[2024-01-24 10:58:06,469] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:58:06,472] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:58:06,472] [INFO] DQC Reference Directory: /var/lib/cwl/stged60ef67-6447-414b-9fda-4bd6e1bca22c/dqc_reference
[2024-01-24 10:58:09,633] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:58:09,634] [INFO] Task started: Prodigal
[2024-01-24 10:58:09,635] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b278d74-36bc-4a1e-8211-65b110e71f93/GCF_006385135.1_ASM638513v1_genomic.fna.gz | prodigal -d GCF_006385135.1_ASM638513v1_genomic.fna/cds.fna -a GCF_006385135.1_ASM638513v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:21,933] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:21,934] [INFO] Task started: HMMsearch
[2024-01-24 10:58:21,934] [INFO] Running command: hmmsearch --tblout GCF_006385135.1_ASM638513v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged60ef67-6447-414b-9fda-4bd6e1bca22c/dqc_reference/reference_markers.hmm GCF_006385135.1_ASM638513v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:22,246] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:22,247] [INFO] Found 6/6 markers.
[2024-01-24 10:58:22,286] [INFO] Query marker FASTA was written to GCF_006385135.1_ASM638513v1_genomic.fna/markers.fasta
[2024-01-24 10:58:22,286] [INFO] Task started: Blastn
[2024-01-24 10:58:22,286] [INFO] Running command: blastn -query GCF_006385135.1_ASM638513v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged60ef67-6447-414b-9fda-4bd6e1bca22c/dqc_reference/reference_markers.fasta -out GCF_006385135.1_ASM638513v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:22,986] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:22,991] [INFO] Selected 22 target genomes.
[2024-01-24 10:58:22,992] [INFO] Target genome list was writen to GCF_006385135.1_ASM638513v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:23,044] [INFO] Task started: fastANI
[2024-01-24 10:58:23,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b278d74-36bc-4a1e-8211-65b110e71f93/GCF_006385135.1_ASM638513v1_genomic.fna.gz --refList GCF_006385135.1_ASM638513v1_genomic.fna/target_genomes.txt --output GCF_006385135.1_ASM638513v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:37,889] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:37,889] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged60ef67-6447-414b-9fda-4bd6e1bca22c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:37,890] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged60ef67-6447-414b-9fda-4bd6e1bca22c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:37,901] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:58:37,902] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:37,902] [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
Paremcibacter congregatus	strain=ZYLT	GCA_006385135.1	2043170	2043170	type	True	100.0	1393	1396	95	conclusive
Paremcibacter congregatus	strain=ZYL	GCA_002740695.1	2043170	2043170	type	True	99.9712	1364	1396	95	conclusive
Emcibacter nanhaiensis	strain=MCCC 1A06723	GCA_006385175.1	1505037	1505037	type	True	77.5746	206	1396	95	below_threshold
Luteithermobacter gelatinilyticus	strain=MEBiC09520	GCA_005849285.1	2582913	2582913	type	True	76.7098	144	1396	95	below_threshold
Kordiimonas marina	strain=A6E486	GCA_023006325.1	2872312	2872312	type	True	76.3931	54	1396	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:37,904] [INFO] DFAST Taxonomy check result was written to GCF_006385135.1_ASM638513v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:37,904] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:37,904] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:37,904] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged60ef67-6447-414b-9fda-4bd6e1bca22c/dqc_reference/checkm_data
[2024-01-24 10:58:37,905] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:37,949] [INFO] Task started: CheckM
[2024-01-24 10:58:37,949] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006385135.1_ASM638513v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006385135.1_ASM638513v1_genomic.fna/checkm_input GCF_006385135.1_ASM638513v1_genomic.fna/checkm_result
[2024-01-24 10:59:19,035] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:19,037] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:19,060] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:19,060] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:19,061] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006385135.1_ASM638513v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:19,061] [INFO] Task started: Blastn
[2024-01-24 10:59:19,061] [INFO] Running command: blastn -query GCF_006385135.1_ASM638513v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged60ef67-6447-414b-9fda-4bd6e1bca22c/dqc_reference/reference_markers_gtdb.fasta -out GCF_006385135.1_ASM638513v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:20,286] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:20,290] [INFO] Selected 18 target genomes.
[2024-01-24 10:59:20,290] [INFO] Target genome list was writen to GCF_006385135.1_ASM638513v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:20,330] [INFO] Task started: fastANI
[2024-01-24 10:59:20,331] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b278d74-36bc-4a1e-8211-65b110e71f93/GCF_006385135.1_ASM638513v1_genomic.fna.gz --refList GCF_006385135.1_ASM638513v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006385135.1_ASM638513v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:32,318] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:32,339] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:32,339] [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_006385135.1	s__Paremcibacter congregatus	100.0	1393	1396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Paremcibacter	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCA_002401455.1	s__Paremcibacter sp002401455	77.6534	244	1396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Paremcibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013152755.1	s__Paremcibacter sp013152755	77.4767	261	1396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Paremcibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051815.1	s__Paremcibacter sp011051815	77.4349	159	1396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Paremcibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385175.1	s__Emcibacter nanhaiensis	77.4114	203	1396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Emcibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002749135.1	s__Paremcibacter sp002749135	77.3851	270	1396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Paremcibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016765435.1	s__Paremcibacter sp016765435	77.3414	156	1396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Paremcibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002401545.1	s__Paremcibacter sp002401545	77.0799	220	1396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Paremcibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013152615.1	s__Paremcibacter sp013152615	76.9636	158	1396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Paremcibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005849285.1	s__Luteithermobacter gelatinilyticus	76.7264	143	1396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Emcibacteraceae;g__Luteithermobacter	95.0	99.04	99.04	0.96	0.96	2	-
GCA_006226495.1	s__Kordiimonas sp006226495	75.7593	57	1396	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:32,341] [INFO] GTDB search result was written to GCF_006385135.1_ASM638513v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:32,343] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:32,349] [INFO] DFAST_QC result json was written to GCF_006385135.1_ASM638513v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:32,349] [INFO] DFAST_QC completed!
[2024-01-24 10:59:32,350] [INFO] Total running time: 0h1m26s