[2024-01-24 14:53:50,249] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:53:50,251] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:53:50,251] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f2f2213-9922-486f-8b42-e2e5a5e71376/dqc_reference
[2024-01-24 14:53:51,466] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:53:51,467] [INFO] Task started: Prodigal
[2024-01-24 14:53:51,467] [INFO] Running command: gunzip -c /var/lib/cwl/stg67ba0ae9-9ec9-45ab-8760-0b48912aca2e/GCF_003063475.1_ASM306347v1_genomic.fna.gz | prodigal -d GCF_003063475.1_ASM306347v1_genomic.fna/cds.fna -a GCF_003063475.1_ASM306347v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:54:03,945] [INFO] Task succeeded: Prodigal
[2024-01-24 14:54:03,946] [INFO] Task started: HMMsearch
[2024-01-24 14:54:03,946] [INFO] Running command: hmmsearch --tblout GCF_003063475.1_ASM306347v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f2f2213-9922-486f-8b42-e2e5a5e71376/dqc_reference/reference_markers.hmm GCF_003063475.1_ASM306347v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:54:04,254] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:54:04,255] [INFO] Found 6/6 markers.
[2024-01-24 14:54:04,284] [INFO] Query marker FASTA was written to GCF_003063475.1_ASM306347v1_genomic.fna/markers.fasta
[2024-01-24 14:54:04,284] [INFO] Task started: Blastn
[2024-01-24 14:54:04,285] [INFO] Running command: blastn -query GCF_003063475.1_ASM306347v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f2f2213-9922-486f-8b42-e2e5a5e71376/dqc_reference/reference_markers.fasta -out GCF_003063475.1_ASM306347v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:54:04,998] [INFO] Task succeeded: Blastn
[2024-01-24 14:54:05,026] [INFO] Selected 22 target genomes.
[2024-01-24 14:54:05,027] [INFO] Target genome list was writen to GCF_003063475.1_ASM306347v1_genomic.fna/target_genomes.txt
[2024-01-24 14:54:05,044] [INFO] Task started: fastANI
[2024-01-24 14:54:05,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg67ba0ae9-9ec9-45ab-8760-0b48912aca2e/GCF_003063475.1_ASM306347v1_genomic.fna.gz --refList GCF_003063475.1_ASM306347v1_genomic.fna/target_genomes.txt --output GCF_003063475.1_ASM306347v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:54:21,652] [INFO] Task succeeded: fastANI
[2024-01-24 14:54:21,653] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f2f2213-9922-486f-8b42-e2e5a5e71376/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:54:21,654] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f2f2213-9922-486f-8b42-e2e5a5e71376/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:54:21,675] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:54:21,675] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:54:21,675] [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
Limnohabitans curvus	strain=MWH-C5	GCA_003063475.1	323423	323423	type	True	100.0	1007	1009	95	conclusive
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	79.6525	357	1009	95	below_threshold
Limnohabitans parvus	strain=II-B4	GCA_003063455.1	540061	540061	type	True	79.5721	365	1009	95	below_threshold
Limnohabitans planktonicus	strain=II-D5	GCA_001270065.2	540060	540060	type	True	79.3068	354	1009	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	78.2283	214	1009	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	78.0282	285	1009	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	77.944	296	1009	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	77.8442	291	1009	95	below_threshold
Rhodoferax aquaticus	strain=Gr-4	GCA_006974105.1	2527691	2527691	type	True	77.8119	234	1009	95	below_threshold
Hydrogenophaga pseudoflava	strain=NBRC 102511	GCA_001592285.1	47421	47421	type	True	77.6751	224	1009	95	below_threshold
Comamonas aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	77.5796	224	1009	95	below_threshold
Hydrogenophaga flava	strain=NBRC 102514	GCA_001571145.1	65657	65657	type	True	77.5377	223	1009	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	77.4666	217	1009	95	below_threshold
Hydrogenophaga palleronii	strain=NBRC 102513	GCA_001571225.1	65655	65655	type	True	77.4277	252	1009	95	below_threshold
Rhodoferax antarcticus	strain=DSM 24876	GCA_001955735.1	81479	81479	type	True	77.4048	210	1009	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	77.349	211	1009	95	below_threshold
Simplicispira suum	strain=SC1-8	GCA_003008595.1	2109915	2109915	type	True	77.2846	203	1009	95	below_threshold
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	77.2462	198	1009	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	77.2394	220	1009	95	below_threshold
Simplicispira hankyongi	strain=NY-02	GCA_003570885.1	2315688	2315688	type	True	77.2096	208	1009	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	76.848	182	1009	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	76.2712	53	1009	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:54:21,677] [INFO] DFAST Taxonomy check result was written to GCF_003063475.1_ASM306347v1_genomic.fna/tc_result.tsv
[2024-01-24 14:54:21,677] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:54:21,677] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:54:21,678] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f2f2213-9922-486f-8b42-e2e5a5e71376/dqc_reference/checkm_data
[2024-01-24 14:54:21,679] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:54:21,710] [INFO] Task started: CheckM
[2024-01-24 14:54:21,710] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003063475.1_ASM306347v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003063475.1_ASM306347v1_genomic.fna/checkm_input GCF_003063475.1_ASM306347v1_genomic.fna/checkm_result
[2024-01-24 14:55:03,818] [INFO] Task succeeded: CheckM
[2024-01-24 14:55:03,820] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:55:03,836] [INFO] ===== Completeness check finished =====
[2024-01-24 14:55:03,836] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:55:03,836] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003063475.1_ASM306347v1_genomic.fna/markers.fasta)
[2024-01-24 14:55:03,837] [INFO] Task started: Blastn
[2024-01-24 14:55:03,837] [INFO] Running command: blastn -query GCF_003063475.1_ASM306347v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f2f2213-9922-486f-8b42-e2e5a5e71376/dqc_reference/reference_markers_gtdb.fasta -out GCF_003063475.1_ASM306347v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:04,947] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:04,950] [INFO] Selected 11 target genomes.
[2024-01-24 14:55:04,950] [INFO] Target genome list was writen to GCF_003063475.1_ASM306347v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:55:04,981] [INFO] Task started: fastANI
[2024-01-24 14:55:04,981] [INFO] Running command: fastANI --query /var/lib/cwl/stg67ba0ae9-9ec9-45ab-8760-0b48912aca2e/GCF_003063475.1_ASM306347v1_genomic.fna.gz --refList GCF_003063475.1_ASM306347v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003063475.1_ASM306347v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:55:12,412] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:12,420] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:55:12,420] [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_003063475.1	s__Limnohabitans curvus	100.0	1007	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	98.49	98.49	0.87	0.87	2	conclusive
GCA_002282445.1	s__Limnohabitans sp002282445	87.0423	618	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	100.00	100.00	0.99	0.99	3	-
GCF_003063545.1	s__Limnohabitans sp003063545	86.9756	650	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903886485.1	s__Limnohabitans sp903886485	85.2443	643	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.98	99.98	0.98	0.98	3	-
GCA_903952885.1	s__Limnohabitans sp903952885	85.2087	422	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.13	99.13	0.83	0.83	2	-
GCF_002778325.1	s__Limnohabitans sp002778325	83.9328	611	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903892175.1	s__Limnohabitans sp903892175	80.8599	457	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	98.61	96.75	0.84	0.82	4	-
GCF_016735515.1	s__Rhizobacter sp016735515	76.9456	151	1009	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:55:12,422] [INFO] GTDB search result was written to GCF_003063475.1_ASM306347v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:55:12,422] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:55:12,427] [INFO] DFAST_QC result json was written to GCF_003063475.1_ASM306347v1_genomic.fna/dqc_result.json
[2024-01-24 14:55:12,427] [INFO] DFAST_QC completed!
[2024-01-24 14:55:12,428] [INFO] Total running time: 0h1m22s