[2024-01-25 19:33:20,970] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:33:20,972] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:33:20,972] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8e72a8e-38e9-4ea5-97ef-996c0321a5da/dqc_reference
[2024-01-25 19:33:22,143] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:33:22,144] [INFO] Task started: Prodigal
[2024-01-25 19:33:22,144] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ddc44c7-9318-4f5c-b91d-6a6daa300bf1/GCF_018336155.1_ASM1833615v1_genomic.fna.gz | prodigal -d GCF_018336155.1_ASM1833615v1_genomic.fna/cds.fna -a GCF_018336155.1_ASM1833615v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:33:38,646] [INFO] Task succeeded: Prodigal
[2024-01-25 19:33:38,646] [INFO] Task started: HMMsearch
[2024-01-25 19:33:38,647] [INFO] Running command: hmmsearch --tblout GCF_018336155.1_ASM1833615v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8e72a8e-38e9-4ea5-97ef-996c0321a5da/dqc_reference/reference_markers.hmm GCF_018336155.1_ASM1833615v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:33:38,929] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:33:38,930] [INFO] Found 6/6 markers.
[2024-01-25 19:33:38,978] [INFO] Query marker FASTA was written to GCF_018336155.1_ASM1833615v1_genomic.fna/markers.fasta
[2024-01-25 19:33:38,978] [INFO] Task started: Blastn
[2024-01-25 19:33:38,978] [INFO] Running command: blastn -query GCF_018336155.1_ASM1833615v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8e72a8e-38e9-4ea5-97ef-996c0321a5da/dqc_reference/reference_markers.fasta -out GCF_018336155.1_ASM1833615v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:33:39,806] [INFO] Task succeeded: Blastn
[2024-01-25 19:33:39,811] [INFO] Selected 13 target genomes.
[2024-01-25 19:33:39,811] [INFO] Target genome list was writen to GCF_018336155.1_ASM1833615v1_genomic.fna/target_genomes.txt
[2024-01-25 19:33:39,815] [INFO] Task started: fastANI
[2024-01-25 19:33:39,816] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ddc44c7-9318-4f5c-b91d-6a6daa300bf1/GCF_018336155.1_ASM1833615v1_genomic.fna.gz --refList GCF_018336155.1_ASM1833615v1_genomic.fna/target_genomes.txt --output GCF_018336155.1_ASM1833615v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:34:01,714] [INFO] Task succeeded: fastANI
[2024-01-25 19:34:01,714] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8e72a8e-38e9-4ea5-97ef-996c0321a5da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:34:01,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8e72a8e-38e9-4ea5-97ef-996c0321a5da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:34:01,724] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:34:01,724] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:34:01,724] [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 crudilactis	strain=UCMA 17988	GCA_013433315.1	2697028	2697028	type	True	90.3838	1583	1934	95	below_threshold
Pseudomonas tensinigenes	strain=ZA 5.3	GCA_014268445.2	2745511	2745511	type	True	90.3738	1586	1934	95	below_threshold
Pseudomonas neuropathica	strain=P155	GCA_015461835.1	2730425	2730425	type	True	90.2263	1552	1934	95	below_threshold
Pseudomonas zeae	strain=OE 48.2	GCA_014268485.2	2745510	2745510	type	True	90.221	1554	1934	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	90.1568	1561	1934	95	below_threshold
Pseudomonas baetica	strain=a390	GCA_003031005.1	674054	674054	type	True	89.3045	1459	1934	95	below_threshold
Pseudomonas baetica	strain=LMG 25716	GCA_002813455.1	674054	674054	type	True	89.2607	1520	1934	95	below_threshold
Pseudomonas allokribbensis	strain=IzPS23	GCA_014863605.1	2774460	2774460	type	True	88.0603	1515	1934	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	88.0448	1490	1934	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	87.9374	1471	1934	95	below_threshold
Pseudomonas laurylsulfativorans	strain=AP3_22	GCA_002906155.1	1943631	1943631	type	True	85.5532	1327	1934	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	83.1713	1164	1934	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	81.4799	771	1934	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:34:01,726] [INFO] DFAST Taxonomy check result was written to GCF_018336155.1_ASM1833615v1_genomic.fna/tc_result.tsv
[2024-01-25 19:34:01,726] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:34:01,726] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:34:01,726] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8e72a8e-38e9-4ea5-97ef-996c0321a5da/dqc_reference/checkm_data
[2024-01-25 19:34:01,727] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:34:01,781] [INFO] Task started: CheckM
[2024-01-25 19:34:01,782] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018336155.1_ASM1833615v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018336155.1_ASM1833615v1_genomic.fna/checkm_input GCF_018336155.1_ASM1833615v1_genomic.fna/checkm_result
[2024-01-25 19:34:50,563] [INFO] Task succeeded: CheckM
[2024-01-25 19:34:50,565] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:34:50,586] [INFO] ===== Completeness check finished =====
[2024-01-25 19:34:50,586] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:34:50,587] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018336155.1_ASM1833615v1_genomic.fna/markers.fasta)
[2024-01-25 19:34:50,587] [INFO] Task started: Blastn
[2024-01-25 19:34:50,587] [INFO] Running command: blastn -query GCF_018336155.1_ASM1833615v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8e72a8e-38e9-4ea5-97ef-996c0321a5da/dqc_reference/reference_markers_gtdb.fasta -out GCF_018336155.1_ASM1833615v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:34:51,978] [INFO] Task succeeded: Blastn
[2024-01-25 19:34:51,981] [INFO] Selected 22 target genomes.
[2024-01-25 19:34:51,981] [INFO] Target genome list was writen to GCF_018336155.1_ASM1833615v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:34:51,992] [INFO] Task started: fastANI
[2024-01-25 19:34:51,992] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ddc44c7-9318-4f5c-b91d-6a6daa300bf1/GCF_018336155.1_ASM1833615v1_genomic.fna.gz --refList GCF_018336155.1_ASM1833615v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018336155.1_ASM1833615v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:35:31,386] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:31,401] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:35:31,401] [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_001269815.1	s__Pseudomonas_E sp001269815	97.4181	1705	1934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.38	97.36	0.89	0.88	4	conclusive
GCF_000282515.1	s__Pseudomonas_E sp000282515	91.8954	1497	1934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.31	97.31	0.87	0.87	2	-
GCF_004124275.1	s__Pseudomonas_E sp004124275	90.7624	1571	1934	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_018138145.1	s__Pseudomonas_E koreensis_A	90.657	1572	1934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.53	97.00	0.95	0.94	5	-
GCF_001297015.1	s__Pseudomonas_E sp001297015	90.5992	1579	1934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.81	98.77	0.95	0.94	9	-
GCF_001648775.1	s__Pseudomonas_E fluorescens_M	90.5843	1572	1934	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_009764645.1	s__Pseudomonas_E sp009764645	90.5354	1464	1934	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_000783395.1	s__Pseudomonas_E helmanticensis	90.5293	1538	1934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.23	95.21	0.89	0.89	3	-
GCF_900580865.1	s__Pseudomonas_E sp900580865	90.4681	1577	1934	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_014268445.2	s__Pseudomonas_E sp900187515	90.3938	1584	1934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.92	96.07	0.93	0.91	8	-
GCF_009834515.1	s__Pseudomonas_E sp009834515	90.3843	1535	1934	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_902497745.1	s__Pseudomonas_E fluorescens_BM	90.3762	1564	1934	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_013433315.1	s__Pseudomonas_E crudilactis	90.3759	1583	1934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.42	98.37	0.96	0.95	4	-
GCF_900187605.1	s__Pseudomonas_E sp900187605	90.3279	1557	1934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.55	98.53	0.93	0.93	4	-
GCF_015461835.1	s__Pseudomonas_E neuropathica	90.222	1552	1934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.00	95.48	0.91	0.90	7	-
GCF_016650635.1	s__Pseudomonas_E sp016650635	90.0004	1581	1934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.85	97.85	0.86	0.86	2	-
GCF_017980685.1	s__Pseudomonas_E iridis	88.806	1452	1934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.83	96.38	0.88	0.86	9	-
GCF_016651255.1	s__Pseudomonas_E sp016651255	88.3808	991	1934	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_004682045.1	s__Pseudomonas_E nabeulensis	83.149	1119	1934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.61	95.59	0.85	0.85	3	-
GCF_019139815.1	s__Pseudomonas_E sp900005815	83.0303	1110	1934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.55	99.31	0.95	0.92	7	-
GCF_001439845.1	s__Pseudomonas_E lactis	82.8116	1135	1934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.24	95.50	0.88	0.81	30	-
GCF_900105675.1	s__Pseudomonas_E synxantha	82.5839	1131	1934	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.7053	98.15	96.46	0.93	0.84	14	-
--------------------------------------------------------------------------------
[2024-01-25 19:35:31,404] [INFO] GTDB search result was written to GCF_018336155.1_ASM1833615v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:35:31,405] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:35:31,408] [INFO] DFAST_QC result json was written to GCF_018336155.1_ASM1833615v1_genomic.fna/dqc_result.json
[2024-01-25 19:35:31,408] [INFO] DFAST_QC completed!
[2024-01-25 19:35:31,408] [INFO] Total running time: 0h2m10s