[2024-01-24 12:14:34,104] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:34,105] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:34,105] [INFO] DQC Reference Directory: /var/lib/cwl/stgcbb081db-90a6-4809-9dbf-727badb61a49/dqc_reference
[2024-01-24 12:14:35,262] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,262] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,262] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd6f48cd-2f4e-4363-bc6d-3fee34c9c2cd/GCF_003384935.1_ASM338493v1_genomic.fna.gz | prodigal -d GCF_003384935.1_ASM338493v1_genomic.fna/cds.fna -a GCF_003384935.1_ASM338493v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:43,459] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:43,459] [INFO] Task started: HMMsearch
[2024-01-24 12:14:43,459] [INFO] Running command: hmmsearch --tblout GCF_003384935.1_ASM338493v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcbb081db-90a6-4809-9dbf-727badb61a49/dqc_reference/reference_markers.hmm GCF_003384935.1_ASM338493v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:43,765] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:43,766] [INFO] Found 6/6 markers.
[2024-01-24 12:14:43,795] [INFO] Query marker FASTA was written to GCF_003384935.1_ASM338493v1_genomic.fna/markers.fasta
[2024-01-24 12:14:43,795] [INFO] Task started: Blastn
[2024-01-24 12:14:43,795] [INFO] Running command: blastn -query GCF_003384935.1_ASM338493v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbb081db-90a6-4809-9dbf-727badb61a49/dqc_reference/reference_markers.fasta -out GCF_003384935.1_ASM338493v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:44,503] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:44,506] [INFO] Selected 13 target genomes.
[2024-01-24 12:14:44,506] [INFO] Target genome list was writen to GCF_003384935.1_ASM338493v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:44,572] [INFO] Task started: fastANI
[2024-01-24 12:14:44,572] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd6f48cd-2f4e-4363-bc6d-3fee34c9c2cd/GCF_003384935.1_ASM338493v1_genomic.fna.gz --refList GCF_003384935.1_ASM338493v1_genomic.fna/target_genomes.txt --output GCF_003384935.1_ASM338493v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:53,958] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:53,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcbb081db-90a6-4809-9dbf-727badb61a49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:53,958] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcbb081db-90a6-4809-9dbf-727badb61a49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:53,967] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:14:53,967] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:53,967] [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
Lutibacter oceani	strain=325-5	GCA_003384935.1	1853311	1853311	type	True	100.0	1119	1120	95	conclusive
Lutibacter oceani	strain=JCM30924	GCA_003426875.1	1853311	1853311	type	True	99.9979	1118	1120	95	conclusive
Lutibacter flavus	strain=DSM 27993	GCA_900188355.1	691689	691689	type	True	82.5323	819	1120	95	below_threshold
Lutibacter citreus	strain=1KV19	GCA_003260195.1	2138210	2138210	type	True	80.4941	623	1120	95	below_threshold
Lutibacter maritimus	strain=DSM 24450	GCA_900116115.1	593133	593133	type	True	80.2502	654	1120	95	below_threshold
Lutibacter agarilyticus	strain=DSM 29150	GCA_900188235.1	1109740	1109740	type	True	80.0581	579	1120	95	below_threshold
Lutibacter oricola	strain=DSM 24956	GCA_900106565.1	762486	762486	type	True	79.5971	561	1120	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	77.3527	231	1120	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	77.3303	261	1120	95	below_threshold
Polaribacter vadi	strain=LPB0003	GCA_001761365.1	1774273	1774273	type	True	77.066	263	1120	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	77.0234	223	1120	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	77.0064	241	1120	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.7557	227	1120	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:53,968] [INFO] DFAST Taxonomy check result was written to GCF_003384935.1_ASM338493v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:53,969] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:53,969] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:53,969] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcbb081db-90a6-4809-9dbf-727badb61a49/dqc_reference/checkm_data
[2024-01-24 12:14:53,970] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:54,006] [INFO] Task started: CheckM
[2024-01-24 12:14:54,006] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003384935.1_ASM338493v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003384935.1_ASM338493v1_genomic.fna/checkm_input GCF_003384935.1_ASM338493v1_genomic.fna/checkm_result
[2024-01-24 12:15:21,321] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:21,322] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:21,351] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:21,351] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:21,352] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003384935.1_ASM338493v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:21,352] [INFO] Task started: Blastn
[2024-01-24 12:15:21,352] [INFO] Running command: blastn -query GCF_003384935.1_ASM338493v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcbb081db-90a6-4809-9dbf-727badb61a49/dqc_reference/reference_markers_gtdb.fasta -out GCF_003384935.1_ASM338493v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:22,302] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:22,305] [INFO] Selected 14 target genomes.
[2024-01-24 12:15:22,305] [INFO] Target genome list was writen to GCF_003384935.1_ASM338493v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:22,312] [INFO] Task started: fastANI
[2024-01-24 12:15:22,313] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd6f48cd-2f4e-4363-bc6d-3fee34c9c2cd/GCF_003384935.1_ASM338493v1_genomic.fna.gz --refList GCF_003384935.1_ASM338493v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003384935.1_ASM338493v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:32,238] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:32,246] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:32,247] [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_003384935.1	s__Lutibacter oceani	100.0	1119	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900188355.1	s__Lutibacter flavus	82.557	816	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646675.1	s__Lutibacter litoralis	81.6945	745	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003260195.1	s__Lutibacter citreus	80.504	621	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116115.1	s__Lutibacter maritimus	80.2657	652	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016342705.1	s__Lutibacter sp016342705	80.1318	654	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188235.1	s__Lutibacter agarilyticus	80.0403	581	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004195315.1	s__Lutibacter sp004195315	79.9459	383	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139515.1	s__Lutibacter sp013139515	79.8408	490	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012524075.1	s__Lutibacter sp012524075	79.8197	548	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004121075.1	s__Lutibacter sp004121075	79.5751	533	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013041805.1	s__Lutibacter sp013041805	79.532	495	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	0.99	0.99	2	-
GCA_015767395.1	s__Lutibacter sp015767395	78.9646	355	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018054895.1	s__Lutibacter sp018054895	78.8014	385	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:32,248] [INFO] GTDB search result was written to GCF_003384935.1_ASM338493v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:32,248] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:32,250] [INFO] DFAST_QC result json was written to GCF_003384935.1_ASM338493v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:32,250] [INFO] DFAST_QC completed!
[2024-01-24 12:15:32,251] [INFO] Total running time: 0h0m58s