[2024-01-24 11:59:35,678] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:35,681] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:35,682] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b53432f-2d36-4d7e-b573-b1517310e61e/dqc_reference
[2024-01-24 11:59:36,902] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:36,903] [INFO] Task started: Prodigal
[2024-01-24 11:59:36,904] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0ccd02d-e3d7-4e92-8c17-d5e3ee9881a0/GCF_004833285.1_ASM483328v1_genomic.fna.gz | prodigal -d GCF_004833285.1_ASM483328v1_genomic.fna/cds.fna -a GCF_004833285.1_ASM483328v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:51,359] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:51,359] [INFO] Task started: HMMsearch
[2024-01-24 11:59:51,360] [INFO] Running command: hmmsearch --tblout GCF_004833285.1_ASM483328v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b53432f-2d36-4d7e-b573-b1517310e61e/dqc_reference/reference_markers.hmm GCF_004833285.1_ASM483328v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:51,688] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:51,691] [INFO] Found 6/6 markers.
[2024-01-24 11:59:51,725] [INFO] Query marker FASTA was written to GCF_004833285.1_ASM483328v1_genomic.fna/markers.fasta
[2024-01-24 11:59:51,725] [INFO] Task started: Blastn
[2024-01-24 11:59:51,726] [INFO] Running command: blastn -query GCF_004833285.1_ASM483328v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b53432f-2d36-4d7e-b573-b1517310e61e/dqc_reference/reference_markers.fasta -out GCF_004833285.1_ASM483328v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:52,428] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:52,432] [INFO] Selected 24 target genomes.
[2024-01-24 11:59:52,432] [INFO] Target genome list was writen to GCF_004833285.1_ASM483328v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:52,441] [INFO] Task started: fastANI
[2024-01-24 11:59:52,441] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0ccd02d-e3d7-4e92-8c17-d5e3ee9881a0/GCF_004833285.1_ASM483328v1_genomic.fna.gz --refList GCF_004833285.1_ASM483328v1_genomic.fna/target_genomes.txt --output GCF_004833285.1_ASM483328v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:09,070] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:09,070] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b53432f-2d36-4d7e-b573-b1517310e61e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:09,071] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b53432f-2d36-4d7e-b573-b1517310e61e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:09,091] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:00:09,091] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:00:09,092] [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
Lampropedia puyangensis	strain=2-bin	GCA_004833285.1	1330072	1330072	type	True	100.0	1288	1291	95	conclusive
Lampropedia aestuarii	strain=YIM MLB12	GCA_004803635.1	2562762	2562762	type	True	79.1649	459	1291	95	below_threshold
Lampropedia hyalina	strain=DSM 16112	GCA_900129055.1	198706	198706	type	True	77.0897	137	1291	95	below_threshold
Comamonas avium	strain=Sa2CVA6	GCA_014836675.1	2762231	2762231	type	True	76.8432	112	1291	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	76.8415	95	1291	95	below_threshold
Simplicispira metamorpha	strain=NBRC 13960	GCA_003568725.1	80881	80881	type	True	76.7781	119	1291	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_001298675.1	343013	343013	type	True	76.7338	101	1291	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	76.7051	96	1291	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	76.6948	87	1291	95	below_threshold
Acidovorax caeni	strain=R-24608	GCA_900116825.1	343013	343013	type	True	76.6504	101	1291	95	below_threshold
Comamonas fluminis	strain=CJ34	GCA_019186805.1	2796366	2796366	type	True	76.5629	118	1291	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	76.5419	94	1291	95	below_threshold
Diaphorobacter ruginosibacter	strain=DSM 27467	GCA_014395975.1	1715720	1715720	type	True	76.5373	100	1291	95	below_threshold
Comamonas terrigena	strain=NCTC1937	GCA_900461435.1	32013	32013	type	True	76.4861	115	1291	95	below_threshold
Comamonas suwonensis	strain=EJ-4	GCA_012844455.2	2606214	2606214	type	True	76.4484	117	1291	95	below_threshold
Polaromonas jejuensis	strain=NBRC 106434	GCA_001598235.1	457502	457502	type	True	76.4222	94	1291	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	76.4083	102	1291	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	76.3336	98	1291	95	below_threshold
Rhodoferax antarcticus	strain=DSM 24876	GCA_001955735.1	81479	81479	type	True	76.1649	70	1291	95	below_threshold
Rhodoferax antarcticus	strain=ANT.BR	GCA_001938565.1	81479	81479	type	True	76.1609	71	1291	95	below_threshold
Simplicispira suum	strain=SC1-8	GCA_003008595.1	2109915	2109915	type	True	76.1246	85	1291	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:09,093] [INFO] DFAST Taxonomy check result was written to GCF_004833285.1_ASM483328v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:09,094] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:09,094] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:09,094] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b53432f-2d36-4d7e-b573-b1517310e61e/dqc_reference/checkm_data
[2024-01-24 12:00:09,095] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:09,138] [INFO] Task started: CheckM
[2024-01-24 12:00:09,138] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004833285.1_ASM483328v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004833285.1_ASM483328v1_genomic.fna/checkm_input GCF_004833285.1_ASM483328v1_genomic.fna/checkm_result
[2024-01-24 12:00:54,716] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:54,718] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:54,745] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:54,746] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:54,746] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004833285.1_ASM483328v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:54,747] [INFO] Task started: Blastn
[2024-01-24 12:00:54,747] [INFO] Running command: blastn -query GCF_004833285.1_ASM483328v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b53432f-2d36-4d7e-b573-b1517310e61e/dqc_reference/reference_markers_gtdb.fasta -out GCF_004833285.1_ASM483328v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:55,962] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:55,969] [INFO] Selected 20 target genomes.
[2024-01-24 12:00:55,969] [INFO] Target genome list was writen to GCF_004833285.1_ASM483328v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:55,990] [INFO] Task started: fastANI
[2024-01-24 12:00:55,991] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0ccd02d-e3d7-4e92-8c17-d5e3ee9881a0/GCF_004833285.1_ASM483328v1_genomic.fna.gz --refList GCF_004833285.1_ASM483328v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004833285.1_ASM483328v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:01:07,248] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:07,270] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:01:07,271] [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_004833285.1	s__Lampropedia puyangensis	100.0	1288	1291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lampropedia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004803635.1	s__Lampropedia aestuarii	79.1845	457	1291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lampropedia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002285265.1	s__Lampropedia sp002285265	77.2603	190	1291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lampropedia	95.0	96.24	95.49	0.89	0.89	3	-
GCA_002285285.1	s__Lampropedia sp002285285	77.1659	201	1291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lampropedia	95.0	97.35	97.22	0.92	0.90	6	-
GCF_003063545.1	s__Limnohabitans sp003063545	77.119	95	1291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001005215.1	s__Lampropedia cohaerens	77.0984	159	1291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lampropedia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129055.1	s__Lampropedia hyalina	77.0897	137	1291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lampropedia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836675.1	s__Comamonas sp014836675	76.8432	112	1291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Comamonas	95.0	98.72	98.72	0.93	0.93	2	-
GCF_001298675.1	s__Acidovorax_C caeni	76.7576	100	1291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax_C	95.0	99.98	99.98	0.98	0.98	2	-
GCA_002633085.1	s__Hylemonella sp002633085	76.7418	72	1291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	96.79	96.79	0.90	0.90	2	-
GCA_017986605.1	s__Limnohabitans_A sp017986605	76.6308	58	1291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002282445.1	s__Limnohabitans sp002282445	76.5825	87	1291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	100.00	100.00	0.99	0.99	3	-
GCF_002157145.1	s__Acidovorax carolinensis	76.5419	94	1291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	97.15	97.05	0.89	0.88	4	-
GCA_903832625.1	s__Limnohabitans sp903832625	76.5319	91	1291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	97.24	97.19	0.90	0.89	4	-
GCF_001269365.1	s__Limnohabitans_A sp001269365	76.4894	77	1291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598235.1	s__Polaromonas jejuensis	76.4222	94	1291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097105.1	s__Rhodoferax_B sp003097105	76.4062	84	1291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011620245.1	s__Acidovorax sp011620245	76.2016	54	1291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903925445.1	s__Limnohabitans sp903925445	75.7571	52	1291	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:01:07,272] [INFO] GTDB search result was written to GCF_004833285.1_ASM483328v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:01:07,273] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:01:07,277] [INFO] DFAST_QC result json was written to GCF_004833285.1_ASM483328v1_genomic.fna/dqc_result.json
[2024-01-24 12:01:07,277] [INFO] DFAST_QC completed!
[2024-01-24 12:01:07,277] [INFO] Total running time: 0h1m32s