[2024-01-24 14:05:48,650] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:48,652] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:48,652] [INFO] DQC Reference Directory: /var/lib/cwl/stg9fcf1299-b6be-454d-ba8a-45a1930bbcba/dqc_reference
[2024-01-24 14:05:50,025] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:50,026] [INFO] Task started: Prodigal
[2024-01-24 14:05:50,026] [INFO] Running command: gunzip -c /var/lib/cwl/stga1c7fecc-aad2-4300-a009-8597bcf91383/GCF_006385705.1_ASM638570v1_genomic.fna.gz | prodigal -d GCF_006385705.1_ASM638570v1_genomic.fna/cds.fna -a GCF_006385705.1_ASM638570v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:16,709] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:16,710] [INFO] Task started: HMMsearch
[2024-01-24 14:06:16,710] [INFO] Running command: hmmsearch --tblout GCF_006385705.1_ASM638570v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9fcf1299-b6be-454d-ba8a-45a1930bbcba/dqc_reference/reference_markers.hmm GCF_006385705.1_ASM638570v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:17,097] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:17,099] [INFO] Found 6/6 markers.
[2024-01-24 14:06:17,142] [INFO] Query marker FASTA was written to GCF_006385705.1_ASM638570v1_genomic.fna/markers.fasta
[2024-01-24 14:06:17,142] [INFO] Task started: Blastn
[2024-01-24 14:06:17,142] [INFO] Running command: blastn -query GCF_006385705.1_ASM638570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fcf1299-b6be-454d-ba8a-45a1930bbcba/dqc_reference/reference_markers.fasta -out GCF_006385705.1_ASM638570v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:17,828] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:17,832] [INFO] Selected 12 target genomes.
[2024-01-24 14:06:17,832] [INFO] Target genome list was writen to GCF_006385705.1_ASM638570v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:17,837] [INFO] Task started: fastANI
[2024-01-24 14:06:17,838] [INFO] Running command: fastANI --query /var/lib/cwl/stga1c7fecc-aad2-4300-a009-8597bcf91383/GCF_006385705.1_ASM638570v1_genomic.fna.gz --refList GCF_006385705.1_ASM638570v1_genomic.fna/target_genomes.txt --output GCF_006385705.1_ASM638570v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:31,648] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:31,649] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9fcf1299-b6be-454d-ba8a-45a1930bbcba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:31,649] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9fcf1299-b6be-454d-ba8a-45a1930bbcba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:31,661] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:31,661] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:31,662] [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 mangrovi	strain=HB172049	GCA_006385705.1	2589816	2589816	type	True	100.0	1608	1609	95	conclusive
Pontibacter flavimaris	strain=S10-8	GCA_001907195.1	1797110	1797110	type	True	82.8842	1040	1609	95	below_threshold
Pontibacter mucosus	strain=DSM 100162	GCA_003054055.1	1649266	1649266	type	True	82.0402	1003	1609	95	below_threshold
Pontibacter chinhatensis	strain=LP51	GCA_900113285.1	1436961	1436961	type	True	81.7175	979	1609	95	below_threshold
Pontibacter actiniarum	strain=DSM 19842	GCA_003585765.1	323450	323450	type	True	81.5715	888	1609	95	below_threshold
Pontibacter actiniarum	strain=DSM 19842	GCA_000472485.1	323450	323450	type	True	81.5715	887	1609	95	below_threshold
Pontibacter oryzae	strain=KIRAN	GCA_003576375.1	2304593	2304593	type	True	80.2157	675	1609	95	below_threshold
Pontibacter korlensis	strain=X14-1T	GCA_000973725.1	400092	400092	type	True	79.8914	758	1609	95	below_threshold
Pontibacter ruber	strain=JC213	GCA_023630205.1	1343895	1343895	type	True	78.9415	583	1609	95	below_threshold
Pontibacter pamirensis	strain=TRT317	GCA_010015475.1	2562824	2562824	type	True	78.4052	486	1609	95	below_threshold
Pontibacter deserti	strain=JC215	GCA_023630255.1	1343896	1343896	type	True	78.0825	381	1609	95	below_threshold
Pontibacter silvestris	strain=XAAS-R86T	GCA_020907275.1	2305183	2305183	type	True	77.7434	208	1609	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:31,663] [INFO] DFAST Taxonomy check result was written to GCF_006385705.1_ASM638570v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:31,664] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:31,664] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:31,664] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9fcf1299-b6be-454d-ba8a-45a1930bbcba/dqc_reference/checkm_data
[2024-01-24 14:06:31,666] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:31,728] [INFO] Task started: CheckM
[2024-01-24 14:06:31,728] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006385705.1_ASM638570v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006385705.1_ASM638570v1_genomic.fna/checkm_input GCF_006385705.1_ASM638570v1_genomic.fna/checkm_result
[2024-01-24 14:07:42,510] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:42,512] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:42,530] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:42,530] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:42,530] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006385705.1_ASM638570v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:42,531] [INFO] Task started: Blastn
[2024-01-24 14:07:42,531] [INFO] Running command: blastn -query GCF_006385705.1_ASM638570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fcf1299-b6be-454d-ba8a-45a1930bbcba/dqc_reference/reference_markers_gtdb.fasta -out GCF_006385705.1_ASM638570v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:43,357] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:43,360] [INFO] Selected 7 target genomes.
[2024-01-24 14:07:43,361] [INFO] Target genome list was writen to GCF_006385705.1_ASM638570v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:43,366] [INFO] Task started: fastANI
[2024-01-24 14:07:43,367] [INFO] Running command: fastANI --query /var/lib/cwl/stga1c7fecc-aad2-4300-a009-8597bcf91383/GCF_006385705.1_ASM638570v1_genomic.fna.gz --refList GCF_006385705.1_ASM638570v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006385705.1_ASM638570v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:52,060] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:52,073] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:52,073] [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_006385705.1	s__Pontibacter sp006385705	100.0	1608	1609	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_001907195.1	s__Pontibacter sp001907195	82.912	1037	1609	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	82.0482	1002	1609	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	81.7406	976	1609	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	81.5921	886	1609	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003576375.1	s__Pontibacter oryzae	80.2211	674	1609	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000973725.1	s__Pontibacter korlensis	79.9134	757	1609	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:52,075] [INFO] GTDB search result was written to GCF_006385705.1_ASM638570v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:52,075] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:52,078] [INFO] DFAST_QC result json was written to GCF_006385705.1_ASM638570v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:52,078] [INFO] DFAST_QC completed!
[2024-01-24 14:07:52,078] [INFO] Total running time: 0h2m3s