[2024-01-24 11:35:22,743] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:22,749] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:22,749] [INFO] DQC Reference Directory: /var/lib/cwl/stg5525c9fb-b9a3-404a-b31e-4014249d5e4b/dqc_reference
[2024-01-24 11:35:26,248] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:26,249] [INFO] Task started: Prodigal
[2024-01-24 11:35:26,249] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d37f8b7-c7c9-4d3b-8e8a-c4434fbb1496/GCF_010686685.1_ASM1068668v1_genomic.fna.gz | prodigal -d GCF_010686685.1_ASM1068668v1_genomic.fna/cds.fna -a GCF_010686685.1_ASM1068668v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:44,964] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:44,964] [INFO] Task started: HMMsearch
[2024-01-24 11:35:44,964] [INFO] Running command: hmmsearch --tblout GCF_010686685.1_ASM1068668v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5525c9fb-b9a3-404a-b31e-4014249d5e4b/dqc_reference/reference_markers.hmm GCF_010686685.1_ASM1068668v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:45,303] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:45,305] [INFO] Found 6/6 markers.
[2024-01-24 11:35:45,346] [INFO] Query marker FASTA was written to GCF_010686685.1_ASM1068668v1_genomic.fna/markers.fasta
[2024-01-24 11:35:45,346] [INFO] Task started: Blastn
[2024-01-24 11:35:45,347] [INFO] Running command: blastn -query GCF_010686685.1_ASM1068668v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5525c9fb-b9a3-404a-b31e-4014249d5e4b/dqc_reference/reference_markers.fasta -out GCF_010686685.1_ASM1068668v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:45,975] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:45,980] [INFO] Selected 15 target genomes.
[2024-01-24 11:35:45,980] [INFO] Target genome list was writen to GCF_010686685.1_ASM1068668v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:45,987] [INFO] Task started: fastANI
[2024-01-24 11:35:45,988] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d37f8b7-c7c9-4d3b-8e8a-c4434fbb1496/GCF_010686685.1_ASM1068668v1_genomic.fna.gz --refList GCF_010686685.1_ASM1068668v1_genomic.fna/target_genomes.txt --output GCF_010686685.1_ASM1068668v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:59,953] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:59,953] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5525c9fb-b9a3-404a-b31e-4014249d5e4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:59,954] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5525c9fb-b9a3-404a-b31e-4014249d5e4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:59,970] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:59,970] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:59,971] [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 burrus	strain=BT327	GCA_010686685.1	2704466	2704466	type	True	100.0	1424	1425	95	conclusive
Pontibacter pudoricolor	strain=BT214	GCA_010092985.1	2694930	2694930	type	True	81.528	847	1425	95	below_threshold
Pontibacter fetidus	strain=BT213	GCA_010119545.1	2700082	2700082	type	True	81.4818	786	1425	95	below_threshold
Pontibacter deserti	strain=JC215	GCA_023630255.1	1343896	1343896	type	True	80.9361	732	1425	95	below_threshold
Pontibacter ruber	strain=JC213	GCA_023630205.1	1343895	1343895	type	True	78.73	477	1425	95	below_threshold
Pontibacter arcticus	strain=2b14	GCA_003284895.1	2080288	2080288	type	True	78.412	391	1425	95	below_threshold
Pontibacter cellulosilyticus	strain=SD6	GCA_014306105.1	1720253	1720253	type	True	78.2979	423	1425	95	below_threshold
Pontibacter mangrovi	strain=HB172049	GCA_006385705.1	2589816	2589816	type	True	78.2272	400	1425	95	below_threshold
Pontibacter aquaedesilientis	strain=JH31	GCA_014773225.1	2766980	2766980	type	True	78.1688	327	1425	95	below_threshold
Pontibacter actiniarum	strain=DSM 19842	GCA_000472485.1	323450	323450	type	True	78.1265	365	1425	95	below_threshold
Pontibacter actiniarum	strain=DSM 19842	GCA_003585765.1	323450	323450	type	True	78.1105	370	1425	95	below_threshold
Pontibacter pamirensis	strain=TRT317	GCA_010015475.1	2562824	2562824	type	True	77.5892	318	1425	95	below_threshold
Pontibacter silvestris	strain=XAAS-R86T	GCA_020907275.1	2305183	2305183	type	True	77.5758	212	1425	95	below_threshold
Adhaeribacter arboris	strain=HMF7605	GCA_003023845.1	2072846	2072846	type	True	75.9989	73	1425	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:59,975] [INFO] DFAST Taxonomy check result was written to GCF_010686685.1_ASM1068668v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:59,975] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:59,976] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:59,976] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5525c9fb-b9a3-404a-b31e-4014249d5e4b/dqc_reference/checkm_data
[2024-01-24 11:35:59,977] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:36:00,025] [INFO] Task started: CheckM
[2024-01-24 11:36:00,026] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010686685.1_ASM1068668v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010686685.1_ASM1068668v1_genomic.fna/checkm_input GCF_010686685.1_ASM1068668v1_genomic.fna/checkm_result
[2024-01-24 11:36:53,725] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:53,727] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:53,746] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:53,747] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:53,747] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010686685.1_ASM1068668v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:53,747] [INFO] Task started: Blastn
[2024-01-24 11:36:53,748] [INFO] Running command: blastn -query GCF_010686685.1_ASM1068668v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5525c9fb-b9a3-404a-b31e-4014249d5e4b/dqc_reference/reference_markers_gtdb.fasta -out GCF_010686685.1_ASM1068668v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:54,626] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:54,631] [INFO] Selected 10 target genomes.
[2024-01-24 11:36:54,631] [INFO] Target genome list was writen to GCF_010686685.1_ASM1068668v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:54,639] [INFO] Task started: fastANI
[2024-01-24 11:36:54,639] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d37f8b7-c7c9-4d3b-8e8a-c4434fbb1496/GCF_010686685.1_ASM1068668v1_genomic.fna.gz --refList GCF_010686685.1_ASM1068668v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010686685.1_ASM1068668v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:05,454] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:05,466] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:37:05,466] [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_010686685.1	s__Pontibacter burrus	100.0	1424	1425	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_014212495.1	s__Pontibacter sp014212495	83.5685	998	1425	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	81.5348	858	1425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010092985.1	s__Pontibacter pudoricolor	81.5091	852	1425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119545.1	s__Pontibacter fetidus	81.4968	783	1425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297265.1	s__Pontibacter sp014297265	80.896	738	1425	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	78.1113	370	1425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010015475.1	s__Pontibacter sp010015475	77.5705	320	1425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003023845.1	s__Adhaeribacter arboris	75.9785	74	1425	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Adhaeribacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:37:05,467] [INFO] GTDB search result was written to GCF_010686685.1_ASM1068668v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:05,468] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:05,472] [INFO] DFAST_QC result json was written to GCF_010686685.1_ASM1068668v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:05,472] [INFO] DFAST_QC completed!
[2024-01-24 11:37:05,472] [INFO] Total running time: 0h1m43s