[2024-01-25 19:10:50,716] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:10:50,718] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:10:50,718] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2c5be20-8195-469a-9531-a0f400dcf38c/dqc_reference
[2024-01-25 19:10:51,872] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:10:51,872] [INFO] Task started: Prodigal
[2024-01-25 19:10:51,872] [INFO] Running command: gunzip -c /var/lib/cwl/stg39706a71-9281-4821-ba98-6f1501e092ff/GCF_003568725.2_ASM356872v2_genomic.fna.gz | prodigal -d GCF_003568725.2_ASM356872v2_genomic.fna/cds.fna -a GCF_003568725.2_ASM356872v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:11:04,096] [INFO] Task succeeded: Prodigal
[2024-01-25 19:11:04,096] [INFO] Task started: HMMsearch
[2024-01-25 19:11:04,096] [INFO] Running command: hmmsearch --tblout GCF_003568725.2_ASM356872v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2c5be20-8195-469a-9531-a0f400dcf38c/dqc_reference/reference_markers.hmm GCF_003568725.2_ASM356872v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:11:04,384] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:11:04,386] [INFO] Found 6/6 markers.
[2024-01-25 19:11:04,418] [INFO] Query marker FASTA was written to GCF_003568725.2_ASM356872v2_genomic.fna/markers.fasta
[2024-01-25 19:11:04,418] [INFO] Task started: Blastn
[2024-01-25 19:11:04,418] [INFO] Running command: blastn -query GCF_003568725.2_ASM356872v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2c5be20-8195-469a-9531-a0f400dcf38c/dqc_reference/reference_markers.fasta -out GCF_003568725.2_ASM356872v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:05,219] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:05,228] [INFO] Selected 16 target genomes.
[2024-01-25 19:11:05,228] [INFO] Target genome list was writen to GCF_003568725.2_ASM356872v2_genomic.fna/target_genomes.txt
[2024-01-25 19:11:05,247] [INFO] Task started: fastANI
[2024-01-25 19:11:05,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg39706a71-9281-4821-ba98-6f1501e092ff/GCF_003568725.2_ASM356872v2_genomic.fna.gz --refList GCF_003568725.2_ASM356872v2_genomic.fna/target_genomes.txt --output GCF_003568725.2_ASM356872v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:11:20,670] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:20,670] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2c5be20-8195-469a-9531-a0f400dcf38c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:11:20,671] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2c5be20-8195-469a-9531-a0f400dcf38c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:11:20,681] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:11:20,681] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:11:20,681] [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
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	100.0	1196	1201	95	conclusive
Simplicispira metamorpha	strain=DSM 1837	GCA_004341365.1	80881	80881	type	True	99.9954	1195	1201	95	conclusive
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	82.2812	663	1201	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	82.1721	690	1201	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	81.7018	701	1201	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	81.5984	685	1201	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	81.2846	666	1201	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	81.2816	672	1201	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	81.2536	624	1201	95	below_threshold
Simplicispira psychrophila	strain=DSM 11588	GCA_000688255.1	80882	80882	type	True	81.2237	680	1201	95	below_threshold
Simplicispira hankyongi	strain=NY-02	GCA_003570885.1	2315688	2315688	type	True	80.7354	564	1201	95	below_threshold
Comamonas aquatica	strain=NBRC 14918	GCA_000739875.1	225991	225991	type	True	80.3231	506	1201	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.5291	480	1201	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	78.9653	413	1201	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	78.9611	452	1201	95	below_threshold
Diaphorobacter aerolatus	strain=KACC 16536	GCA_014489535.1	1288495	1288495	type	True	78.8701	435	1201	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:11:20,683] [INFO] DFAST Taxonomy check result was written to GCF_003568725.2_ASM356872v2_genomic.fna/tc_result.tsv
[2024-01-25 19:11:20,683] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:11:20,683] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:11:20,683] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2c5be20-8195-469a-9531-a0f400dcf38c/dqc_reference/checkm_data
[2024-01-25 19:11:20,684] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:11:20,723] [INFO] Task started: CheckM
[2024-01-25 19:11:20,724] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003568725.2_ASM356872v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003568725.2_ASM356872v2_genomic.fna/checkm_input GCF_003568725.2_ASM356872v2_genomic.fna/checkm_result
[2024-01-25 19:12:03,519] [INFO] Task succeeded: CheckM
[2024-01-25 19:12:03,520] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:12:03,542] [INFO] ===== Completeness check finished =====
[2024-01-25 19:12:03,543] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:12:03,545] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003568725.2_ASM356872v2_genomic.fna/markers.fasta)
[2024-01-25 19:12:03,546] [INFO] Task started: Blastn
[2024-01-25 19:12:03,546] [INFO] Running command: blastn -query GCF_003568725.2_ASM356872v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2c5be20-8195-469a-9531-a0f400dcf38c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003568725.2_ASM356872v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:12:05,079] [INFO] Task succeeded: Blastn
[2024-01-25 19:12:05,084] [INFO] Selected 21 target genomes.
[2024-01-25 19:12:05,084] [INFO] Target genome list was writen to GCF_003568725.2_ASM356872v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:12:05,110] [INFO] Task started: fastANI
[2024-01-25 19:12:05,110] [INFO] Running command: fastANI --query /var/lib/cwl/stg39706a71-9281-4821-ba98-6f1501e092ff/GCF_003568725.2_ASM356872v2_genomic.fna.gz --refList GCF_003568725.2_ASM356872v2_genomic.fna/target_genomes_gtdb.txt --output GCF_003568725.2_ASM356872v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:12:23,547] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:23,559] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:12:23,560] [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_004341365.1	s__Giesbergeria metamorpha	99.9954	1195	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	99.27	98.54	0.92	0.85	3	conclusive
GCF_012932145.1	s__Giesbergeria sp012932145	82.6156	680	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	98.72	98.72	0.89	0.89	2	-
GCF_001633105.1	s__Acidovorax sp001633105	82.4386	732	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003604195.1	s__Giesbergeria lacusdiani	82.3811	686	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002176815.1	s__Acidovorax sp002176815	82.2891	680	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	98.23	97.20	0.91	0.82	4	-
GCF_900107605.1	s__Acidovorax soli	82.2729	664	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	95.72	95.72	0.84	0.84	2	-
GCF_002157145.1	s__Acidovorax carolinensis	82.1794	690	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.15	97.05	0.89	0.88	4	-
GCA_001770955.1	s__Giesbergeria sp001770955	82.0404	635	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	97.11	95.02	0.83	0.80	5	-
GCF_003852545.1	s__Acidovorax sp003852545	82.0179	694	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001714725.1	s__Acidovorax sp001714725	81.6668	636	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003669015.1	s__Acidovorax sp002754495	81.6006	675	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.04	96.96	0.91	0.90	3	-
GCF_003096555.1	s__Giesbergeria sp003096555	81.4975	619	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	99.19	98.39	0.95	0.90	3	-
GCF_001422735.1	s__Acidovorax sp001422735	81.3357	675	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424425.1	s__Acidovorax sp001424425	81.3341	693	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	99.93	99.87	0.98	0.97	3	-
GCF_900113035.1	s__Acidovorax_A wautersii	81.2605	623	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408765.1	s__Acidovorax sp013408765	81.2437	705	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017998735.1	s__Giesbergeria sp017998735	80.9257	383	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017988165.1	s__Giesbergeria sp017988165	80.7013	399	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017985015.1	s__Giesbergeria sp017985015	80.5299	507	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	99.01	95.86	0.92	0.90	6	-
GCF_003008595.1	s__Giesbergeria suum	80.3062	550	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017987055.1	s__Giesbergeria sp017987055	80.2594	338	1201	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	99.05	99.05	0.76	0.76	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:12:23,563] [INFO] GTDB search result was written to GCF_003568725.2_ASM356872v2_genomic.fna/result_gtdb.tsv
[2024-01-25 19:12:23,563] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:12:23,567] [INFO] DFAST_QC result json was written to GCF_003568725.2_ASM356872v2_genomic.fna/dqc_result.json
[2024-01-25 19:12:23,567] [INFO] DFAST_QC completed!
[2024-01-25 19:12:23,567] [INFO] Total running time: 0h1m33s