[2024-01-24 13:49:55,414] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:55,416] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:55,416] [INFO] DQC Reference Directory: /var/lib/cwl/stg0aab3f3c-26cd-4a28-b787-ab8fb8fb2293/dqc_reference
[2024-01-24 13:49:56,674] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:56,675] [INFO] Task started: Prodigal
[2024-01-24 13:49:56,675] [INFO] Running command: gunzip -c /var/lib/cwl/stgf840a2cd-488b-4d39-bed6-3a170ab5e469/GCF_001679645.1_ASM167964v1_genomic.fna.gz | prodigal -d GCF_001679645.1_ASM167964v1_genomic.fna/cds.fna -a GCF_001679645.1_ASM167964v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:17,656] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:17,656] [INFO] Task started: HMMsearch
[2024-01-24 13:50:17,656] [INFO] Running command: hmmsearch --tblout GCF_001679645.1_ASM167964v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0aab3f3c-26cd-4a28-b787-ab8fb8fb2293/dqc_reference/reference_markers.hmm GCF_001679645.1_ASM167964v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:17,963] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:17,965] [INFO] Found 6/6 markers.
[2024-01-24 13:50:18,012] [INFO] Query marker FASTA was written to GCF_001679645.1_ASM167964v1_genomic.fna/markers.fasta
[2024-01-24 13:50:18,012] [INFO] Task started: Blastn
[2024-01-24 13:50:18,013] [INFO] Running command: blastn -query GCF_001679645.1_ASM167964v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0aab3f3c-26cd-4a28-b787-ab8fb8fb2293/dqc_reference/reference_markers.fasta -out GCF_001679645.1_ASM167964v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:19,049] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:19,052] [INFO] Selected 14 target genomes.
[2024-01-24 13:50:19,052] [INFO] Target genome list was writen to GCF_001679645.1_ASM167964v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:19,059] [INFO] Task started: fastANI
[2024-01-24 13:50:19,059] [INFO] Running command: fastANI --query /var/lib/cwl/stgf840a2cd-488b-4d39-bed6-3a170ab5e469/GCF_001679645.1_ASM167964v1_genomic.fna.gz --refList GCF_001679645.1_ASM167964v1_genomic.fna/target_genomes.txt --output GCF_001679645.1_ASM167964v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:41,651] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:41,651] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0aab3f3c-26cd-4a28-b787-ab8fb8fb2293/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:41,652] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0aab3f3c-26cd-4a28-b787-ab8fb8fb2293/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:41,664] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:41,664] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:41,664] [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 bananamidigenes	strain=BW11P2	GCA_001679645.1	2843610	2843610	type	True	100.0	1918	1931	95	conclusive
Pseudomonas kribbensis	strain=46-2	GCA_003352185.1	1628086	1628086	type	True	92.2126	1746	1931	95	below_threshold
Pseudomonas allokribbensis	strain=IzPS23	GCA_014863605.1	2774460	2774460	type	True	91.4532	1708	1931	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	90.2696	1617	1931	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	90.2617	1638	1931	95	below_threshold
Pseudomonas koreensis	strain=DSM 16610	GCA_012986595.1	198620	198620	suspected-type	True	88.0753	1585	1931	95	below_threshold
Pseudomonas monsensis	strain=PGSB 8459	GCA_014268495.2	2745509	2745509	type	True	87.5312	1590	1931	95	below_threshold
Pseudomonas zeae	strain=OE 48.2	GCA_014268485.2	2745510	2745510	type	True	87.1519	1604	1931	95	below_threshold
Pseudomonas crudilactis	strain=UCMA 17988	GCA_013433315.1	2697028	2697028	type	True	87.1157	1593	1931	95	below_threshold
Pseudomonas tensinigenes	strain=ZA 5.3	GCA_014268445.2	2745511	2745511	type	True	87.0705	1607	1931	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	87.0536	1589	1931	95	below_threshold
Pseudomonas moorei	strain=CCUG 53114	GCA_008801475.1	395599	395599	type	True	85.319	1299	1931	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	83.1594	1187	1931	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	81.9419	842	1931	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:41,666] [INFO] DFAST Taxonomy check result was written to GCF_001679645.1_ASM167964v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:41,667] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:41,667] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:41,667] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0aab3f3c-26cd-4a28-b787-ab8fb8fb2293/dqc_reference/checkm_data
[2024-01-24 13:50:41,668] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:41,724] [INFO] Task started: CheckM
[2024-01-24 13:50:41,724] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001679645.1_ASM167964v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001679645.1_ASM167964v1_genomic.fna/checkm_input GCF_001679645.1_ASM167964v1_genomic.fna/checkm_result
[2024-01-24 13:51:43,957] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:43,958] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:43,977] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:43,977] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:43,978] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001679645.1_ASM167964v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:43,978] [INFO] Task started: Blastn
[2024-01-24 13:51:43,978] [INFO] Running command: blastn -query GCF_001679645.1_ASM167964v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0aab3f3c-26cd-4a28-b787-ab8fb8fb2293/dqc_reference/reference_markers_gtdb.fasta -out GCF_001679645.1_ASM167964v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:45,748] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:45,751] [INFO] Selected 15 target genomes.
[2024-01-24 13:51:45,752] [INFO] Target genome list was writen to GCF_001679645.1_ASM167964v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:45,773] [INFO] Task started: fastANI
[2024-01-24 13:51:45,773] [INFO] Running command: fastANI --query /var/lib/cwl/stgf840a2cd-488b-4d39-bed6-3a170ab5e469/GCF_001679645.1_ASM167964v1_genomic.fna.gz --refList GCF_001679645.1_ASM167964v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001679645.1_ASM167964v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:52:08,258] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:08,271] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:52:08,271] [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_001679645.1	s__Pseudomonas_E fluorescens_K	100.0	1918	1931	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003352185.1	s__Pseudomonas_E kribbensis	92.2048	1747	1931	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.22	95.68	0.92	0.89	10	-
GCF_002112385.1	s__Pseudomonas_E sp002112385	91.6654	1703	1931	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	7	-
GCF_012974785.1	s__Pseudomonas_E fluorescens_BT	91.5602	1708	1931	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.87	98.87	0.96	0.96	2	-
GCF_014863605.1	s__Pseudomonas_E allokribbensis	91.4532	1708	1931	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.79	97.76	0.93	0.92	10	-
GCF_004006335.1	s__Pseudomonas_E sp002112885	90.6267	1681	1931	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.01	95.48	0.92	0.90	14	-
GCF_003352875.1	s__Pseudomonas_E fluorescens_BF	90.6133	1685	1931	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_002113045.1	s__Pseudomonas_E sp002113045	90.5036	1658	1931	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.93	98.93	0.93	0.93	2	-
GCF_014863585.1	s__Pseudomonas_E gozinkensis	90.4758	1676	1931	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_001594225.2	s__Pseudomonas_E glycinae	90.2381	1687	1931	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.56	95.98	0.93	0.88	9	-
GCF_002878485.1	s__Pseudomonas_E sp002878485	87.7761	1578	1931	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	87.5285	1590	1931	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_009834515.1	s__Pseudomonas_E sp009834515	87.081	1602	1931	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_005938625.1	s__Pseudomonas_E fluorescens_BD	87.0586	1587	1931	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_004124275.1	s__Pseudomonas_E sp004124275	87.028	1602	1931	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 13:52:08,273] [INFO] GTDB search result was written to GCF_001679645.1_ASM167964v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:52:08,274] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:52:08,278] [INFO] DFAST_QC result json was written to GCF_001679645.1_ASM167964v1_genomic.fna/dqc_result.json
[2024-01-24 13:52:08,278] [INFO] DFAST_QC completed!
[2024-01-24 13:52:08,278] [INFO] Total running time: 0h2m13s