[2024-01-24 10:48:09,163] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:48:09,168] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:48:09,168] [INFO] DQC Reference Directory: /var/lib/cwl/stga2de5e95-db83-4859-9940-454367419301/dqc_reference
[2024-01-24 10:48:23,956] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:48:23,958] [INFO] Task started: Prodigal
[2024-01-24 10:48:23,959] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a262910-7981-487c-aebe-961170f66bf0/GCF_014651555.1_ASM1465155v1_genomic.fna.gz | prodigal -d GCF_014651555.1_ASM1465155v1_genomic.fna/cds.fna -a GCF_014651555.1_ASM1465155v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:50,174] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:50,174] [INFO] Task started: HMMsearch
[2024-01-24 10:48:50,174] [INFO] Running command: hmmsearch --tblout GCF_014651555.1_ASM1465155v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2de5e95-db83-4859-9940-454367419301/dqc_reference/reference_markers.hmm GCF_014651555.1_ASM1465155v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:50,480] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:50,481] [INFO] Found 6/6 markers.
[2024-01-24 10:48:50,525] [INFO] Query marker FASTA was written to GCF_014651555.1_ASM1465155v1_genomic.fna/markers.fasta
[2024-01-24 10:48:50,525] [INFO] Task started: Blastn
[2024-01-24 10:48:50,526] [INFO] Running command: blastn -query GCF_014651555.1_ASM1465155v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2de5e95-db83-4859-9940-454367419301/dqc_reference/reference_markers.fasta -out GCF_014651555.1_ASM1465155v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:51,150] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:51,155] [INFO] Selected 15 target genomes.
[2024-01-24 10:48:51,155] [INFO] Target genome list was writen to GCF_014651555.1_ASM1465155v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:51,205] [INFO] Task started: fastANI
[2024-01-24 10:48:51,205] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a262910-7981-487c-aebe-961170f66bf0/GCF_014651555.1_ASM1465155v1_genomic.fna.gz --refList GCF_014651555.1_ASM1465155v1_genomic.fna/target_genomes.txt --output GCF_014651555.1_ASM1465155v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:49:07,915] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:07,915] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2de5e95-db83-4859-9940-454367419301/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:49:07,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2de5e95-db83-4859-9940-454367419301/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:49:07,928] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 10:49:07,929] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:49:07,929] [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 akesuensis	strain=KCTC 12758	GCA_014651555.1	388950	388950	type	True	100.0	1600	1600	95	conclusive
Pontibacter akesuensis	strain=AKS 1T	GCA_001611675.1	388950	388950	type	True	99.9987	1598	1600	95	conclusive
Pontibacter akesuensis	strain=DSM 18820	GCA_900116885.1	388950	388950	type	True	99.994	1596	1600	95	conclusive
Pontibacter actiniarum	strain=DSM 19842	GCA_000472485.1	323450	323450	type	True	80.0804	802	1600	95	below_threshold
Pontibacter actiniarum	strain=DSM 19842	GCA_003585765.1	323450	323450	type	True	80.074	807	1600	95	below_threshold
Pontibacter mangrovi	strain=HB172049	GCA_006385705.1	2589816	2589816	type	True	79.7467	732	1600	95	below_threshold
Pontibacter mucosus	strain=DSM 100162	GCA_003054055.1	1649266	1649266	type	True	79.3003	715	1600	95	below_threshold
Pontibacter chinhatensis	strain=LP51	GCA_900113285.1	1436961	1436961	type	True	79.1322	702	1600	95	below_threshold
Pontibacter oryzae	strain=KIRAN	GCA_003576375.1	2304593	2304593	type	True	79.0454	599	1600	95	below_threshold
Pontibacter russatus	strain=BT326	GCA_009931655.1	2694929	2694929	type	True	78.6409	619	1600	95	below_threshold
Pontibacter pamirensis	strain=TRT317	GCA_010015475.1	2562824	2562824	type	True	78.4509	555	1600	95	below_threshold
Pontibacter ummariensis	strain=NKM1	GCA_900188175.1	1610492	1610492	type	True	78.3472	522	1600	95	below_threshold
Pontibacter ruber	strain=JC213	GCA_023630205.1	1343895	1343895	type	True	78.2665	519	1600	95	below_threshold
Pontibacter deserti	strain=JC215	GCA_023630255.1	1343896	1343896	type	True	77.6696	365	1600	95	below_threshold
Pontibacter arcticus	strain=2b14	GCA_003284895.1	2080288	2080288	type	True	77.4389	364	1600	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:49:07,932] [INFO] DFAST Taxonomy check result was written to GCF_014651555.1_ASM1465155v1_genomic.fna/tc_result.tsv
[2024-01-24 10:49:07,932] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:49:07,933] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:49:07,933] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2de5e95-db83-4859-9940-454367419301/dqc_reference/checkm_data
[2024-01-24 10:49:07,934] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:49:07,988] [INFO] Task started: CheckM
[2024-01-24 10:49:07,988] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651555.1_ASM1465155v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651555.1_ASM1465155v1_genomic.fna/checkm_input GCF_014651555.1_ASM1465155v1_genomic.fna/checkm_result
[2024-01-24 10:50:19,935] [INFO] Task succeeded: CheckM
[2024-01-24 10:50:19,937] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:50:19,963] [INFO] ===== Completeness check finished =====
[2024-01-24 10:50:19,964] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:50:19,964] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651555.1_ASM1465155v1_genomic.fna/markers.fasta)
[2024-01-24 10:50:19,965] [INFO] Task started: Blastn
[2024-01-24 10:50:19,965] [INFO] Running command: blastn -query GCF_014651555.1_ASM1465155v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga2de5e95-db83-4859-9940-454367419301/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651555.1_ASM1465155v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:50:20,793] [INFO] Task succeeded: Blastn
[2024-01-24 10:50:20,797] [INFO] Selected 11 target genomes.
[2024-01-24 10:50:20,797] [INFO] Target genome list was writen to GCF_014651555.1_ASM1465155v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:50:20,826] [INFO] Task started: fastANI
[2024-01-24 10:50:20,826] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a262910-7981-487c-aebe-961170f66bf0/GCF_014651555.1_ASM1465155v1_genomic.fna.gz --refList GCF_014651555.1_ASM1465155v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651555.1_ASM1465155v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:50:32,174] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:32,187] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:50:32,187] [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_001611675.1	s__Pontibacter akesuensis	99.9987	1598	1600	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_003585765.1	s__Pontibacter actiniarum	80.0915	804	1600	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	79.7541	731	1600	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	79.5717	770	1600	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	79.2901	717	1600	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	79.1219	704	1600	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	79.0527	598	1600	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	78.6439	618	1600	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	78.4373	579	1600	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188175.1	s__Pontibacter ummariensis	78.3482	523	1600	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000373265.1	s__Pontibacter roseus	78.2057	504	1600	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 10:50:32,188] [INFO] GTDB search result was written to GCF_014651555.1_ASM1465155v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:50:32,189] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:50:32,192] [INFO] DFAST_QC result json was written to GCF_014651555.1_ASM1465155v1_genomic.fna/dqc_result.json
[2024-01-24 10:50:32,193] [INFO] DFAST_QC completed!
[2024-01-24 10:50:32,193] [INFO] Total running time: 0h2m23s