[2024-01-24 15:10:19,842] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:19,844] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:19,844] [INFO] DQC Reference Directory: /var/lib/cwl/stg2cf4104c-dccf-4440-844a-3e68f96b22f3/dqc_reference
[2024-01-24 15:10:22,720] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:22,720] [INFO] Task started: Prodigal
[2024-01-24 15:10:22,721] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa3d89e2-ae2b-469d-9509-4da61d2c8563/GCF_028830055.1_ASM2883005v1_genomic.fna.gz | prodigal -d GCF_028830055.1_ASM2883005v1_genomic.fna/cds.fna -a GCF_028830055.1_ASM2883005v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:42,879] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:42,879] [INFO] Task started: HMMsearch
[2024-01-24 15:10:42,880] [INFO] Running command: hmmsearch --tblout GCF_028830055.1_ASM2883005v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2cf4104c-dccf-4440-844a-3e68f96b22f3/dqc_reference/reference_markers.hmm GCF_028830055.1_ASM2883005v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:43,199] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:43,201] [INFO] Found 6/6 markers.
[2024-01-24 15:10:43,249] [INFO] Query marker FASTA was written to GCF_028830055.1_ASM2883005v1_genomic.fna/markers.fasta
[2024-01-24 15:10:43,250] [INFO] Task started: Blastn
[2024-01-24 15:10:43,250] [INFO] Running command: blastn -query GCF_028830055.1_ASM2883005v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cf4104c-dccf-4440-844a-3e68f96b22f3/dqc_reference/reference_markers.fasta -out GCF_028830055.1_ASM2883005v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:44,290] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:44,295] [INFO] Selected 15 target genomes.
[2024-01-24 15:10:44,295] [INFO] Target genome list was writen to GCF_028830055.1_ASM2883005v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:44,302] [INFO] Task started: fastANI
[2024-01-24 15:10:44,302] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa3d89e2-ae2b-469d-9509-4da61d2c8563/GCF_028830055.1_ASM2883005v1_genomic.fna.gz --refList GCF_028830055.1_ASM2883005v1_genomic.fna/target_genomes.txt --output GCF_028830055.1_ASM2883005v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:11,366] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:11,366] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2cf4104c-dccf-4440-844a-3e68f96b22f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:11,367] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2cf4104c-dccf-4440-844a-3e68f96b22f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:11,386] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:11:11,386] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:11:11,386] [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
Pseudomonas koreensis	strain=JCM 14769	GCA_014646955.1	198620	198620	suspected-type	True	93.0005	1737	1999	95	below_threshold
Pseudomonas koreensis	strain=DSM 16610	GCA_012986595.1	198620	198620	suspected-type	True	92.9992	1730	1999	95	below_threshold
Pseudomonas koreensis	strain=CCUG 51519	GCA_008801535.1	198620	198620	suspected-type	True	92.9464	1750	1999	95	below_threshold
Pseudomonas monsensis	strain=PGSB 8459	GCA_014268495.2	2745509	2745509	type	True	90.3283	1686	1999	95	below_threshold
Pseudomonas zeae	strain=OE 48.2	GCA_014268485.2	2745510	2745510	type	True	89.1574	1687	1999	95	below_threshold
Pseudomonas tensinigenes	strain=ZA 5.3	GCA_014268445.2	2745511	2745511	type	True	89.0629	1719	1999	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	89.0598	1715	1999	95	below_threshold
Pseudomonas allokribbensis	strain=IzPS23	GCA_014863605.1	2774460	2774460	type	True	88.9892	1668	1999	95	below_threshold
Pseudomonas kribbensis	strain=46-2	GCA_003352185.1	1628086	1628086	type	True	88.8599	1642	1999	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	88.8593	1596	1999	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	88.8368	1656	1999	95	below_threshold
Pseudomonas iranensis	strain=SWRI54	GCA_014268585.2	2745503	2745503	type	True	88.104	1584	1999	95	below_threshold
Pseudomonas atacamensis	strain=M7D1	GCA_004801935.1	2565368	2565368	type	True	88.0799	1582	1999	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	83.5943	1251	1999	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	83.5365	1302	1999	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:11,389] [INFO] DFAST Taxonomy check result was written to GCF_028830055.1_ASM2883005v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:11,390] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:11,390] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:11,391] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2cf4104c-dccf-4440-844a-3e68f96b22f3/dqc_reference/checkm_data
[2024-01-24 15:11:11,392] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:11,452] [INFO] Task started: CheckM
[2024-01-24 15:11:11,453] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028830055.1_ASM2883005v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028830055.1_ASM2883005v1_genomic.fna/checkm_input GCF_028830055.1_ASM2883005v1_genomic.fna/checkm_result
[2024-01-24 15:12:17,160] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:17,161] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:17,181] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:17,182] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:17,182] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028830055.1_ASM2883005v1_genomic.fna/markers.fasta)
[2024-01-24 15:12:17,183] [INFO] Task started: Blastn
[2024-01-24 15:12:17,183] [INFO] Running command: blastn -query GCF_028830055.1_ASM2883005v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2cf4104c-dccf-4440-844a-3e68f96b22f3/dqc_reference/reference_markers_gtdb.fasta -out GCF_028830055.1_ASM2883005v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:19,084] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:19,089] [INFO] Selected 14 target genomes.
[2024-01-24 15:12:19,089] [INFO] Target genome list was writen to GCF_028830055.1_ASM2883005v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:19,101] [INFO] Task started: fastANI
[2024-01-24 15:12:19,101] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa3d89e2-ae2b-469d-9509-4da61d2c8563/GCF_028830055.1_ASM2883005v1_genomic.fna.gz --refList GCF_028830055.1_ASM2883005v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028830055.1_ASM2883005v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:44,685] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:44,704] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:44,704] [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_003999415.1	s__Pseudomonas_E koreensis_E	98.5748	1880	1999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.57	98.57	0.92	0.92	2	conclusive
GCF_012986595.1	s__Pseudomonas_E koreensis	92.9992	1730	1999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.85	97.85	0.96	0.91	8	-
GCF_002878485.1	s__Pseudomonas_E sp002878485	92.8792	1703	1999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000633255.1	s__Pseudomonas_E sp000633255	92.496	1737	1999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000631985.1	s__Pseudomonas_E sp000631985	92.0314	1738	1999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282275.2	s__Pseudomonas_E sp000282275	92.0123	1699	1999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004683905.1	s__Pseudomonas_E putida_A	91.9516	1731	1999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.80	95.08	0.93	0.90	22	-
GCF_000292795.1	s__Pseudomonas_E fluorescens_H	91.8261	1723	1999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.99	97.99	0.94	0.93	3	-
GCF_002287825.1	s__Pseudomonas_E koreensis_B	91.7109	1750	1999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.58	96.55	0.92	0.86	13	-
GCF_003061005.1	s__Pseudomonas_E sp003061005	91.6371	1591	1999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014268495.2	s__Pseudomonas_E fluorescens_BC	90.3208	1687	1999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.66	98.66	0.95	0.95	2	-
GCF_016651305.1	s__Pseudomonas_E sp016651305	89.2171	1687	1999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011755.1	s__Pseudomonas_E sp004011755	89.09	1702	1999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.20	98.13	0.94	0.93	4	-
GCF_014863585.1	s__Pseudomonas_E gozinkensis	88.8541	1675	1999	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:44,780] [INFO] GTDB search result was written to GCF_028830055.1_ASM2883005v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:44,781] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:44,788] [INFO] DFAST_QC result json was written to GCF_028830055.1_ASM2883005v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:44,788] [INFO] DFAST_QC completed!
[2024-01-24 15:12:44,789] [INFO] Total running time: 0h2m25s