[2023-06-05 04:00:05,188] [INFO] DFAST_QC pipeline started.
[2023-06-05 04:00:05,192] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 04:00:05,192] [INFO] DQC Reference Directory: /var/lib/cwl/stg07904751-4b9d-49a2-b5f7-8bd6ac16974e/dqc_reference
[2023-06-05 04:00:07,488] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 04:00:07,489] [INFO] Task started: Prodigal
[2023-06-05 04:00:07,489] [INFO] Running command: gunzip -c /var/lib/cwl/stgf394e077-5545-4d85-87ce-31417c8bbf2c/GCA_004173315.1_ASM417331v1_genomic.fna.gz | prodigal -d GCA_004173315.1_ASM417331v1_genomic.fna/cds.fna -a GCA_004173315.1_ASM417331v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 04:00:32,881] [INFO] Task succeeded: Prodigal
[2023-06-05 04:00:32,882] [INFO] Task started: HMMsearch
[2023-06-05 04:00:32,882] [INFO] Running command: hmmsearch --tblout GCA_004173315.1_ASM417331v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07904751-4b9d-49a2-b5f7-8bd6ac16974e/dqc_reference/reference_markers.hmm GCA_004173315.1_ASM417331v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 04:00:33,143] [INFO] Task succeeded: HMMsearch
[2023-06-05 04:00:33,144] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf394e077-5545-4d85-87ce-31417c8bbf2c/GCA_004173315.1_ASM417331v1_genomic.fna.gz]
[2023-06-05 04:00:33,187] [INFO] Query marker FASTA was written to GCA_004173315.1_ASM417331v1_genomic.fna/markers.fasta
[2023-06-05 04:00:33,188] [INFO] Task started: Blastn
[2023-06-05 04:00:33,188] [INFO] Running command: blastn -query GCA_004173315.1_ASM417331v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07904751-4b9d-49a2-b5f7-8bd6ac16974e/dqc_reference/reference_markers.fasta -out GCA_004173315.1_ASM417331v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 04:00:33,754] [INFO] Task succeeded: Blastn
[2023-06-05 04:00:33,758] [INFO] Selected 8 target genomes.
[2023-06-05 04:00:33,759] [INFO] Target genome list was writen to GCA_004173315.1_ASM417331v1_genomic.fna/target_genomes.txt
[2023-06-05 04:00:33,762] [INFO] Task started: fastANI
[2023-06-05 04:00:33,762] [INFO] Running command: fastANI --query /var/lib/cwl/stgf394e077-5545-4d85-87ce-31417c8bbf2c/GCA_004173315.1_ASM417331v1_genomic.fna.gz --refList GCA_004173315.1_ASM417331v1_genomic.fna/target_genomes.txt --output GCA_004173315.1_ASM417331v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 04:00:40,309] [INFO] Task succeeded: fastANI
[2023-06-05 04:00:40,310] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07904751-4b9d-49a2-b5f7-8bd6ac16974e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 04:00:40,311] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07904751-4b9d-49a2-b5f7-8bd6ac16974e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 04:00:40,324] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 04:00:40,324] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 04:00:40,324] [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
Hymenobacter setariae	strain=Fur1	GCA_007713685.1	2594794	2594794	type	True	81.5175	386	585	95	below_threshold
Hymenobacter polaris	strain=RP-2-7	GCA_012927305.1	2682546	2682546	type	True	80.9804	369	585	95	below_threshold
Hymenobacter ginkgonis	strain=HMF4947	GCA_009755225.1	2682976	2682976	type	True	80.8682	359	585	95	below_threshold
Hymenobacter baengnokdamensis	strain=BRD72	GCA_008728635.1	2615203	2615203	type	True	80.4123	295	585	95	below_threshold
Hymenobacter frigidus	strain=CGMCC 1.14966	GCA_014640435.1	1524095	1524095	type	True	78.2773	223	585	95	below_threshold
Hymenobacter aerophilus	strain=DSM 13606	GCA_000382225.1	119644	119644	type	True	77.8493	190	585	95	below_threshold
Hymenobacter actinosclerus	strain=DSM 15310	GCA_900111515.1	82805	82805	type	True	77.7753	211	585	95	below_threshold
Hymenobacter metallilatus	strain=9PBR-2	GCA_003944705.1	2493666	2493666	type	True	77.2704	148	585	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 04:00:40,326] [INFO] DFAST Taxonomy check result was written to GCA_004173315.1_ASM417331v1_genomic.fna/tc_result.tsv
[2023-06-05 04:00:40,326] [INFO] ===== Taxonomy check completed =====
[2023-06-05 04:00:40,326] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 04:00:40,326] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07904751-4b9d-49a2-b5f7-8bd6ac16974e/dqc_reference/checkm_data
[2023-06-05 04:00:40,327] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 04:00:40,374] [INFO] Task started: CheckM
[2023-06-05 04:00:40,375] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004173315.1_ASM417331v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004173315.1_ASM417331v1_genomic.fna/checkm_input GCA_004173315.1_ASM417331v1_genomic.fna/checkm_result
[2023-06-05 04:01:45,603] [INFO] Task succeeded: CheckM
[2023-06-05 04:01:45,605] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 16.67%
Contamintation: 20.83%
Strain heterogeneity: 57.14%
--------------------------------------------------------------------------------
[2023-06-05 04:01:45,641] [INFO] ===== Completeness check finished =====
[2023-06-05 04:01:45,641] [INFO] ===== Start GTDB Search =====
[2023-06-05 04:01:45,642] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004173315.1_ASM417331v1_genomic.fna/markers.fasta)
[2023-06-05 04:01:45,642] [INFO] Task started: Blastn
[2023-06-05 04:01:45,642] [INFO] Running command: blastn -query GCA_004173315.1_ASM417331v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07904751-4b9d-49a2-b5f7-8bd6ac16974e/dqc_reference/reference_markers_gtdb.fasta -out GCA_004173315.1_ASM417331v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 04:01:46,372] [INFO] Task succeeded: Blastn
[2023-06-05 04:01:46,377] [INFO] Selected 7 target genomes.
[2023-06-05 04:01:46,377] [INFO] Target genome list was writen to GCA_004173315.1_ASM417331v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 04:01:46,385] [INFO] Task started: fastANI
[2023-06-05 04:01:46,385] [INFO] Running command: fastANI --query /var/lib/cwl/stgf394e077-5545-4d85-87ce-31417c8bbf2c/GCA_004173315.1_ASM417331v1_genomic.fna.gz --refList GCA_004173315.1_ASM417331v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004173315.1_ASM417331v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 04:01:52,741] [INFO] Task succeeded: fastANI
[2023-06-05 04:01:52,760] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 04:01:52,761] [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_016427535.1	s__Hymenobacter sp016427535	81.9474	395	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013256625.1	s__Hymenobacter sp013256625	81.5899	344	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007713685.1	s__Hymenobacter sp007713685	81.5535	384	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004684095.1	s__Hymenobacter sp004684095	81.5234	388	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012927305.1	s__Hymenobacter polaris	81.0108	368	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017571525.1	s__Hymenobacter sp017571525	80.883	353	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728635.1	s__Hymenobacter baengnokdamensis	80.4032	295	585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Hymenobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 04:01:52,763] [INFO] GTDB search result was written to GCA_004173315.1_ASM417331v1_genomic.fna/result_gtdb.tsv
[2023-06-05 04:01:52,764] [INFO] ===== GTDB Search completed =====
[2023-06-05 04:01:52,770] [INFO] DFAST_QC result json was written to GCA_004173315.1_ASM417331v1_genomic.fna/dqc_result.json
[2023-06-05 04:01:52,771] [INFO] DFAST_QC completed!
[2023-06-05 04:01:52,771] [INFO] Total running time: 0h1m48s