[2024-01-24 14:19:31,947] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:31,949] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:31,949] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ddb36f5-bbdf-4d56-902b-a782b7843807/dqc_reference
[2024-01-24 14:19:33,381] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:33,382] [INFO] Task started: Prodigal
[2024-01-24 14:19:33,382] [INFO] Running command: gunzip -c /var/lib/cwl/stgcdb89f62-e0fe-485f-9b95-74acd3ada1d6/GCF_005281475.1_ASM528147v1_genomic.fna.gz | prodigal -d GCF_005281475.1_ASM528147v1_genomic.fna/cds.fna -a GCF_005281475.1_ASM528147v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:08,375] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:08,376] [INFO] Task started: HMMsearch
[2024-01-24 14:20:08,376] [INFO] Running command: hmmsearch --tblout GCF_005281475.1_ASM528147v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ddb36f5-bbdf-4d56-902b-a782b7843807/dqc_reference/reference_markers.hmm GCF_005281475.1_ASM528147v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:08,708] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:08,709] [INFO] Found 6/6 markers.
[2024-01-24 14:20:08,761] [INFO] Query marker FASTA was written to GCF_005281475.1_ASM528147v1_genomic.fna/markers.fasta
[2024-01-24 14:20:08,761] [INFO] Task started: Blastn
[2024-01-24 14:20:08,761] [INFO] Running command: blastn -query GCF_005281475.1_ASM528147v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ddb36f5-bbdf-4d56-902b-a782b7843807/dqc_reference/reference_markers.fasta -out GCF_005281475.1_ASM528147v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:09,446] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:09,449] [INFO] Selected 10 target genomes.
[2024-01-24 14:20:09,450] [INFO] Target genome list was writen to GCF_005281475.1_ASM528147v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:09,462] [INFO] Task started: fastANI
[2024-01-24 14:20:09,462] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdb89f62-e0fe-485f-9b95-74acd3ada1d6/GCF_005281475.1_ASM528147v1_genomic.fna.gz --refList GCF_005281475.1_ASM528147v1_genomic.fna/target_genomes.txt --output GCF_005281475.1_ASM528147v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:31,009] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:31,010] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ddb36f5-bbdf-4d56-902b-a782b7843807/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:31,010] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ddb36f5-bbdf-4d56-902b-a782b7843807/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:31,024] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:20:31,024] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:31,024] [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
Echinicola rosea	strain=JL3085	GCA_005281475.1	1807691	1807691	type	True	100.0	2021	2021	95	conclusive
Echinicola rosea	strain=CGMCC 1.15407	GCA_014642715.1	1807691	1807691	type	True	99.9815	1970	2021	95	conclusive
Echinicola strongylocentroti	strain=MEBiC08714	GCA_003260975.1	1795355	1795355	type	True	85.5147	1352	2021	95	below_threshold
Echinicola soli	strain=LN3S3	GCA_006575665.1	2591634	2591634	type	True	83.0943	1397	2021	95	below_threshold
Echinicola vietnamensis	strain=DSM 17526	GCA_000325705.1	390884	390884	type	True	83.0914	1276	2021	95	below_threshold
Echinicola marina	strain=SCS 3-6	GCA_020463795.1	2859768	2859768	type	True	80.9596	490	2021	95	below_threshold
Cyclobacterium roseum	strain=SYSU L10180	GCA_010119225.1	2666137	2666137	type	True	76.0728	81	2021	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:31,026] [INFO] DFAST Taxonomy check result was written to GCF_005281475.1_ASM528147v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:31,026] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:31,026] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:31,027] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ddb36f5-bbdf-4d56-902b-a782b7843807/dqc_reference/checkm_data
[2024-01-24 14:20:31,028] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:31,087] [INFO] Task started: CheckM
[2024-01-24 14:20:31,088] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005281475.1_ASM528147v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005281475.1_ASM528147v1_genomic.fna/checkm_input GCF_005281475.1_ASM528147v1_genomic.fna/checkm_result
[2024-01-24 14:21:58,608] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:58,610] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:58,640] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:58,640] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:58,640] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005281475.1_ASM528147v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:58,641] [INFO] Task started: Blastn
[2024-01-24 14:21:58,641] [INFO] Running command: blastn -query GCF_005281475.1_ASM528147v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ddb36f5-bbdf-4d56-902b-a782b7843807/dqc_reference/reference_markers_gtdb.fasta -out GCF_005281475.1_ASM528147v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:59,492] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:59,495] [INFO] Selected 11 target genomes.
[2024-01-24 14:21:59,495] [INFO] Target genome list was writen to GCF_005281475.1_ASM528147v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:59,512] [INFO] Task started: fastANI
[2024-01-24 14:21:59,512] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdb89f62-e0fe-485f-9b95-74acd3ada1d6/GCF_005281475.1_ASM528147v1_genomic.fna.gz --refList GCF_005281475.1_ASM528147v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005281475.1_ASM528147v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:22:18,244] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:18,253] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:22:18,254] [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_005281475.1	s__Echinicola rosea	100.0	2021	2021	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_003260975.1	s__Echinicola strongylocentroti	85.5104	1352	2021	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000325705.1	s__Echinicola vietnamensis	83.1276	1274	2021	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006575665.1	s__Echinicola sp006575665	83.0927	1395	2021	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014841125.1	s__Echinicola sp014841125	78.6889	438	2021	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015533855.1	s__Echinicola sp015533855	78.5172	470	2021	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000373245.1	s__Echinicola pacifica	77.8897	340	2021	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000526355.1	s__Algoriphagus marincola_A	77.4324	70	2021	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900188245.1	s__Belliella buryatensis	76.6971	82	2021	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Belliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010119225.1	s__Cyclobacterium sp010119225	76.0467	84	2021	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:22:18,255] [INFO] GTDB search result was written to GCF_005281475.1_ASM528147v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:22:18,256] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:22:18,259] [INFO] DFAST_QC result json was written to GCF_005281475.1_ASM528147v1_genomic.fna/dqc_result.json
[2024-01-24 14:22:18,259] [INFO] DFAST_QC completed!
[2024-01-24 14:22:18,259] [INFO] Total running time: 0h2m46s