[2024-01-24 13:17:12,427] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:12,431] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:12,431] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d5c10e7-14fa-4859-9aee-9c001f2b43c0/dqc_reference
[2024-01-24 13:17:13,673] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:13,674] [INFO] Task started: Prodigal
[2024-01-24 13:17:13,674] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5b2b769-3580-4015-9923-52bea33e81bf/GCF_021271205.1_ASM2127120v1_genomic.fna.gz | prodigal -d GCF_021271205.1_ASM2127120v1_genomic.fna/cds.fna -a GCF_021271205.1_ASM2127120v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:37,013] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:37,013] [INFO] Task started: HMMsearch
[2024-01-24 13:17:37,013] [INFO] Running command: hmmsearch --tblout GCF_021271205.1_ASM2127120v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d5c10e7-14fa-4859-9aee-9c001f2b43c0/dqc_reference/reference_markers.hmm GCF_021271205.1_ASM2127120v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:37,354] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:37,356] [INFO] Found 6/6 markers.
[2024-01-24 13:17:37,408] [INFO] Query marker FASTA was written to GCF_021271205.1_ASM2127120v1_genomic.fna/markers.fasta
[2024-01-24 13:17:37,408] [INFO] Task started: Blastn
[2024-01-24 13:17:37,409] [INFO] Running command: blastn -query GCF_021271205.1_ASM2127120v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d5c10e7-14fa-4859-9aee-9c001f2b43c0/dqc_reference/reference_markers.fasta -out GCF_021271205.1_ASM2127120v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:38,472] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:38,475] [INFO] Selected 16 target genomes.
[2024-01-24 13:17:38,475] [INFO] Target genome list was writen to GCF_021271205.1_ASM2127120v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:38,482] [INFO] Task started: fastANI
[2024-01-24 13:17:38,482] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5b2b769-3580-4015-9923-52bea33e81bf/GCF_021271205.1_ASM2127120v1_genomic.fna.gz --refList GCF_021271205.1_ASM2127120v1_genomic.fna/target_genomes.txt --output GCF_021271205.1_ASM2127120v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:02,086] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:02,087] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d5c10e7-14fa-4859-9aee-9c001f2b43c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:02,087] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d5c10e7-14fa-4859-9aee-9c001f2b43c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:02,104] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:18:02,104] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:18:02,105] [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 mediterranea	strain=DSM 16733	GCA_900106005.1	183795	183795	type	True	87.4613	1601	1971	95	below_threshold
Pseudomonas mediterranea	strain=CFBP 5447	GCA_000774145.1	183795	183795	type	True	87.4498	1585	1971	95	below_threshold
Pseudomonas kilonensis	strain=DSM 13647	GCA_001269885.1	132476	132476	type	True	87.335	1530	1971	95	below_threshold
Pseudomonas brassicacearum	strain=JCM 11938	GCA_012034345.1	930166	930166	suspected-type	True	87.284	1559	1971	95	below_threshold
Pseudomonas brassicacearum subsp. brassicacearum	strain=CCUG 51508	GCA_008801605.1	86264	930166	type	True	87.2644	1560	1971	95	below_threshold
Pseudomonas thivervalensis	strain=DSM 13194	GCA_001269655.1	86265	86265	type	True	87.1974	1567	1971	95	below_threshold
Pseudomonas viciae	strain=11K1	GCA_004786035.1	2505979	2505979	type	True	87.1253	1583	1971	95	below_threshold
Pseudomonas corrugata	strain=NCPPB2445	GCA_003699065.1	47879	47879	type	True	87.0063	1516	1971	95	below_threshold
Pseudomonas corrugata	strain=DSM 7228	GCA_001269905.1	47879	47879	type	True	86.9911	1540	1971	95	below_threshold
Pseudomonas corrugata	strain=NCPPB2445	GCA_001411965.1	47879	47879	type	True	86.9761	1541	1971	95	below_threshold
Pseudomonas zanjanensis	strain=SWRI12	GCA_014268745.2	2745496	2745496	type	True	86.8504	1522	1971	95	below_threshold
Pseudomonas rhizophila	strain=S211	GCA_003033885.1	2045200	2045200	type	True	86.5578	1537	1971	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	83.6077	1227	1971	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	83.5764	1268	1971	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	82.7505	1225	1971	95	below_threshold
Pseudomonas brassicae	strain=MAFF 212427	GCA_010671725.1	2708063	2708063	type	True	81.7869	776	1971	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:02,106] [INFO] DFAST Taxonomy check result was written to GCF_021271205.1_ASM2127120v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:02,107] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:02,107] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:02,107] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d5c10e7-14fa-4859-9aee-9c001f2b43c0/dqc_reference/checkm_data
[2024-01-24 13:18:02,108] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:02,163] [INFO] Task started: CheckM
[2024-01-24 13:18:02,163] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021271205.1_ASM2127120v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021271205.1_ASM2127120v1_genomic.fna/checkm_input GCF_021271205.1_ASM2127120v1_genomic.fna/checkm_result
[2024-01-24 13:19:06,114] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:06,115] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:06,133] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:06,134] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:06,134] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021271205.1_ASM2127120v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:06,135] [INFO] Task started: Blastn
[2024-01-24 13:19:06,135] [INFO] Running command: blastn -query GCF_021271205.1_ASM2127120v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d5c10e7-14fa-4859-9aee-9c001f2b43c0/dqc_reference/reference_markers_gtdb.fasta -out GCF_021271205.1_ASM2127120v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:07,981] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:07,984] [INFO] Selected 13 target genomes.
[2024-01-24 13:19:07,984] [INFO] Target genome list was writen to GCF_021271205.1_ASM2127120v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:08,009] [INFO] Task started: fastANI
[2024-01-24 13:19:08,009] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5b2b769-3580-4015-9923-52bea33e81bf/GCF_021271205.1_ASM2127120v1_genomic.fna.gz --refList GCF_021271205.1_ASM2127120v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021271205.1_ASM2127120v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:29,460] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:29,473] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:29,473] [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_001269775.1	s__Pseudomonas_E sp001269775	99.3518	1862	1971	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_900156465.1	s__Pseudomonas_E sp900156465	89.0691	1683	1971	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.57	99.46	0.97	0.95	10	-
GCF_000774145.1	s__Pseudomonas_E mediterranea	87.4402	1586	1971	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.46	99.30	0.95	0.94	8	-
GCF_014596565.1	s__Pseudomonas_E sp000801235	87.3655	1562	1971	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	0.97	0.97	2	-
GCF_006227205.1	s__Pseudomonas_E sp006227205	87.3337	1584	1971	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.95	98.77	0.93	0.93	3	-
GCF_007828215.1	s__Pseudomonas_E sp007828215	87.283	1550	1971	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.74	99.65	0.96	0.95	6	-
GCF_001623525.1	s__Pseudomonas_E fluorescens_Q	87.2528	1553	1971	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.03	97.11	0.90	0.89	14	-
GCF_001307275.1	s__Pseudomonas_E fluorescens_AA	87.2327	1635	1971	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.99	95.90	0.90	0.85	18	-
GCF_001269655.1	s__Pseudomonas_E thivervalensis	87.1892	1568	1971	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.35	98.81	0.96	0.93	6	-
GCF_004786035.1	s__Pseudomonas_E viciae	87.1358	1582	1971	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_900581005.1	s__Pseudomonas_E sp900581005	87.0981	1556	1971	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_001269905.1	s__Pseudomonas_E corrugata	86.9879	1540	1971	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.75	99.47	0.98	0.95	7	-
GCF_014268745.2	s__Pseudomonas_E sp014268745	86.8612	1521	1971	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.32	95.56	0.90	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:29,484] [INFO] GTDB search result was written to GCF_021271205.1_ASM2127120v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:29,485] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:29,491] [INFO] DFAST_QC result json was written to GCF_021271205.1_ASM2127120v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:29,491] [INFO] DFAST_QC completed!
[2024-01-24 13:19:29,491] [INFO] Total running time: 0h2m17s