[2023-06-29 01:21:38,166] [INFO] DFAST_QC pipeline started.
[2023-06-29 01:21:38,168] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 01:21:38,169] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf06fb09-d880-46bc-85c3-e162a4946819/dqc_reference
[2023-06-29 01:21:39,642] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 01:21:39,643] [INFO] Task started: Prodigal
[2023-06-29 01:21:39,643] [INFO] Running command: gunzip -c /var/lib/cwl/stgd7099be6-7dbf-4fce-891a-a2b2a9726a3c/GCA_020628175.1_ASM2062817v1_genomic.fna.gz | prodigal -d GCA_020628175.1_ASM2062817v1_genomic.fna/cds.fna -a GCA_020628175.1_ASM2062817v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 01:21:43,638] [INFO] Task succeeded: Prodigal
[2023-06-29 01:21:43,638] [INFO] Task started: HMMsearch
[2023-06-29 01:21:43,638] [INFO] Running command: hmmsearch --tblout GCA_020628175.1_ASM2062817v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf06fb09-d880-46bc-85c3-e162a4946819/dqc_reference/reference_markers.hmm GCA_020628175.1_ASM2062817v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 01:21:43,829] [INFO] Task succeeded: HMMsearch
[2023-06-29 01:21:43,830] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgd7099be6-7dbf-4fce-891a-a2b2a9726a3c/GCA_020628175.1_ASM2062817v1_genomic.fna.gz]
[2023-06-29 01:21:43,851] [INFO] Query marker FASTA was written to GCA_020628175.1_ASM2062817v1_genomic.fna/markers.fasta
[2023-06-29 01:21:43,851] [INFO] Task started: Blastn
[2023-06-29 01:21:43,851] [INFO] Running command: blastn -query GCA_020628175.1_ASM2062817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf06fb09-d880-46bc-85c3-e162a4946819/dqc_reference/reference_markers.fasta -out GCA_020628175.1_ASM2062817v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 01:21:44,447] [INFO] Task succeeded: Blastn
[2023-06-29 01:21:44,450] [INFO] Selected 5 target genomes.
[2023-06-29 01:21:44,451] [INFO] Target genome list was writen to GCA_020628175.1_ASM2062817v1_genomic.fna/target_genomes.txt
[2023-06-29 01:21:44,452] [INFO] Task started: fastANI
[2023-06-29 01:21:44,452] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7099be6-7dbf-4fce-891a-a2b2a9726a3c/GCA_020628175.1_ASM2062817v1_genomic.fna.gz --refList GCA_020628175.1_ASM2062817v1_genomic.fna/target_genomes.txt --output GCA_020628175.1_ASM2062817v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 01:21:47,321] [INFO] Task succeeded: fastANI
[2023-06-29 01:21:47,322] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf06fb09-d880-46bc-85c3-e162a4946819/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 01:21:47,322] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf06fb09-d880-46bc-85c3-e162a4946819/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 01:21:47,328] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 01:21:47,329] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 01:21:47,329] [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
Wenyingzhuangia aestuarii	strain=DSM 105044	GCA_011927765.1	1647582	1647582	type	True	80.5204	230	403	95	below_threshold
Wenyingzhuangia heitensis	strain=DSM 101599	GCA_011762155.1	1487859	1487859	type	True	80.2901	219	403	95	below_threshold
Wenyingzhuangia fucanilytica	strain=CZ1127	GCA_001697185.1	1790137	1790137	type	True	80.1138	200	403	95	below_threshold
Wenyingzhuangia marina	strain=DSM 100572	GCA_900130035.1	1195760	1195760	type	True	79.7368	200	403	95	below_threshold
Wenyingzhuangia marina	strain=CGMCC 1.12162	GCA_014636515.1	1195760	1195760	type	True	79.6745	199	403	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 01:21:47,331] [INFO] DFAST Taxonomy check result was written to GCA_020628175.1_ASM2062817v1_genomic.fna/tc_result.tsv
[2023-06-29 01:21:47,332] [INFO] ===== Taxonomy check completed =====
[2023-06-29 01:21:47,332] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 01:21:47,332] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf06fb09-d880-46bc-85c3-e162a4946819/dqc_reference/checkm_data
[2023-06-29 01:21:47,333] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 01:21:47,349] [INFO] Task started: CheckM
[2023-06-29 01:21:47,349] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020628175.1_ASM2062817v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020628175.1_ASM2062817v1_genomic.fna/checkm_input GCA_020628175.1_ASM2062817v1_genomic.fna/checkm_result
[2023-06-29 01:22:06,759] [INFO] Task succeeded: CheckM
[2023-06-29 01:22:06,761] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 01:22:06,783] [INFO] ===== Completeness check finished =====
[2023-06-29 01:22:06,783] [INFO] ===== Start GTDB Search =====
[2023-06-29 01:22:06,783] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020628175.1_ASM2062817v1_genomic.fna/markers.fasta)
[2023-06-29 01:22:06,784] [INFO] Task started: Blastn
[2023-06-29 01:22:06,784] [INFO] Running command: blastn -query GCA_020628175.1_ASM2062817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf06fb09-d880-46bc-85c3-e162a4946819/dqc_reference/reference_markers_gtdb.fasta -out GCA_020628175.1_ASM2062817v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 01:22:07,438] [INFO] Task succeeded: Blastn
[2023-06-29 01:22:07,442] [INFO] Selected 5 target genomes.
[2023-06-29 01:22:07,442] [INFO] Target genome list was writen to GCA_020628175.1_ASM2062817v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 01:22:07,446] [INFO] Task started: fastANI
[2023-06-29 01:22:07,447] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7099be6-7dbf-4fce-891a-a2b2a9726a3c/GCA_020628175.1_ASM2062817v1_genomic.fna.gz --refList GCA_020628175.1_ASM2062817v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020628175.1_ASM2062817v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 01:22:10,420] [INFO] Task succeeded: fastANI
[2023-06-29 01:22:10,431] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 01:22:10,431] [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_011927765.1	s__Wenyingzhuangia aestuarii	80.5204	230	403	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762155.1	s__Wenyingzhuangia heitensis	80.3171	218	403	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001697185.1	s__Wenyingzhuangia fucanilytica	80.0855	201	403	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900130035.1	s__Wenyingzhuangia marina	79.7368	200	403	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wenyingzhuangia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000220525.1	s__Ochrovirga pacifica	78.2633	152	403	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ochrovirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 01:22:10,433] [INFO] GTDB search result was written to GCA_020628175.1_ASM2062817v1_genomic.fna/result_gtdb.tsv
[2023-06-29 01:22:10,434] [INFO] ===== GTDB Search completed =====
[2023-06-29 01:22:10,438] [INFO] DFAST_QC result json was written to GCA_020628175.1_ASM2062817v1_genomic.fna/dqc_result.json
[2023-06-29 01:22:10,439] [INFO] DFAST_QC completed!
[2023-06-29 01:22:10,439] [INFO] Total running time: 0h0m32s