[2024-01-24 11:44:38,163] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:38,164] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:38,165] [INFO] DQC Reference Directory: /var/lib/cwl/stg41a9a6d9-2e84-45d2-a041-e040a774242b/dqc_reference
[2024-01-24 11:44:41,485] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:41,486] [INFO] Task started: Prodigal
[2024-01-24 11:44:41,486] [INFO] Running command: gunzip -c /var/lib/cwl/stg53a30e45-80f9-469b-8f79-daf7b56e356e/GCF_003576375.1_ASM357637v1_genomic.fna.gz | prodigal -d GCF_003576375.1_ASM357637v1_genomic.fna/cds.fna -a GCF_003576375.1_ASM357637v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:45:02,590] [INFO] Task succeeded: Prodigal
[2024-01-24 11:45:02,591] [INFO] Task started: HMMsearch
[2024-01-24 11:45:02,591] [INFO] Running command: hmmsearch --tblout GCF_003576375.1_ASM357637v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41a9a6d9-2e84-45d2-a041-e040a774242b/dqc_reference/reference_markers.hmm GCF_003576375.1_ASM357637v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:45:02,880] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:45:02,882] [INFO] Found 6/6 markers.
[2024-01-24 11:45:02,920] [INFO] Query marker FASTA was written to GCF_003576375.1_ASM357637v1_genomic.fna/markers.fasta
[2024-01-24 11:45:02,921] [INFO] Task started: Blastn
[2024-01-24 11:45:02,921] [INFO] Running command: blastn -query GCF_003576375.1_ASM357637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41a9a6d9-2e84-45d2-a041-e040a774242b/dqc_reference/reference_markers.fasta -out GCF_003576375.1_ASM357637v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:03,514] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:03,518] [INFO] Selected 15 target genomes.
[2024-01-24 11:45:03,518] [INFO] Target genome list was writen to GCF_003576375.1_ASM357637v1_genomic.fna/target_genomes.txt
[2024-01-24 11:45:03,525] [INFO] Task started: fastANI
[2024-01-24 11:45:03,525] [INFO] Running command: fastANI --query /var/lib/cwl/stg53a30e45-80f9-469b-8f79-daf7b56e356e/GCF_003576375.1_ASM357637v1_genomic.fna.gz --refList GCF_003576375.1_ASM357637v1_genomic.fna/target_genomes.txt --output GCF_003576375.1_ASM357637v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:17,285] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:17,286] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41a9a6d9-2e84-45d2-a041-e040a774242b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:17,286] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41a9a6d9-2e84-45d2-a041-e040a774242b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:17,299] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:45:17,299] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:45:17,300] [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 oryzae	strain=KIRAN	GCA_003576375.1	2304593	2304593	type	True	100.0	1402	1405	95	conclusive
Pontibacter actiniarum	strain=DSM 19842	GCA_003585765.1	323450	323450	type	True	80.5098	765	1405	95	below_threshold
Pontibacter actiniarum	strain=DSM 19842	GCA_000472485.1	323450	323450	type	True	80.4996	760	1405	95	below_threshold
Pontibacter mangrovi	strain=HB172049	GCA_006385705.1	2589816	2589816	type	True	80.0675	683	1405	95	below_threshold
Pontibacter flavimaris	strain=S10-8	GCA_001907195.1	1797110	1797110	type	True	79.6937	660	1405	95	below_threshold
Pontibacter chinhatensis	strain=LP51	GCA_900113285.1	1436961	1436961	type	True	79.4557	631	1405	95	below_threshold
Pontibacter mucosus	strain=DSM 100162	GCA_003054055.1	1649266	1649266	type	True	79.4443	626	1405	95	below_threshold
Pontibacter korlensis	strain=X14-1T	GCA_000973725.1	400092	400092	type	True	79.2023	554	1405	95	below_threshold
Pontibacter akesuensis	strain=DSM 18820	GCA_900116885.1	388950	388950	type	True	79.026	599	1405	95	below_threshold
Pontibacter ummariensis	strain=NKM1	GCA_900188175.1	1610492	1610492	type	True	78.3207	434	1405	95	below_threshold
Pontibacter cellulosilyticus	strain=SD6	GCA_014306105.1	1720253	1720253	type	True	78.1983	457	1405	95	below_threshold
Pontibacter arcticus	strain=2b14	GCA_003284895.1	2080288	2080288	type	True	77.7901	362	1405	95	below_threshold
Rufibacter sediminis	strain=CGMCC 1.16289	GCA_024436355.1	2762756	2762756	type	True	76.6327	128	1405	95	below_threshold
Rufibacter hautae	strain=NBS58-1	GCA_008271695.1	2595005	2595005	type	True	76.1583	137	1405	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:45:17,302] [INFO] DFAST Taxonomy check result was written to GCF_003576375.1_ASM357637v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:17,302] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:17,303] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:17,303] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41a9a6d9-2e84-45d2-a041-e040a774242b/dqc_reference/checkm_data
[2024-01-24 11:45:17,305] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:17,347] [INFO] Task started: CheckM
[2024-01-24 11:45:17,347] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003576375.1_ASM357637v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003576375.1_ASM357637v1_genomic.fna/checkm_input GCF_003576375.1_ASM357637v1_genomic.fna/checkm_result
[2024-01-24 11:46:14,609] [INFO] Task succeeded: CheckM
[2024-01-24 11:46:14,611] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:46:14,632] [INFO] ===== Completeness check finished =====
[2024-01-24 11:46:14,633] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:46:14,633] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003576375.1_ASM357637v1_genomic.fna/markers.fasta)
[2024-01-24 11:46:14,634] [INFO] Task started: Blastn
[2024-01-24 11:46:14,634] [INFO] Running command: blastn -query GCF_003576375.1_ASM357637v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41a9a6d9-2e84-45d2-a041-e040a774242b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003576375.1_ASM357637v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:46:15,400] [INFO] Task succeeded: Blastn
[2024-01-24 11:46:15,404] [INFO] Selected 11 target genomes.
[2024-01-24 11:46:15,404] [INFO] Target genome list was writen to GCF_003576375.1_ASM357637v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:46:15,415] [INFO] Task started: fastANI
[2024-01-24 11:46:15,415] [INFO] Running command: fastANI --query /var/lib/cwl/stg53a30e45-80f9-469b-8f79-daf7b56e356e/GCF_003576375.1_ASM357637v1_genomic.fna.gz --refList GCF_003576375.1_ASM357637v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003576375.1_ASM357637v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:25,360] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:25,378] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:25,378] [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_003576375.1	s__Pontibacter oryzae	100.0	1402	1405	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_003585765.1	s__Pontibacter actiniarum	80.5004	767	1405	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	80.0595	684	1405	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	79.6973	660	1405	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	79.4542	632	1405	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	79.4508	626	1405	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	79.1913	555	1405	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001611675.1	s__Pontibacter akesuensis	79.0259	603	1405	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	78.3178	435	1405	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014306105.1	s__Pontibacter sp014306105	78.1903	458	1405	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010686685.1	s__Pontibacter burrus	78.0702	351	1405	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 11:46:25,380] [INFO] GTDB search result was written to GCF_003576375.1_ASM357637v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:25,381] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:25,384] [INFO] DFAST_QC result json was written to GCF_003576375.1_ASM357637v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:25,385] [INFO] DFAST_QC completed!
[2024-01-24 11:46:25,385] [INFO] Total running time: 0h1m47s