[2024-01-24 14:39:34,340] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:34,341] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:34,342] [INFO] DQC Reference Directory: /var/lib/cwl/stgc26da332-f596-4072-9d48-528a76d3d837/dqc_reference
[2024-01-24 14:39:36,894] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:36,898] [INFO] Task started: Prodigal
[2024-01-24 14:39:36,898] [INFO] Running command: gunzip -c /var/lib/cwl/stg65f855df-47a4-4433-a8a5-d3421edfff5d/GCF_003367245.1_ASM336724v1_genomic.fna.gz | prodigal -d GCF_003367245.1_ASM336724v1_genomic.fna/cds.fna -a GCF_003367245.1_ASM336724v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:40:10,403] [INFO] Task succeeded: Prodigal
[2024-01-24 14:40:10,403] [INFO] Task started: HMMsearch
[2024-01-24 14:40:10,403] [INFO] Running command: hmmsearch --tblout GCF_003367245.1_ASM336724v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc26da332-f596-4072-9d48-528a76d3d837/dqc_reference/reference_markers.hmm GCF_003367245.1_ASM336724v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:40:10,771] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:40:10,773] [INFO] Found 6/6 markers.
[2024-01-24 14:40:10,831] [INFO] Query marker FASTA was written to GCF_003367245.1_ASM336724v1_genomic.fna/markers.fasta
[2024-01-24 14:40:10,832] [INFO] Task started: Blastn
[2024-01-24 14:40:10,832] [INFO] Running command: blastn -query GCF_003367245.1_ASM336724v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc26da332-f596-4072-9d48-528a76d3d837/dqc_reference/reference_markers.fasta -out GCF_003367245.1_ASM336724v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:11,449] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:11,453] [INFO] Selected 14 target genomes.
[2024-01-24 14:40:11,453] [INFO] Target genome list was writen to GCF_003367245.1_ASM336724v1_genomic.fna/target_genomes.txt
[2024-01-24 14:40:11,781] [INFO] Task started: fastANI
[2024-01-24 14:40:11,782] [INFO] Running command: fastANI --query /var/lib/cwl/stg65f855df-47a4-4433-a8a5-d3421edfff5d/GCF_003367245.1_ASM336724v1_genomic.fna.gz --refList GCF_003367245.1_ASM336724v1_genomic.fna/target_genomes.txt --output GCF_003367245.1_ASM336724v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:26,953] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:26,954] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc26da332-f596-4072-9d48-528a76d3d837/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:26,954] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc26da332-f596-4072-9d48-528a76d3d837/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:26,967] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:40:26,967] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:26,967] [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
Pontibacter diazotrophicus	strain=H4X	GCA_003367245.1	1400979	1400979	type	True	100.0	2079	2086	95	conclusive
Pontibacter pamirensis	strain=TRT317	GCA_010015475.1	2562824	2562824	type	True	88.5916	1592	2086	95	below_threshold
Pontibacter russatus	strain=BT326	GCA_009931655.1	2694929	2694929	type	True	79.1245	751	2086	95	below_threshold
Pontibacter akesuensis	strain=DSM 18820	GCA_900116885.1	388950	388950	type	True	78.5836	572	2086	95	below_threshold
Pontibacter akesuensis	strain=AKS 1T	GCA_001611675.1	388950	388950	type	True	78.5292	571	2086	95	below_threshold
Pontibacter ummariensis	strain=NKM1	GCA_900188175.1	1610492	1610492	type	True	78.4848	589	2086	95	below_threshold
Pontibacter ummariensis	strain=NKM1	GCA_003002015.1	1610492	1610492	type	True	78.4119	595	2086	95	below_threshold
Pontibacter mangrovi	strain=HB172049	GCA_006385705.1	2589816	2589816	type	True	78.4048	526	2086	95	below_threshold
Pontibacter oryzae	strain=KIRAN	GCA_003576375.1	2304593	2304593	type	True	78.2551	414	2086	95	below_threshold
Pontibacter ruber	strain=JC213	GCA_023630205.1	1343895	1343895	type	True	78.2382	430	2086	95	below_threshold
Pontibacter mucosus	strain=DSM 100162	GCA_003054055.1	1649266	1649266	type	True	78.2125	490	2086	95	below_threshold
Pontibacter chinhatensis	strain=LP51	GCA_900113285.1	1436961	1436961	type	True	78.0157	501	2086	95	below_threshold
Pontibacter deserti	strain=JC215	GCA_023630255.1	1343896	1343896	type	True	77.5913	318	2086	95	below_threshold
Pontibacter silvestris	strain=XAAS-R86T	GCA_020907275.1	2305183	2305183	type	True	77.4157	314	2086	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:26,969] [INFO] DFAST Taxonomy check result was written to GCF_003367245.1_ASM336724v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:26,969] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:26,970] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:26,970] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc26da332-f596-4072-9d48-528a76d3d837/dqc_reference/checkm_data
[2024-01-24 14:40:26,971] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:27,041] [INFO] Task started: CheckM
[2024-01-24 14:40:27,041] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003367245.1_ASM336724v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003367245.1_ASM336724v1_genomic.fna/checkm_input GCF_003367245.1_ASM336724v1_genomic.fna/checkm_result
[2024-01-24 14:41:50,543] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:50,545] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:41:50,568] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:50,568] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:50,569] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003367245.1_ASM336724v1_genomic.fna/markers.fasta)
[2024-01-24 14:41:50,569] [INFO] Task started: Blastn
[2024-01-24 14:41:50,569] [INFO] Running command: blastn -query GCF_003367245.1_ASM336724v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc26da332-f596-4072-9d48-528a76d3d837/dqc_reference/reference_markers_gtdb.fasta -out GCF_003367245.1_ASM336724v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:51,452] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:51,456] [INFO] Selected 12 target genomes.
[2024-01-24 14:41:51,457] [INFO] Target genome list was writen to GCF_003367245.1_ASM336724v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:51,473] [INFO] Task started: fastANI
[2024-01-24 14:41:51,473] [INFO] Running command: fastANI --query /var/lib/cwl/stg65f855df-47a4-4433-a8a5-d3421edfff5d/GCF_003367245.1_ASM336724v1_genomic.fna.gz --refList GCF_003367245.1_ASM336724v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003367245.1_ASM336724v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:42:04,852] [INFO] Task succeeded: fastANI
[2024-01-24 14:42:04,871] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:42:04,872] [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_003367245.1	s__Pontibacter diazotrophicus	100.0	2079	2086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010015475.1	s__Pontibacter sp010015475	88.5801	1593	2086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009931655.1	s__Pontibacter russatus	79.1186	751	2086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003585765.1	s__Pontibacter actiniarum	78.6987	551	2086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001611675.1	s__Pontibacter akesuensis	78.5353	571	2086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	3	-
GCF_900188175.1	s__Pontibacter ummariensis	78.4875	588	2086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006385705.1	s__Pontibacter sp006385705	78.4048	526	2086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001907195.1	s__Pontibacter sp001907195	78.2665	507	2086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576375.1	s__Pontibacter oryzae	78.2551	414	2086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054055.1	s__Pontibacter mucosus	78.2122	490	2086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113285.1	s__Pontibacter chinhatensis	78.0201	501	2086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018122615.1	s__Pontibacter sp018122615	77.6619	323	2086	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:42:04,873] [INFO] GTDB search result was written to GCF_003367245.1_ASM336724v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:42:04,874] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:42:04,878] [INFO] DFAST_QC result json was written to GCF_003367245.1_ASM336724v1_genomic.fna/dqc_result.json
[2024-01-24 14:42:04,878] [INFO] DFAST_QC completed!
[2024-01-24 14:42:04,878] [INFO] Total running time: 0h2m31s