[2023-06-30 01:23:13,470] [INFO] DFAST_QC pipeline started.
[2023-06-30 01:23:13,472] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 01:23:13,472] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a6f71c8-a566-4acd-97c8-1e6f9629531c/dqc_reference
[2023-06-30 01:23:14,713] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 01:23:14,714] [INFO] Task started: Prodigal
[2023-06-30 01:23:14,715] [INFO] Running command: gunzip -c /var/lib/cwl/stg56ecff76-ce2b-454f-9e9d-37d9c45022dc/GCA_024708925.1_ASM2470892v1_genomic.fna.gz | prodigal -d GCA_024708925.1_ASM2470892v1_genomic.fna/cds.fna -a GCA_024708925.1_ASM2470892v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 01:23:22,851] [INFO] Task succeeded: Prodigal
[2023-06-30 01:23:22,852] [INFO] Task started: HMMsearch
[2023-06-30 01:23:22,852] [INFO] Running command: hmmsearch --tblout GCA_024708925.1_ASM2470892v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a6f71c8-a566-4acd-97c8-1e6f9629531c/dqc_reference/reference_markers.hmm GCA_024708925.1_ASM2470892v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 01:23:23,176] [INFO] Task succeeded: HMMsearch
[2023-06-30 01:23:23,177] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg56ecff76-ce2b-454f-9e9d-37d9c45022dc/GCA_024708925.1_ASM2470892v1_genomic.fna.gz]
[2023-06-30 01:23:23,208] [INFO] Query marker FASTA was written to GCA_024708925.1_ASM2470892v1_genomic.fna/markers.fasta
[2023-06-30 01:23:23,208] [INFO] Task started: Blastn
[2023-06-30 01:23:23,208] [INFO] Running command: blastn -query GCA_024708925.1_ASM2470892v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a6f71c8-a566-4acd-97c8-1e6f9629531c/dqc_reference/reference_markers.fasta -out GCA_024708925.1_ASM2470892v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 01:23:24,027] [INFO] Task succeeded: Blastn
[2023-06-30 01:23:24,031] [INFO] Selected 23 target genomes.
[2023-06-30 01:23:24,032] [INFO] Target genome list was writen to GCA_024708925.1_ASM2470892v1_genomic.fna/target_genomes.txt
[2023-06-30 01:23:24,034] [INFO] Task started: fastANI
[2023-06-30 01:23:24,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg56ecff76-ce2b-454f-9e9d-37d9c45022dc/GCA_024708925.1_ASM2470892v1_genomic.fna.gz --refList GCA_024708925.1_ASM2470892v1_genomic.fna/target_genomes.txt --output GCA_024708925.1_ASM2470892v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 01:23:44,182] [INFO] Task succeeded: fastANI
[2023-06-30 01:23:44,183] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a6f71c8-a566-4acd-97c8-1e6f9629531c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 01:23:44,183] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a6f71c8-a566-4acd-97c8-1e6f9629531c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 01:23:44,203] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 01:23:44,204] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 01:23:44,204] [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
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	82.2939	468	727	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	82.2093	460	727	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	81.9449	483	727	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	81.4129	437	727	95	below_threshold
Simplicispira metamorpha	strain=DSM 1837	GCA_004341365.1	80881	80881	type	True	81.3683	420	727	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	81.3384	424	727	95	below_threshold
Acidovorax temperans	strain=DSM 7270	GCA_006716905.1	80878	80878	type	True	81.3152	429	727	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	81.2343	485	727	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	81.1538	483	727	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	80.9773	415	727	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_001298675.1	343013	343013	type	True	80.905	415	727	95	below_threshold
Simplicispira hankyongi	strain=NY-02	GCA_003570885.1	2315688	2315688	type	True	80.4281	423	727	95	below_threshold
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	80.1863	252	727	95	below_threshold
Simplicispira suum	strain=SC1-8	GCA_003008595.1	2109915	2109915	type	True	80.0639	391	727	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.8513	331	727	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	79.8333	382	727	95	below_threshold
Hydrogenophaga palleronii	strain=NBRC 102513	GCA_001571225.1	65655	65655	type	True	79.7853	322	727	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	79.7414	386	727	95	below_threshold
Extensimonas perlucida	strain=HX2-24	GCA_007655255.1	2590786	2590786	type	True	79.431	336	727	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	79.2849	268	727	95	below_threshold
Simplicispira psychrophila	strain=DSM 11588	GCA_000688255.1	80882	80882	type	True	79.1564	355	727	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	79.0991	307	727	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	78.8007	328	727	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 01:23:44,206] [INFO] DFAST Taxonomy check result was written to GCA_024708925.1_ASM2470892v1_genomic.fna/tc_result.tsv
[2023-06-30 01:23:44,207] [INFO] ===== Taxonomy check completed =====
[2023-06-30 01:23:44,207] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 01:23:44,207] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a6f71c8-a566-4acd-97c8-1e6f9629531c/dqc_reference/checkm_data
[2023-06-30 01:23:44,209] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 01:23:44,239] [INFO] Task started: CheckM
[2023-06-30 01:23:44,239] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024708925.1_ASM2470892v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024708925.1_ASM2470892v1_genomic.fna/checkm_input GCA_024708925.1_ASM2470892v1_genomic.fna/checkm_result
[2023-06-30 01:24:15,781] [INFO] Task succeeded: CheckM
[2023-06-30 01:24:15,783] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 01:24:15,804] [INFO] ===== Completeness check finished =====
[2023-06-30 01:24:15,805] [INFO] ===== Start GTDB Search =====
[2023-06-30 01:24:15,805] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024708925.1_ASM2470892v1_genomic.fna/markers.fasta)
[2023-06-30 01:24:15,806] [INFO] Task started: Blastn
[2023-06-30 01:24:15,806] [INFO] Running command: blastn -query GCA_024708925.1_ASM2470892v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a6f71c8-a566-4acd-97c8-1e6f9629531c/dqc_reference/reference_markers_gtdb.fasta -out GCA_024708925.1_ASM2470892v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 01:24:17,171] [INFO] Task succeeded: Blastn
[2023-06-30 01:24:17,175] [INFO] Selected 12 target genomes.
[2023-06-30 01:24:17,175] [INFO] Target genome list was writen to GCA_024708925.1_ASM2470892v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 01:24:17,182] [INFO] Task started: fastANI
[2023-06-30 01:24:17,182] [INFO] Running command: fastANI --query /var/lib/cwl/stg56ecff76-ce2b-454f-9e9d-37d9c45022dc/GCA_024708925.1_ASM2470892v1_genomic.fna.gz --refList GCA_024708925.1_ASM2470892v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024708925.1_ASM2470892v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 01:24:27,498] [INFO] Task succeeded: fastANI
[2023-06-30 01:24:27,514] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 01:24:27,514] [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
GCA_001770955.1	s__Giesbergeria sp001770955	89.2822	552	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	97.11	95.02	0.83	0.80	5	-
GCF_003604195.1	s__Giesbergeria lacusdiani	85.9205	555	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010020825.1	s__Giesbergeria sp010020825	84.261	499	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	98.40	98.40	0.98	0.98	2	-
GCA_016192425.1	s__Giesbergeria sp016192425	83.9494	490	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739995.1	s__Giesbergeria granuli	83.2982	505	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	95.66	95.66	0.85	0.85	2	-
GCF_012932145.1	s__Giesbergeria sp012932145	82.2358	460	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	98.72	98.72	0.89	0.89	2	-
GCF_003852545.1	s__Acidovorax sp003852545	81.8266	504	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019218755.1	s__Acidovorax sp019218755	81.7954	496	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.86	98.86	0.92	0.91	3	-
GCF_001714725.1	s__Acidovorax sp001714725	81.7361	451	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207955.1	s__Acidovorax soli_A	81.7275	486	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053545.1	s__Acidovorax sp003053545	81.722	488	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.66	97.32	0.95	0.90	3	-
GCF_004341365.1	s__Giesbergeria metamorpha	81.3518	421	727	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	99.27	98.54	0.92	0.85	3	-
--------------------------------------------------------------------------------
[2023-06-30 01:24:27,516] [INFO] GTDB search result was written to GCA_024708925.1_ASM2470892v1_genomic.fna/result_gtdb.tsv
[2023-06-30 01:24:27,517] [INFO] ===== GTDB Search completed =====
[2023-06-30 01:24:27,521] [INFO] DFAST_QC result json was written to GCA_024708925.1_ASM2470892v1_genomic.fna/dqc_result.json
[2023-06-30 01:24:27,521] [INFO] DFAST_QC completed!
[2023-06-30 01:24:27,521] [INFO] Total running time: 0h1m14s