[2024-01-24 10:49:34,771] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:49:34,774] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:49:34,774] [INFO] DQC Reference Directory: /var/lib/cwl/stg5030e502-2a48-4439-85a2-993445940cd3/dqc_reference
[2024-01-24 10:49:36,009] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:49:36,010] [INFO] Task started: Prodigal
[2024-01-24 10:49:36,010] [INFO] Running command: gunzip -c /var/lib/cwl/stge747a2f4-428c-40ad-91da-6d2bc9a64b34/GCF_008801535.1_ASM880153v1_genomic.fna.gz | prodigal -d GCF_008801535.1_ASM880153v1_genomic.fna/cds.fna -a GCF_008801535.1_ASM880153v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:49:57,636] [INFO] Task succeeded: Prodigal
[2024-01-24 10:49:57,636] [INFO] Task started: HMMsearch
[2024-01-24 10:49:57,637] [INFO] Running command: hmmsearch --tblout GCF_008801535.1_ASM880153v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5030e502-2a48-4439-85a2-993445940cd3/dqc_reference/reference_markers.hmm GCF_008801535.1_ASM880153v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:49:58,039] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:49:58,041] [INFO] Found 6/6 markers.
[2024-01-24 10:49:58,093] [INFO] Query marker FASTA was written to GCF_008801535.1_ASM880153v1_genomic.fna/markers.fasta
[2024-01-24 10:49:58,093] [INFO] Task started: Blastn
[2024-01-24 10:49:58,094] [INFO] Running command: blastn -query GCF_008801535.1_ASM880153v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5030e502-2a48-4439-85a2-993445940cd3/dqc_reference/reference_markers.fasta -out GCF_008801535.1_ASM880153v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:59,087] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:59,091] [INFO] Selected 16 target genomes.
[2024-01-24 10:49:59,091] [INFO] Target genome list was writen to GCF_008801535.1_ASM880153v1_genomic.fna/target_genomes.txt
[2024-01-24 10:49:59,097] [INFO] Task started: fastANI
[2024-01-24 10:49:59,098] [INFO] Running command: fastANI --query /var/lib/cwl/stge747a2f4-428c-40ad-91da-6d2bc9a64b34/GCF_008801535.1_ASM880153v1_genomic.fna.gz --refList GCF_008801535.1_ASM880153v1_genomic.fna/target_genomes.txt --output GCF_008801535.1_ASM880153v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:50:27,471] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:27,472] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5030e502-2a48-4439-85a2-993445940cd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:50:27,473] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5030e502-2a48-4439-85a2-993445940cd3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:50:27,489] [INFO] Found 16 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 10:50:27,490] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:50:27,490] [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=CCUG 51519	GCA_008801535.1	198620	198620	suspected-type	True	100.0	2015	2017	95	conclusive
Pseudomonas koreensis	strain=DSM 16610	GCA_012986595.1	198620	198620	suspected-type	True	99.9972	2011	2017	95	conclusive
Pseudomonas koreensis	strain=JCM 14769	GCA_014646955.1	198620	198620	suspected-type	True	99.9925	2006	2017	95	conclusive
Pseudomonas monsensis	strain=PGSB 8459	GCA_014268495.2	2745509	2745509	type	True	90.1478	1732	2017	95	below_threshold
Pseudomonas baetica	strain=LMG 25716	GCA_002813455.1	674054	674054	type	True	89.0336	1668	2017	95	below_threshold
Pseudomonas baetica	strain=a390	GCA_003031005.1	674054	674054	type	True	89.0076	1640	2017	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	88.9945	1743	2017	95	below_threshold
Pseudomonas crudilactis	strain=UCMA 17988	GCA_013433315.1	2697028	2697028	type	True	88.9439	1708	2017	95	below_threshold
Pseudomonas kribbensis	strain=46-2	GCA_003352185.1	1628086	1628086	type	True	88.9069	1668	2017	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	88.8272	1680	2017	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	88.7972	1623	2017	95	below_threshold
Pseudomonas iranensis	strain=SWRI54	GCA_014268585.2	2745503	2745503	type	True	88.1468	1568	2017	95	below_threshold
Pseudomonas triticicola	strain=SWRI88	GCA_019145375.1	2842345	2842345	type	True	88.0022	1538	2017	95	below_threshold
Pseudomonas hamedanensis	strain=SWRI65	GCA_014268595.2	2745504	2745504	type	True	87.8048	1569	2017	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	83.4884	1334	2017	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	83.4773	1271	2017	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:50:27,492] [INFO] DFAST Taxonomy check result was written to GCF_008801535.1_ASM880153v1_genomic.fna/tc_result.tsv
[2024-01-24 10:50:27,492] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:50:27,492] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:50:27,493] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5030e502-2a48-4439-85a2-993445940cd3/dqc_reference/checkm_data
[2024-01-24 10:50:27,494] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:50:27,556] [INFO] Task started: CheckM
[2024-01-24 10:50:27,557] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008801535.1_ASM880153v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008801535.1_ASM880153v1_genomic.fna/checkm_input GCF_008801535.1_ASM880153v1_genomic.fna/checkm_result
[2024-01-24 10:51:34,813] [INFO] Task succeeded: CheckM
[2024-01-24 10:51:34,814] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:51:34,838] [INFO] ===== Completeness check finished =====
[2024-01-24 10:51:34,838] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:51:34,839] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008801535.1_ASM880153v1_genomic.fna/markers.fasta)
[2024-01-24 10:51:34,839] [INFO] Task started: Blastn
[2024-01-24 10:51:34,839] [INFO] Running command: blastn -query GCF_008801535.1_ASM880153v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5030e502-2a48-4439-85a2-993445940cd3/dqc_reference/reference_markers_gtdb.fasta -out GCF_008801535.1_ASM880153v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:51:36,771] [INFO] Task succeeded: Blastn
[2024-01-24 10:51:36,776] [INFO] Selected 15 target genomes.
[2024-01-24 10:51:36,776] [INFO] Target genome list was writen to GCF_008801535.1_ASM880153v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:51:36,798] [INFO] Task started: fastANI
[2024-01-24 10:51:36,798] [INFO] Running command: fastANI --query /var/lib/cwl/stge747a2f4-428c-40ad-91da-6d2bc9a64b34/GCF_008801535.1_ASM880153v1_genomic.fna.gz --refList GCF_008801535.1_ASM880153v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008801535.1_ASM880153v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:52:03,658] [INFO] Task succeeded: fastANI
[2024-01-24 10:52:03,682] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:52:03,682] [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_012986595.1	s__Pseudomonas_E koreensis	99.9972	2011	2017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.85	97.85	0.96	0.91	8	conclusive
GCF_003999415.1	s__Pseudomonas_E koreensis_E	92.8845	1737	2017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.57	98.57	0.92	0.92	2	-
GCF_002878485.1	s__Pseudomonas_E sp002878485	92.3181	1686	2017	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	92.0944	1784	2017	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	92.082	1773	2017	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_000633255.1	s__Pseudomonas_E sp000633255	92.0676	1743	2017	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	91.9812	1750	2017	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	91.9607	1741	2017	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_002287825.1	s__Pseudomonas_E koreensis_B	91.7105	1750	2017	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	91.5426	1624	2017	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	90.1401	1733	2017	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_018326005.1	s__Pseudomonas_E sp002901475	89.4058	1738	2017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.45	98.45	0.94	0.94	2	-
GCF_016651305.1	s__Pseudomonas_E sp016651305	89.1514	1724	2017	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_002813455.1	s__Pseudomonas_E baetica	89.057	1666	2017	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.98	95.55	0.93	0.86	4	-
GCF_014472415.1	s__Pseudomonas_E sp014472415	89.0033	1599	2017	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 10:52:03,684] [INFO] GTDB search result was written to GCF_008801535.1_ASM880153v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:52:03,685] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:52:03,688] [INFO] DFAST_QC result json was written to GCF_008801535.1_ASM880153v1_genomic.fna/dqc_result.json
[2024-01-24 10:52:03,689] [INFO] DFAST_QC completed!
[2024-01-24 10:52:03,689] [INFO] Total running time: 0h2m29s