] [INFO] Task succeeded: Prodigal
[2024-01-25 18:50:31,133] [INFO] Task started: HMMsearch
[2024-01-25 18:50:31,133] [INFO] Running command: hmmsearch --tblout GCF_025460835.1_ASM2546083v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61755243-e65a-4ff5-b745-cf928a0508ed/dqc_reference/reference_markers.hmm GCF_025460835.1_ASM2546083v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:50:31,395] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:50:31,396] [INFO] Found 6/6 markers.
[2024-01-25 18:50:31,440] [INFO] Query marker FASTA was written to GCF_025460835.1_ASM2546083v1_genomic.fna/markers.fasta
[2024-01-25 18:50:31,440] [INFO] Task started: Blastn
[2024-01-25 18:50:31,440] [INFO] Running command: blastn -query GCF_025460835.1_ASM2546083v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61755243-e65a-4ff5-b745-cf928a0508ed/dqc_reference/reference_markers.fasta -out GCF_025460835.1_ASM2546083v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:31,987] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:31,989] [INFO] Selected 22 target genomes.
[2024-01-25 18:50:31,990] [INFO] Target genome list was writen to GCF_025460835.1_ASM2546083v1_genomic.fna/target_genomes.txt
[2024-01-25 18:50:32,006] [INFO] Task started: fastANI
[2024-01-25 18:50:32,006] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb1bded5-5179-4cad-ba01-599d70bdbe87/GCF_025460835.1_ASM2546083v1_genomic.fna.gz --refList GCF_025460835.1_ASM2546083v1_genomic.fna/target_genomes.txt --output GCF_025460835.1_ASM2546083v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:50:48,799] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:48,799] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61755243-e65a-4ff5-b745-cf928a0508ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:50:48,800] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61755243-e65a-4ff5-b745-cf928a0508ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:50:48,806] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:50:48,806] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:50:48,806] [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
Parapedobacter soli	strain=KCTC 12984	GCA_025460835.1	416955	416955	type	True	100.0	1637	1645	95	conclusive
Parapedobacter indicus	strain=RK1	GCA_002934635.1	1477437	1477437	type	True	77.9102	297	1645	95	below_threshold
Parapedobacter indicus	strain=RK1	GCA_900113765.1	1477437	1477437	type	True	77.8696	299	1645	95	below_threshold
Parapedobacter pyrenivorans	strain=CGMCC 1.12195	GCA_014636865.1	1305674	1305674	type	True	77.8395	353	1645	95	below_threshold
Parapedobacter composti	strain=DSM 22900	GCA_900112315.1	623281	623281	type	True	77.577	203	1645	95	below_threshold
Parapedobacter defluvii	strain=CGMCC 1.15342	GCA_014642075.1	2045106	2045106	type	True	77.5139	282	1645	95	below_threshold
Parapedobacter koreensis	strain=Jip14	GCA_900109365.1	332977	332977	type	True	77.5001	218	1645	95	below_threshold
Parapedobacter luteus	strain=DSM 22899	GCA_900168055.1	623280	623280	type	True	77.24	213	1645	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:50:48,807] [INFO] DFAST Taxonomy check result was written to GCF_025460835.1_ASM2546083v1_genomic.fna/tc_result.tsv
[2024-01-25 18:50:48,808] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:50:48,808] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:50:48,808] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61755243-e65a-4ff5-b745-cf928a0508ed/dqc_reference/checkm_data
[2024-01-25 18:50:48,809] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:50:48,860] [INFO] Task started: CheckM
[2024-01-25 18:50:48,860] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025460835.1_ASM2546083v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025460835.1_ASM2546083v1_genomic.fna/checkm_input GCF_025460835.1_ASM2546083v1_genomic.fna/checkm_result
[2024-01-25 18:51:54,663] [INFO] Task succeeded: CheckM
[2024-01-25 18:51:54,664] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:51:54,700] [INFO] ===== Completeness check finished =====
[2024-01-25 18:51:54,700] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:51:54,701] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025460835.1_ASM2546083v1_genomic.fna/markers.fasta)
[2024-01-25 18:51:54,702] [INFO] Task started: Blastn
[2024-01-25 18:51:54,702] [INFO] Running command: blastn -query GCF_025460835.1_ASM2546083v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61755243-e65a-4ff5-b745-cf928a0508ed/dqc_reference/reference_markers_gtdb.fasta -out GCF_025460835.1_ASM2546083v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:55,509] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:55,512] [INFO] Selected 27 target genomes.
[2024-01-25 18:51:55,513] [INFO] Target genome list was writen to GCF_025460835.1_ASM2546083v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:51:55,567] [INFO] Task started: fastANI
[2024-01-25 18:51:55,568] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb1bded5-5179-4cad-ba01-599d70bdbe87/GCF_025460835.1_ASM2546083v1_genomic.fna.gz --refList GCF_025460835.1_ASM2546083v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025460835.1_ASM2546083v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:52:15,648] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:15,654] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:52:15,654] [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_011030405.1	s__Sphingobacterium sp011030405	78.2436	54	1645	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113765.1	s__Parapedobacter indicus	77.8635	301	1645	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Parapedobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014636865.1	s__Parapedobacter pyrenivorans	77.83	356	1645	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Parapedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112315.1	s__Parapedobacter composti	77.5573	202	1645	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Parapedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014642075.1	s__Parapedobacter defluvii	77.5209	282	1645	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Parapedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109365.1	s__Parapedobacter koreensis	77.4728	220	1645	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Parapedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168055.1	s__Parapedobacter luteus	77.2255	215	1645	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Parapedobacter	95.0	99.02	99.02	0.90	0.90	2	-
GCF_009768885.1	s__Sphingobacterium humi	76.9433	60	1645	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:52:15,656] [INFO] GTDB search result was written to GCF_025460835.1_ASM2546083v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:52:15,657] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:52:15,661] [INFO] DFAST_QC result json was written to GCF_025460835.1_ASM2546083v1_genomic.fna/dqc_result.json
[2024-01-25 18:52:15,661] [INFO] DFAST_QC completed!
[2024-01-25 18:52:15,661] [INFO] Total running time: 0h2m10s