[2023-06-27 20:56:33,784] [INFO] DFAST_QC pipeline started.
[2023-06-27 20:56:33,786] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 20:56:33,786] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4b3ffee-66d0-48d3-9796-3511139d858c/dqc_reference
[2023-06-27 20:56:35,024] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 20:56:35,024] [INFO] Task started: Prodigal
[2023-06-27 20:56:35,025] [INFO] Running command: gunzip -c /var/lib/cwl/stg94e67516-7f5f-4fc4-8384-216e26533818/GCA_026400175.1_ASM2640017v1_genomic.fna.gz | prodigal -d GCA_026400175.1_ASM2640017v1_genomic.fna/cds.fna -a GCA_026400175.1_ASM2640017v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 20:56:43,158] [INFO] Task succeeded: Prodigal
[2023-06-27 20:56:43,159] [INFO] Task started: HMMsearch
[2023-06-27 20:56:43,159] [INFO] Running command: hmmsearch --tblout GCA_026400175.1_ASM2640017v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4b3ffee-66d0-48d3-9796-3511139d858c/dqc_reference/reference_markers.hmm GCA_026400175.1_ASM2640017v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 20:56:43,438] [INFO] Task succeeded: HMMsearch
[2023-06-27 20:56:43,439] [INFO] Found 6/6 markers.
[2023-06-27 20:56:43,463] [INFO] Query marker FASTA was written to GCA_026400175.1_ASM2640017v1_genomic.fna/markers.fasta
[2023-06-27 20:56:43,464] [INFO] Task started: Blastn
[2023-06-27 20:56:43,464] [INFO] Running command: blastn -query GCA_026400175.1_ASM2640017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4b3ffee-66d0-48d3-9796-3511139d858c/dqc_reference/reference_markers.fasta -out GCA_026400175.1_ASM2640017v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 20:56:44,192] [INFO] Task succeeded: Blastn
[2023-06-27 20:56:44,196] [INFO] Selected 24 target genomes.
[2023-06-27 20:56:44,196] [INFO] Target genome list was writen to GCA_026400175.1_ASM2640017v1_genomic.fna/target_genomes.txt
[2023-06-27 20:56:44,198] [INFO] Task started: fastANI
[2023-06-27 20:56:44,198] [INFO] Running command: fastANI --query /var/lib/cwl/stg94e67516-7f5f-4fc4-8384-216e26533818/GCA_026400175.1_ASM2640017v1_genomic.fna.gz --refList GCA_026400175.1_ASM2640017v1_genomic.fna/target_genomes.txt --output GCA_026400175.1_ASM2640017v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 20:57:01,605] [INFO] Task succeeded: fastANI
[2023-06-27 20:57:01,606] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4b3ffee-66d0-48d3-9796-3511139d858c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 20:57:01,606] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4b3ffee-66d0-48d3-9796-3511139d858c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 20:57:01,632] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 20:57:01,632] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 20:57:01,632] [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	78.6146	280	797	95	below_threshold
Limnohabitans planktonicus	strain=II-D5	GCA_001270065.2	540060	540060	type	True	77.7359	131	797	95	below_threshold
Limnohabitans parvus	strain=II-B4	GCA_003063455.1	540061	540061	type	True	77.2395	149	797	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	77.1594	128	797	95	below_threshold
Acidovorax carolinensis	strain=NA3	GCA_002157145.1	553814	553814	type	True	77.0805	88	797	95	below_threshold
Hydrogenophaga crassostreae	strain=LPB0072	GCA_001640105.1	1763535	1763535	type	True	77.0101	93	797	95	below_threshold
Hydrogenophaga crassostreae	strain=LPB0072	GCA_001761385.1	1763535	1763535	type	True	76.9944	93	797	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	76.9822	101	797	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	76.9271	104	797	95	below_threshold
Comamonas avium	strain=Sa2CVA6	GCA_014836675.1	2762231	2762231	type	True	76.9053	68	797	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	76.8873	96	797	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	76.8616	103	797	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	76.8421	58	797	95	below_threshold
Polaromonas jejuensis	strain=NBRC 106434	GCA_001598235.1	457502	457502	type	True	76.7397	87	797	95	below_threshold
Hydrogenophaga palleronii	strain=NBRC 102513	GCA_001571225.1	65655	65655	type	True	76.7378	96	797	95	below_threshold
Diaphorobacter caeni	strain=NR2-3-3-1	GCA_015354245.1	2784387	2784387	type	True	76.7251	65	797	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	76.7005	99	797	95	below_threshold
Simplicispira hankyongi	strain=NY-02	GCA_003570885.1	2315688	2315688	type	True	76.6572	81	797	95	below_threshold
Serpentinimonas barnesii	strain=H1	GCA_000696225.1	1458427	1458427	type	True	76.6053	74	797	95	below_threshold
Extensimonas perlucida	strain=HX2-24	GCA_007655255.1	2590786	2590786	type	True	76.5052	62	797	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 20:57:01,634] [INFO] DFAST Taxonomy check result was written to GCA_026400175.1_ASM2640017v1_genomic.fna/tc_result.tsv
[2023-06-27 20:57:01,635] [INFO] ===== Taxonomy check completed =====
[2023-06-27 20:57:01,635] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 20:57:01,635] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4b3ffee-66d0-48d3-9796-3511139d858c/dqc_reference/checkm_data
[2023-06-27 20:57:01,636] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 20:57:01,666] [INFO] Task started: CheckM
[2023-06-27 20:57:01,666] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026400175.1_ASM2640017v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026400175.1_ASM2640017v1_genomic.fna/checkm_input GCA_026400175.1_ASM2640017v1_genomic.fna/checkm_result
[2023-06-27 20:57:30,651] [INFO] Task succeeded: CheckM
[2023-06-27 20:57:30,653] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 20:57:30,675] [INFO] ===== Completeness check finished =====
[2023-06-27 20:57:30,675] [INFO] ===== Start GTDB Search =====
[2023-06-27 20:57:30,676] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026400175.1_ASM2640017v1_genomic.fna/markers.fasta)
[2023-06-27 20:57:30,676] [INFO] Task started: Blastn
[2023-06-27 20:57:30,676] [INFO] Running command: blastn -query GCA_026400175.1_ASM2640017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4b3ffee-66d0-48d3-9796-3511139d858c/dqc_reference/reference_markers_gtdb.fasta -out GCA_026400175.1_ASM2640017v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 20:57:31,903] [INFO] Task succeeded: Blastn
[2023-06-27 20:57:31,908] [INFO] Selected 15 target genomes.
[2023-06-27 20:57:31,909] [INFO] Target genome list was writen to GCA_026400175.1_ASM2640017v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 20:57:31,912] [INFO] Task started: fastANI
[2023-06-27 20:57:31,912] [INFO] Running command: fastANI --query /var/lib/cwl/stg94e67516-7f5f-4fc4-8384-216e26533818/GCA_026400175.1_ASM2640017v1_genomic.fna.gz --refList GCA_026400175.1_ASM2640017v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026400175.1_ASM2640017v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 20:57:39,164] [INFO] Task succeeded: fastANI
[2023-06-27 20:57:39,190] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 20:57:39,190] [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_005786815.1	s__Limnohabitans sp005786815	94.6199	293	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009923345.1	s__Limnohabitans sp009923345	91.2979	429	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903880855.1	s__Limnohabitans sp903880855	90.1975	612	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.14	98.09	0.92	0.91	4	-
GCA_018969975.1	s__Limnohabitans sp018969975	86.4976	490	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002347905.1	s__Limnohabitans sp002347905	84.6689	370	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	98.39	98.39	0.80	0.80	2	-
GCA_002342165.1	s__Hylemonella sp002342165	78.9992	69	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hylemonella	95.0	99.18	99.01	0.79	0.72	4	-
GCF_002778315.1	s__Limnohabitans sp002778315	78.8064	266	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	98.08	98.08	0.92	0.92	2	-
GCF_003063545.1	s__Limnohabitans sp003063545	78.7469	252	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063475.1	s__Limnohabitans curvus	78.6146	280	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	98.49	98.49	0.87	0.87	2	-
GCA_002282445.1	s__Limnohabitans sp002282445	78.5403	260	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	100.00	100.00	0.99	0.99	3	-
GCA_903832625.1	s__Limnohabitans sp903832625	78.4824	256	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	97.24	97.19	0.90	0.89	4	-
GCA_903952885.1	s__Limnohabitans sp903952885	78.1641	197	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.13	99.13	0.83	0.83	2	-
GCA_903892175.1	s__Limnohabitans sp903892175	78.1146	253	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	98.61	96.75	0.84	0.82	4	-
GCA_903856875.1	s__Limnohabitans_A sp903856875	77.3881	88	797	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_016000195.1	s__Polaromonas sp016000195	76.3996	74	797	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	98.70	98.70	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-06-27 20:57:39,193] [INFO] GTDB search result was written to GCA_026400175.1_ASM2640017v1_genomic.fna/result_gtdb.tsv
[2023-06-27 20:57:39,194] [INFO] ===== GTDB Search completed =====
[2023-06-27 20:57:39,200] [INFO] DFAST_QC result json was written to GCA_026400175.1_ASM2640017v1_genomic.fna/dqc_result.json
[2023-06-27 20:57:39,201] [INFO] DFAST_QC completed!
[2023-06-27 20:57:39,201] [INFO] Total running time: 0h1m5s