[2023-06-08 20:36:19,336] [INFO] DFAST_QC pipeline started.
[2023-06-08 20:36:19,341] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 20:36:19,341] [INFO] DQC Reference Directory: /var/lib/cwl/stgc988f843-d703-47dd-a500-9176dcb1537d/dqc_reference
[2023-06-08 20:36:20,691] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 20:36:20,692] [INFO] Task started: Prodigal
[2023-06-08 20:36:20,692] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b0be4f1-82b9-48a3-8439-641a9fc46aa5/GCA_947504255.1_ZH-3nov15-180_genomic.fna.gz | prodigal -d GCA_947504255.1_ZH-3nov15-180_genomic.fna/cds.fna -a GCA_947504255.1_ZH-3nov15-180_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 20:36:33,544] [INFO] Task succeeded: Prodigal
[2023-06-08 20:36:33,544] [INFO] Task started: HMMsearch
[2023-06-08 20:36:33,545] [INFO] Running command: hmmsearch --tblout GCA_947504255.1_ZH-3nov15-180_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc988f843-d703-47dd-a500-9176dcb1537d/dqc_reference/reference_markers.hmm GCA_947504255.1_ZH-3nov15-180_genomic.fna/protein.faa > /dev/null
[2023-06-08 20:36:33,857] [INFO] Task succeeded: HMMsearch
[2023-06-08 20:36:33,858] [INFO] Found 6/6 markers.
[2023-06-08 20:36:33,889] [INFO] Query marker FASTA was written to GCA_947504255.1_ZH-3nov15-180_genomic.fna/markers.fasta
[2023-06-08 20:36:33,890] [INFO] Task started: Blastn
[2023-06-08 20:36:33,890] [INFO] Running command: blastn -query GCA_947504255.1_ZH-3nov15-180_genomic.fna/markers.fasta -db /var/lib/cwl/stgc988f843-d703-47dd-a500-9176dcb1537d/dqc_reference/reference_markers.fasta -out GCA_947504255.1_ZH-3nov15-180_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:36:34,642] [INFO] Task succeeded: Blastn
[2023-06-08 20:36:34,647] [INFO] Selected 24 target genomes.
[2023-06-08 20:36:34,647] [INFO] Target genome list was writen to GCA_947504255.1_ZH-3nov15-180_genomic.fna/target_genomes.txt
[2023-06-08 20:36:34,650] [INFO] Task started: fastANI
[2023-06-08 20:36:34,651] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b0be4f1-82b9-48a3-8439-641a9fc46aa5/GCA_947504255.1_ZH-3nov15-180_genomic.fna.gz --refList GCA_947504255.1_ZH-3nov15-180_genomic.fna/target_genomes.txt --output GCA_947504255.1_ZH-3nov15-180_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 20:36:52,147] [INFO] Task succeeded: fastANI
[2023-06-08 20:36:52,148] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc988f843-d703-47dd-a500-9176dcb1537d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 20:36:52,148] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc988f843-d703-47dd-a500-9176dcb1537d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 20:36:52,164] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 20:36:52,164] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 20:36:52,164] [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 parvus	strain=II-B4	GCA_003063455.1	540061	540061	type	True	78.2441	296	1034	95	below_threshold
Limnohabitans planktonicus	strain=II-D5	GCA_001270065.2	540060	540060	type	True	78.1819	320	1034	95	below_threshold
Limnohabitans curvus	strain=MWH-C5	GCA_003063475.1	323423	323423	type	True	78.0261	222	1034	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	77.8794	271	1034	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	77.3445	190	1034	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	77.262	138	1034	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	77.1817	164	1034	95	below_threshold
Hydrogenophaga crassostreae	strain=LPB0072	GCA_001761385.1	1763535	1763535	type	True	77.0983	161	1034	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	77.0686	203	1034	95	below_threshold
Hydrogenophaga crassostreae	strain=LPB0072	GCA_001640105.1	1763535	1763535	type	True	77.0633	161	1034	95	below_threshold
Hydrogenophaga taeniospiralis	strain=NBRC 102512	GCA_001592305.1	65656	65656	type	True	77.0408	158	1034	95	below_threshold
Hydrogenophaga palleronii	strain=NBRC 102513	GCA_001571225.1	65655	65655	type	True	77.0275	155	1034	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	77.0124	201	1034	95	below_threshold
Variovorax soli	strain=NBRC 106424	GCA_001591385.1	376815	376815	type	True	76.941	138	1034	95	below_threshold
Simplicispira psychrophila	strain=DSM 11588	GCA_000688255.1	80882	80882	type	True	76.8	156	1034	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	76.7942	170	1034	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	76.7867	178	1034	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	76.7412	178	1034	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	76.7228	163	1034	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	76.597	127	1034	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	75.9955	88	1034	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 20:36:52,170] [INFO] DFAST Taxonomy check result was written to GCA_947504255.1_ZH-3nov15-180_genomic.fna/tc_result.tsv
[2023-06-08 20:36:52,170] [INFO] ===== Taxonomy check completed =====
[2023-06-08 20:36:52,170] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 20:36:52,171] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc988f843-d703-47dd-a500-9176dcb1537d/dqc_reference/checkm_data
[2023-06-08 20:36:52,172] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 20:36:52,211] [INFO] Task started: CheckM
[2023-06-08 20:36:52,211] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947504255.1_ZH-3nov15-180_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947504255.1_ZH-3nov15-180_genomic.fna/checkm_input GCA_947504255.1_ZH-3nov15-180_genomic.fna/checkm_result
[2023-06-08 20:37:34,482] [INFO] Task succeeded: CheckM
[2023-06-08 20:37:34,484] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 20:37:34,507] [INFO] ===== Completeness check finished =====
[2023-06-08 20:37:34,507] [INFO] ===== Start GTDB Search =====
[2023-06-08 20:37:34,508] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947504255.1_ZH-3nov15-180_genomic.fna/markers.fasta)
[2023-06-08 20:37:34,508] [INFO] Task started: Blastn
[2023-06-08 20:37:34,509] [INFO] Running command: blastn -query GCA_947504255.1_ZH-3nov15-180_genomic.fna/markers.fasta -db /var/lib/cwl/stgc988f843-d703-47dd-a500-9176dcb1537d/dqc_reference/reference_markers_gtdb.fasta -out GCA_947504255.1_ZH-3nov15-180_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:37:35,816] [INFO] Task succeeded: Blastn
[2023-06-08 20:37:35,821] [INFO] Selected 16 target genomes.
[2023-06-08 20:37:35,821] [INFO] Target genome list was writen to GCA_947504255.1_ZH-3nov15-180_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 20:37:35,824] [INFO] Task started: fastANI
[2023-06-08 20:37:35,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b0be4f1-82b9-48a3-8439-641a9fc46aa5/GCA_947504255.1_ZH-3nov15-180_genomic.fna.gz --refList GCA_947504255.1_ZH-3nov15-180_genomic.fna/target_genomes_gtdb.txt --output GCA_947504255.1_ZH-3nov15-180_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 20:37:44,547] [INFO] Task succeeded: fastANI
[2023-06-08 20:37:44,565] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 20:37:44,565] [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_903870145.1	s__Limnohabitans_A sp903870145	99.8588	864	1034	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	99.83	99.72	0.91	0.84	26	conclusive
GCF_001412575.1	s__Limnohabitans_A sp001412575	79.5345	432	1034	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	97.90	97.72	0.94	0.91	3	-
GCA_903856875.1	s__Limnohabitans_A sp903856875	79.0318	249	1034	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_003063375.1	s__Limnohabitans_A sp003063375	79.0197	378	1034	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_001269365.1	s__Limnohabitans_A sp001269365	78.9745	415	1034	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_009928125.1	s__Limnohabitans_A sp009928125	78.6233	288	1034	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	98.84	98.65	0.83	0.81	5	-
GCA_005789685.1	s__Limnohabitans_A sp005789685	78.3746	222	1034	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_017848645.1	s__Limnohabitans_A sp017848645	78.262	306	1034	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	97.74	96.96	0.88	0.84	5	-
GCA_903961095.1	s__Limnohabitans_A sp903961095	78.254	329	1034	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	99.26	99.25	0.86	0.84	3	-
GCF_000293865.2	s__Limnohabitans_A sp000293865	78.1658	301	1034	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_003063355.1	s__Limnohabitans_A sp003063355	78.1117	313	1034	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_002255935.1	s__Limnohabitans_A sp002255935	78.097	306	1034	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_903822825.1	s__Limnohabitans_A sp903822825	77.856	259	1034	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans_A	95.0	99.95	99.93	0.93	0.91	3	-
GCA_903840825.1	s__Rhodoferax sp903840825	76.9865	123	1034	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103645.1	s__Oryzisolibacter propanilivorax	76.7452	120	1034	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oryzisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780365.1	s__Acidovorax sp018780365	76.5001	131	1034	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Acidovorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 20:37:44,567] [INFO] GTDB search result was written to GCA_947504255.1_ZH-3nov15-180_genomic.fna/result_gtdb.tsv
[2023-06-08 20:37:44,568] [INFO] ===== GTDB Search completed =====
[2023-06-08 20:37:44,572] [INFO] DFAST_QC result json was written to GCA_947504255.1_ZH-3nov15-180_genomic.fna/dqc_result.json
[2023-06-08 20:37:44,573] [INFO] DFAST_QC completed!
[2023-06-08 20:37:44,573] [INFO] Total running time: 0h1m25s