[2024-01-24 13:57:55,732] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:55,734] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:55,734] [INFO] DQC Reference Directory: /var/lib/cwl/stgfbea0738-cd44-4b1f-b241-1fbfabf39b34/dqc_reference
[2024-01-24 13:57:57,072] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:57,073] [INFO] Task started: Prodigal
[2024-01-24 13:57:57,073] [INFO] Running command: gunzip -c /var/lib/cwl/stg73a948d0-e5c4-4a7e-88cb-560fd2a143f4/GCF_020531905.1_ASM2053190v1_genomic.fna.gz | prodigal -d GCF_020531905.1_ASM2053190v1_genomic.fna/cds.fna -a GCF_020531905.1_ASM2053190v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:06,734] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:06,735] [INFO] Task started: HMMsearch
[2024-01-24 13:58:06,735] [INFO] Running command: hmmsearch --tblout GCF_020531905.1_ASM2053190v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfbea0738-cd44-4b1f-b241-1fbfabf39b34/dqc_reference/reference_markers.hmm GCF_020531905.1_ASM2053190v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:07,023] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:07,024] [INFO] Found 6/6 markers.
[2024-01-24 13:58:07,051] [INFO] Query marker FASTA was written to GCF_020531905.1_ASM2053190v1_genomic.fna/markers.fasta
[2024-01-24 13:58:07,051] [INFO] Task started: Blastn
[2024-01-24 13:58:07,051] [INFO] Running command: blastn -query GCF_020531905.1_ASM2053190v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbea0738-cd44-4b1f-b241-1fbfabf39b34/dqc_reference/reference_markers.fasta -out GCF_020531905.1_ASM2053190v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:07,743] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:07,746] [INFO] Selected 13 target genomes.
[2024-01-24 13:58:07,746] [INFO] Target genome list was writen to GCF_020531905.1_ASM2053190v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:07,749] [INFO] Task started: fastANI
[2024-01-24 13:58:07,749] [INFO] Running command: fastANI --query /var/lib/cwl/stg73a948d0-e5c4-4a7e-88cb-560fd2a143f4/GCF_020531905.1_ASM2053190v1_genomic.fna.gz --refList GCF_020531905.1_ASM2053190v1_genomic.fna/target_genomes.txt --output GCF_020531905.1_ASM2053190v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:17,867] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:17,868] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfbea0738-cd44-4b1f-b241-1fbfabf39b34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:17,868] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfbea0738-cd44-4b1f-b241-1fbfabf39b34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:17,877] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:17,878] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:17,878] [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
Deefgea salmonis	strain=H3-26	GCA_020531905.1	2875502	2875502	type	True	100.0	1073	1076	95	conclusive
Deefgea rivuli	strain=DSM 18356	GCA_000620145.1	400948	400948	type	True	80.4191	591	1076	95	below_threshold
Deefgea chitinilytica	strain=LMG 24817	GCA_016881405.1	570276	570276	type	True	79.7692	520	1076	95	below_threshold
Chitinibacter bivalviorum	strain=2T18	GCA_013403565.1	2739434	2739434	type	True	78.2481	329	1076	95	below_threshold
Chitinibacter fontanus	strain=STM-7	GCA_013423785.1	1737446	1737446	type	True	77.9595	322	1076	95	below_threshold
Chitinibacter tainanensis	strain=DSM 15459	GCA_000429785.1	230667	230667	type	True	77.3176	255	1076	95	below_threshold
Iodobacter ciconiae	strain=H11R3	GCA_003952345.1	2496266	2496266	type	True	77.1012	131	1076	95	below_threshold
Iodobacter fluviatilis	strain=NCTC11159	GCA_900451195.1	537	537	type	True	76.9665	158	1076	95	below_threshold
Iodobacter fluviatilis	strain=DSM 3764	GCA_004346505.1	537	537	type	True	76.8319	155	1076	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:17,879] [INFO] DFAST Taxonomy check result was written to GCF_020531905.1_ASM2053190v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:17,880] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:17,880] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:17,881] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfbea0738-cd44-4b1f-b241-1fbfabf39b34/dqc_reference/checkm_data
[2024-01-24 13:58:17,883] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:17,923] [INFO] Task started: CheckM
[2024-01-24 13:58:17,923] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020531905.1_ASM2053190v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020531905.1_ASM2053190v1_genomic.fna/checkm_input GCF_020531905.1_ASM2053190v1_genomic.fna/checkm_result
[2024-01-24 13:58:51,981] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:51,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:52,009] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:52,009] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:52,010] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020531905.1_ASM2053190v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:52,010] [INFO] Task started: Blastn
[2024-01-24 13:58:52,011] [INFO] Running command: blastn -query GCF_020531905.1_ASM2053190v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbea0738-cd44-4b1f-b241-1fbfabf39b34/dqc_reference/reference_markers_gtdb.fasta -out GCF_020531905.1_ASM2053190v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:53,257] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:53,260] [INFO] Selected 11 target genomes.
[2024-01-24 13:58:53,261] [INFO] Target genome list was writen to GCF_020531905.1_ASM2053190v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:53,265] [INFO] Task started: fastANI
[2024-01-24 13:58:53,265] [INFO] Running command: fastANI --query /var/lib/cwl/stg73a948d0-e5c4-4a7e-88cb-560fd2a143f4/GCF_020531905.1_ASM2053190v1_genomic.fna.gz --refList GCF_020531905.1_ASM2053190v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020531905.1_ASM2053190v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:01,592] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:01,603] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:59:01,603] [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_013284055.1	s__Deefgea sp013284055	90.3751	924	1076	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Deefgea	95.0	95.22	95.22	0.87	0.87	2	-
GCF_000620145.1	s__Deefgea rivuli	80.4319	589	1076	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Deefgea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016881405.1	s__Deefgea chitinilytica	79.7536	521	1076	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Deefgea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013403565.1	s__Chitinibacter sp013403565	78.2479	329	1076	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013423785.1	s__Chitinibacter fontanus	77.9677	320	1076	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009760905.1	s__Chitinibacter sp009760905	77.7506	305	1076	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429785.1	s__Chitinibacter tainanensis	77.3289	254	1076	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinibacter	95.0	96.34	96.34	0.90	0.90	2	-
GCF_011601265.1	s__Iodobacter sp011601265	77.1393	156	1076	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Iodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900451195.1	s__Iodobacter fluviatilis	76.9528	159	1076	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Iodobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002735645.1	s__Iodobacter sp002735645	76.8196	156	1076	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Iodobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:01,608] [INFO] GTDB search result was written to GCF_020531905.1_ASM2053190v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:01,609] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:01,612] [INFO] DFAST_QC result json was written to GCF_020531905.1_ASM2053190v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:01,613] [INFO] DFAST_QC completed!
[2024-01-24 13:59:01,613] [INFO] Total running time: 0h1m6s