[2024-01-24 13:18:41,588] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:41,592] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:41,593] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6ce52c5-6959-461c-8241-d68280809bb0/dqc_reference
[2024-01-24 13:18:43,041] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:43,042] [INFO] Task started: Prodigal
[2024-01-24 13:18:43,042] [INFO] Running command: gunzip -c /var/lib/cwl/stg0195fdd1-e63c-4e88-9c13-baacc90b9238/GCF_014332515.1_ASM1433251v1_genomic.fna.gz | prodigal -d GCF_014332515.1_ASM1433251v1_genomic.fna/cds.fna -a GCF_014332515.1_ASM1433251v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:11,686] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:11,687] [INFO] Task started: HMMsearch
[2024-01-24 13:19:11,687] [INFO] Running command: hmmsearch --tblout GCF_014332515.1_ASM1433251v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6ce52c5-6959-461c-8241-d68280809bb0/dqc_reference/reference_markers.hmm GCF_014332515.1_ASM1433251v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:12,000] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:12,002] [INFO] Found 6/6 markers.
[2024-01-24 13:19:12,046] [INFO] Query marker FASTA was written to GCF_014332515.1_ASM1433251v1_genomic.fna/markers.fasta
[2024-01-24 13:19:12,047] [INFO] Task started: Blastn
[2024-01-24 13:19:12,047] [INFO] Running command: blastn -query GCF_014332515.1_ASM1433251v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6ce52c5-6959-461c-8241-d68280809bb0/dqc_reference/reference_markers.fasta -out GCF_014332515.1_ASM1433251v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:12,661] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:12,666] [INFO] Selected 18 target genomes.
[2024-01-24 13:19:12,667] [INFO] Target genome list was writen to GCF_014332515.1_ASM1433251v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:12,678] [INFO] Task started: fastANI
[2024-01-24 13:19:12,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg0195fdd1-e63c-4e88-9c13-baacc90b9238/GCF_014332515.1_ASM1433251v1_genomic.fna.gz --refList GCF_014332515.1_ASM1433251v1_genomic.fna/target_genomes.txt --output GCF_014332515.1_ASM1433251v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:28,969] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:28,970] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6ce52c5-6959-461c-8241-d68280809bb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:28,970] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6ce52c5-6959-461c-8241-d68280809bb0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:28,991] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:28,991] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:28,992] [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 beigongshangensis	strain=T6-1	GCA_014332515.1	2574733	2574733	type	True	100.0	1881	1886	95	conclusive
Botryobacter ruber	strain=SYSU D60016	GCA_003347595.2	2171629	2171629	type	True	78.444	671	1886	95	below_threshold
Pontibacter mangrovi	strain=HB172049	GCA_006385705.1	2589816	2589816	type	True	78.1382	463	1886	95	below_threshold
Pontibacter flavimaris	strain=S10-8	GCA_001907195.1	1797110	1797110	type	True	77.9976	482	1886	95	below_threshold
Pontibacter russatus	strain=BT326	GCA_009931655.1	2694929	2694929	type	True	77.9958	511	1886	95	below_threshold
Pontibacter actiniarum	strain=DSM 19842	GCA_003585765.1	323450	323450	type	True	77.9275	434	1886	95	below_threshold
Pontibacter ruber	strain=JC213	GCA_023630205.1	1343895	1343895	type	True	77.89	427	1886	95	below_threshold
Pontibacter lucknowensis	strain=DM9	GCA_900156415.1	1077936	1077936	type	True	77.8854	346	1886	95	below_threshold
Pontibacter actiniarum	strain=DSM 19842	GCA_000472485.1	323450	323450	type	True	77.8779	440	1886	95	below_threshold
Pontibacter ramchanderi	strain=LP43	GCA_002846395.1	1179743	1179743	type	True	77.7605	400	1886	95	below_threshold
Pontibacter mucosus	strain=DSM 100162	GCA_003054055.1	1649266	1649266	type	True	77.7446	468	1886	95	below_threshold
Pontibacter akesuensis	strain=DSM 18820	GCA_900116885.1	388950	388950	type	True	77.7324	404	1886	95	below_threshold
Pontibacter virosus	strain=DSM 100231	GCA_003096355.1	1765052	1765052	type	True	77.694	407	1886	95	below_threshold
Pontibacter oryzae	strain=KIRAN	GCA_003576375.1	2304593	2304593	type	True	77.6768	307	1886	95	below_threshold
Pontibacter aquaedesilientis	strain=JH31	GCA_014773225.1	2766980	2766980	type	True	77.6491	351	1886	95	below_threshold
Pontibacter silvestris	strain=XAAS-R86T	GCA_020907275.1	2305183	2305183	type	True	77.5618	208	1886	95	below_threshold
Pontibacter pamirensis	strain=TRT317	GCA_010015475.1	2562824	2562824	type	True	77.4484	364	1886	95	below_threshold
Pontibacter deserti	strain=JC215	GCA_023630255.1	1343896	1343896	type	True	77.4397	257	1886	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:28,995] [INFO] DFAST Taxonomy check result was written to GCF_014332515.1_ASM1433251v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:28,995] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:28,995] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:28,996] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6ce52c5-6959-461c-8241-d68280809bb0/dqc_reference/checkm_data
[2024-01-24 13:19:28,997] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:29,067] [INFO] Task started: CheckM
[2024-01-24 13:19:29,067] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014332515.1_ASM1433251v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014332515.1_ASM1433251v1_genomic.fna/checkm_input GCF_014332515.1_ASM1433251v1_genomic.fna/checkm_result
[2024-01-24 13:20:44,090] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:44,091] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:44,114] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:44,114] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:44,115] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014332515.1_ASM1433251v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:44,115] [INFO] Task started: Blastn
[2024-01-24 13:20:44,115] [INFO] Running command: blastn -query GCF_014332515.1_ASM1433251v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6ce52c5-6959-461c-8241-d68280809bb0/dqc_reference/reference_markers_gtdb.fasta -out GCF_014332515.1_ASM1433251v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:44,953] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:44,957] [INFO] Selected 12 target genomes.
[2024-01-24 13:20:44,958] [INFO] Target genome list was writen to GCF_014332515.1_ASM1433251v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:44,984] [INFO] Task started: fastANI
[2024-01-24 13:20:44,984] [INFO] Running command: fastANI --query /var/lib/cwl/stg0195fdd1-e63c-4e88-9c13-baacc90b9238/GCF_014332515.1_ASM1433251v1_genomic.fna.gz --refList GCF_014332515.1_ASM1433251v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014332515.1_ASM1433251v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:57,305] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:57,321] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:57,321] [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_014332515.1	s__Botryobacter beigongshangensis	100.0	1881	1886	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Botryobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008017455.1	s__Botryobacter sp008017455	81.7656	1087	1886	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Botryobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003347595.2	s__Botryobacter ruber	78.4516	668	1886	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Botryobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385705.1	s__Pontibacter sp006385705	78.1382	463	1886	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	78.0028	510	1886	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	77.9174	436	1886	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	77.8774	435	1886	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015686655.1	s__Pontibacter sp015686655	77.8122	346	1886	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846395.1	s__Pontibacter ramchanderi	77.7768	398	1886	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	77.7449	468	1886	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	77.6969	305	1886	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__Pontibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005491705.1	s__SGAir0037 sp005491705	77.2548	313	1886	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Hymenobacteraceae;g__SGAir0037	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:57,323] [INFO] GTDB search result was written to GCF_014332515.1_ASM1433251v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:57,324] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:57,327] [INFO] DFAST_QC result json was written to GCF_014332515.1_ASM1433251v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:57,327] [INFO] DFAST_QC completed!
[2024-01-24 13:20:57,327] [INFO] Total running time: 0h2m16s