[2024-01-24 12:14:35,322] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:35,323] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:35,327] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d2b4918-cba2-41f2-84c9-a47307a7a5dc/dqc_reference
[2024-01-24 12:14:36,731] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:36,732] [INFO] Task started: Prodigal
[2024-01-24 12:14:36,733] [INFO] Running command: gunzip -c /var/lib/cwl/stg0d1d7128-6199-4344-b20c-8744f8f27f5c/GCF_010119545.1_ASM1011954v1_genomic.fna.gz | prodigal -d GCF_010119545.1_ASM1011954v1_genomic.fna/cds.fna -a GCF_010119545.1_ASM1011954v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:54,163] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:54,163] [INFO] Task started: HMMsearch
[2024-01-24 12:14:54,163] [INFO] Running command: hmmsearch --tblout GCF_010119545.1_ASM1011954v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d2b4918-cba2-41f2-84c9-a47307a7a5dc/dqc_reference/reference_markers.hmm GCF_010119545.1_ASM1011954v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:54,454] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:54,455] [INFO] Found 6/6 markers.
[2024-01-24 12:14:54,494] [INFO] Query marker FASTA was written to GCF_010119545.1_ASM1011954v1_genomic.fna/markers.fasta
[2024-01-24 12:14:54,495] [INFO] Task started: Blastn
[2024-01-24 12:14:54,495] [INFO] Running command: blastn -query GCF_010119545.1_ASM1011954v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d2b4918-cba2-41f2-84c9-a47307a7a5dc/dqc_reference/reference_markers.fasta -out GCF_010119545.1_ASM1011954v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:55,118] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:55,122] [INFO] Selected 9 target genomes.
[2024-01-24 12:14:55,123] [INFO] Target genome list was writen to GCF_010119545.1_ASM1011954v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:55,127] [INFO] Task started: fastANI
[2024-01-24 12:14:55,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d1d7128-6199-4344-b20c-8744f8f27f5c/GCF_010119545.1_ASM1011954v1_genomic.fna.gz --refList GCF_010119545.1_ASM1011954v1_genomic.fna/target_genomes.txt --output GCF_010119545.1_ASM1011954v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:04,273] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:04,274] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d2b4918-cba2-41f2-84c9-a47307a7a5dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:04,274] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d2b4918-cba2-41f2-84c9-a47307a7a5dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:04,283] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:04,284] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:04,284] [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 fetidus	strain=BT213	GCA_010119545.1	2700082	2700082	type	True	100.0	1331	1334	95	conclusive
Pontibacter pudoricolor	strain=BT214	GCA_010092985.1	2694930	2694930	type	True	83.2604	942	1334	95	below_threshold
Pontibacter deserti	strain=JC215	GCA_023630255.1	1343896	1343896	type	True	82.5706	878	1334	95	below_threshold
Pontibacter burrus	strain=BT327	GCA_010686685.1	2704466	2704466	type	True	81.538	799	1334	95	below_threshold
Pontibacter ruber	strain=JC213	GCA_023630205.1	1343895	1343895	type	True	78.8465	530	1334	95	below_threshold
Pontibacter arcticus	strain=2b14	GCA_003284895.1	2080288	2080288	type	True	78.5022	462	1334	95	below_threshold
Pontibacter cellulosilyticus	strain=SD6	GCA_014306105.1	1720253	1720253	type	True	78.4301	467	1334	95	below_threshold
Pontibacter mangrovi	strain=HB172049	GCA_006385705.1	2589816	2589816	type	True	78.1644	418	1334	95	below_threshold
Pontibacter silvestris	strain=XAAS-R86T	GCA_020907275.1	2305183	2305183	type	True	77.3345	220	1334	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:04,285] [INFO] DFAST Taxonomy check result was written to GCF_010119545.1_ASM1011954v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:04,286] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:04,286] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:04,286] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d2b4918-cba2-41f2-84c9-a47307a7a5dc/dqc_reference/checkm_data
[2024-01-24 12:15:04,288] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:04,330] [INFO] Task started: CheckM
[2024-01-24 12:15:04,331] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010119545.1_ASM1011954v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010119545.1_ASM1011954v1_genomic.fna/checkm_input GCF_010119545.1_ASM1011954v1_genomic.fna/checkm_result
[2024-01-24 12:15:54,483] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:54,484] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:54,505] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:54,506] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:54,506] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010119545.1_ASM1011954v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:54,507] [INFO] Task started: Blastn
[2024-01-24 12:15:54,507] [INFO] Running command: blastn -query GCF_010119545.1_ASM1011954v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d2b4918-cba2-41f2-84c9-a47307a7a5dc/dqc_reference/reference_markers_gtdb.fasta -out GCF_010119545.1_ASM1011954v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:55,294] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:55,298] [INFO] Selected 6 target genomes.
[2024-01-24 12:15:55,298] [INFO] Target genome list was writen to GCF_010119545.1_ASM1011954v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:55,304] [INFO] Task started: fastANI
[2024-01-24 12:15:55,304] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d1d7128-6199-4344-b20c-8744f8f27f5c/GCF_010119545.1_ASM1011954v1_genomic.fna.gz --refList GCF_010119545.1_ASM1011954v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010119545.1_ASM1011954v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:03,052] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:03,064] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:03,064] [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_010119545.1	s__Pontibacter fetidus	100.0	1331	1334	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_010092985.1	s__Pontibacter pudoricolor	83.2488	943	1334	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	83.2365	912	1334	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014297265.1	s__Pontibacter sp014297265	82.6403	868	1334	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212495.1	s__Pontibacter sp014212495	82.2809	889	1334	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	81.565	795	1334	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 12:16:03,067] [INFO] GTDB search result was written to GCF_010119545.1_ASM1011954v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:03,067] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:03,074] [INFO] DFAST_QC result json was written to GCF_010119545.1_ASM1011954v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:03,074] [INFO] DFAST_QC completed!
[2024-01-24 12:16:03,075] [INFO] Total running time: 0h1m28s