[2024-01-24 12:06:24,376] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:24,379] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:24,379] [INFO] DQC Reference Directory: /var/lib/cwl/stgef1dd1a1-060f-4d87-b7e9-4bba75f1c109/dqc_reference
[2024-01-24 12:06:25,675] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:25,676] [INFO] Task started: Prodigal
[2024-01-24 12:06:25,676] [INFO] Running command: gunzip -c /var/lib/cwl/stgd04fff9d-2b62-4534-8454-7e53c7ef257d/GCF_021495345.1_ASM2149534v2_genomic.fna.gz | prodigal -d GCF_021495345.1_ASM2149534v2_genomic.fna/cds.fna -a GCF_021495345.1_ASM2149534v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:42,436] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:42,437] [INFO] Task started: HMMsearch
[2024-01-24 12:06:42,437] [INFO] Running command: hmmsearch --tblout GCF_021495345.1_ASM2149534v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef1dd1a1-060f-4d87-b7e9-4bba75f1c109/dqc_reference/reference_markers.hmm GCF_021495345.1_ASM2149534v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:42,715] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:42,716] [INFO] Found 6/6 markers.
[2024-01-24 12:06:42,767] [INFO] Query marker FASTA was written to GCF_021495345.1_ASM2149534v2_genomic.fna/markers.fasta
[2024-01-24 12:06:42,768] [INFO] Task started: Blastn
[2024-01-24 12:06:42,768] [INFO] Running command: blastn -query GCF_021495345.1_ASM2149534v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgef1dd1a1-060f-4d87-b7e9-4bba75f1c109/dqc_reference/reference_markers.fasta -out GCF_021495345.1_ASM2149534v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:43,913] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:43,917] [INFO] Selected 13 target genomes.
[2024-01-24 12:06:43,917] [INFO] Target genome list was writen to GCF_021495345.1_ASM2149534v2_genomic.fna/target_genomes.txt
[2024-01-24 12:06:43,922] [INFO] Task started: fastANI
[2024-01-24 12:06:43,923] [INFO] Running command: fastANI --query /var/lib/cwl/stgd04fff9d-2b62-4534-8454-7e53c7ef257d/GCF_021495345.1_ASM2149534v2_genomic.fna.gz --refList GCF_021495345.1_ASM2149534v2_genomic.fna/target_genomes.txt --output GCF_021495345.1_ASM2149534v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:01,118] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:01,119] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef1dd1a1-060f-4d87-b7e9-4bba75f1c109/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:01,119] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef1dd1a1-060f-4d87-b7e9-4bba75f1c109/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:01,131] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:01,131] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:01,131] [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 hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	100.0	1762	1763	95	conclusive
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	91.95	1388	1763	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	89.7449	1326	1763	95	below_threshold
Pseudomonas sihuiensis	strain=KCTC 32246	GCA_900106015.1	1274359	1274359	type	True	89.271	1355	1763	95	below_threshold
Pseudomonas toyotomiensis	strain=DSM 26169	GCA_002741095.1	554344	554344	type	True	89.2496	1360	1763	95	below_threshold
Pseudomonas toyotomiensis	strain=JCM 15604	GCA_900115695.1	554344	554344	type	True	89.2367	1373	1763	95	below_threshold
Pseudomonas alcaliphila	strain=JCM 10630	GCA_900101755.1	101564	101564	type	True	89.0669	1348	1763	95	below_threshold
Pseudomonas alcaliphila	strain=NBRC 102411	GCA_002091495.1	101564	101564	type	True	89.058	1335	1763	95	below_threshold
Pseudomonas mendocina	strain=NBRC 14162	GCA_000813265.1	300	300	suspected-type	True	88.1628	1308	1763	95	below_threshold
Pseudomonas mendocina	strain=NCTC10897	GCA_900636545.1	300	300	suspected-type	True	88.1217	1340	1763	95	below_threshold
Pseudomonas composti	strain=CCUG 59231	GCA_900115475.1	658457	658457	type	True	87.9888	1322	1763	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	84.8633	996	1763	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	82.8987	950	1763	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:01,133] [INFO] DFAST Taxonomy check result was written to GCF_021495345.1_ASM2149534v2_genomic.fna/tc_result.tsv
[2024-01-24 12:07:01,133] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:01,134] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:01,134] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef1dd1a1-060f-4d87-b7e9-4bba75f1c109/dqc_reference/checkm_data
[2024-01-24 12:07:01,135] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:01,185] [INFO] Task started: CheckM
[2024-01-24 12:07:01,186] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021495345.1_ASM2149534v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021495345.1_ASM2149534v2_genomic.fna/checkm_input GCF_021495345.1_ASM2149534v2_genomic.fna/checkm_result
[2024-01-24 12:07:49,609] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:49,610] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:49,630] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:49,630] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:49,630] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021495345.1_ASM2149534v2_genomic.fna/markers.fasta)
[2024-01-24 12:07:49,631] [INFO] Task started: Blastn
[2024-01-24 12:07:49,631] [INFO] Running command: blastn -query GCF_021495345.1_ASM2149534v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgef1dd1a1-060f-4d87-b7e9-4bba75f1c109/dqc_reference/reference_markers_gtdb.fasta -out GCF_021495345.1_ASM2149534v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:51,735] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:51,738] [INFO] Selected 15 target genomes.
[2024-01-24 12:07:51,738] [INFO] Target genome list was writen to GCF_021495345.1_ASM2149534v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:51,748] [INFO] Task started: fastANI
[2024-01-24 12:07:51,749] [INFO] Running command: fastANI --query /var/lib/cwl/stgd04fff9d-2b62-4534-8454-7e53c7ef257d/GCF_021495345.1_ASM2149534v2_genomic.fna.gz --refList GCF_021495345.1_ASM2149534v2_genomic.fna/target_genomes_gtdb.txt --output GCF_021495345.1_ASM2149534v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:10,737] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:10,750] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:10,751] [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_000016565.1	s__Pseudomonas_E mendocina_A	97.8977	1531	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.76	97.37	0.90	0.88	7	conclusive
GCF_900104265.1	s__Pseudomonas_E guguanensis	91.95	1388	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.13	97.13	0.85	0.85	2	-
GCF_000418555.1	s__Pseudomonas_E sp000418555	90.5496	1332	1763	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_009932725.1	s__Pseudomonas_E sp009932725	89.7449	1326	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.40	98.35	0.94	0.88	4	-
GCF_002803095.1	s__Pseudomonas_E sp002803095	89.693	1355	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.6432	99.96	99.96	0.99	0.99	2	-
GCF_003696305.1	s__Pseudomonas_E sp003696305	89.6169	1281	1763	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_900106015.1	s__Pseudomonas_E sihuiensis	89.271	1355	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.7402	N/A	N/A	N/A	N/A	1	-
GCF_900115695.1	s__Pseudomonas_E toyotomiensis	89.2475	1372	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.1942	98.17	97.23	0.91	0.85	7	-
GCF_001941865.1	s__Pseudomonas_E alcaliphila_B	89.0853	1316	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.7502	96.52	96.24	0.87	0.86	3	-
GCF_016008875.1	s__Pseudomonas_E sp002439135	88.7176	1298	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.91	96.75	0.87	0.85	5	-
GCF_003052605.1	s__Pseudomonas_E indoloxydans	88.4037	1157	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.52	N/A	N/A	N/A	N/A	1	-
GCF_008041835.1	s__Pseudomonas_E sp002282595	88.3496	1085	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.53	95.53	0.75	0.75	2	-
GCF_004521985.1	s__Pseudomonas_E khazarica	87.9253	1288	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.35	98.01	0.91	0.87	12	-
GCF_003008615.1	s__Pseudomonas_E mendocina_C	87.0711	1299	1763	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_014109765.1	s__Pseudomonas_E oleovorans_B	87.0491	1308	1763	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.92	96.88	0.93	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:10,752] [INFO] GTDB search result was written to GCF_021495345.1_ASM2149534v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:10,753] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:10,757] [INFO] DFAST_QC result json was written to GCF_021495345.1_ASM2149534v2_genomic.fna/dqc_result.json
[2024-01-24 12:08:10,757] [INFO] DFAST_QC completed!
[2024-01-24 12:08:10,758] [INFO] Total running time: 0h1m46s