[2024-01-24 10:57:06,595] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:06,599] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:06,599] [INFO] DQC Reference Directory: /var/lib/cwl/stge5c38a94-a0a9-47a1-90ad-877fced6bd50/dqc_reference
[2024-01-24 10:57:07,867] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:07,868] [INFO] Task started: Prodigal
[2024-01-24 10:57:07,868] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ece4c15-a76f-42d0-9255-943512cee8f9/GCF_019655855.2_ASM1965585v2_genomic.fna.gz | prodigal -d GCF_019655855.2_ASM1965585v2_genomic.fna/cds.fna -a GCF_019655855.2_ASM1965585v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:23,681] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:23,681] [INFO] Task started: HMMsearch
[2024-01-24 10:57:23,681] [INFO] Running command: hmmsearch --tblout GCF_019655855.2_ASM1965585v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5c38a94-a0a9-47a1-90ad-877fced6bd50/dqc_reference/reference_markers.hmm GCF_019655855.2_ASM1965585v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:23,980] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:23,981] [INFO] Found 6/6 markers.
[2024-01-24 10:57:24,026] [INFO] Query marker FASTA was written to GCF_019655855.2_ASM1965585v2_genomic.fna/markers.fasta
[2024-01-24 10:57:24,027] [INFO] Task started: Blastn
[2024-01-24 10:57:24,027] [INFO] Running command: blastn -query GCF_019655855.2_ASM1965585v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge5c38a94-a0a9-47a1-90ad-877fced6bd50/dqc_reference/reference_markers.fasta -out GCF_019655855.2_ASM1965585v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:25,169] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:25,190] [INFO] Selected 23 target genomes.
[2024-01-24 10:57:25,190] [INFO] Target genome list was writen to GCF_019655855.2_ASM1965585v2_genomic.fna/target_genomes.txt
[2024-01-24 10:57:25,211] [INFO] Task started: fastANI
[2024-01-24 10:57:25,211] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ece4c15-a76f-42d0-9255-943512cee8f9/GCF_019655855.2_ASM1965585v2_genomic.fna.gz --refList GCF_019655855.2_ASM1965585v2_genomic.fna/target_genomes.txt --output GCF_019655855.2_ASM1965585v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:54,065] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:54,066] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5c38a94-a0a9-47a1-90ad-877fced6bd50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:54,066] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5c38a94-a0a9-47a1-90ad-877fced6bd50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:54,094] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:57:54,094] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:57:54,094] [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 alcaligenes	strain=NCTC10367	GCA_900455475.1	43263	43263	type	True	88.2652	1114	1781	95	below_threshold
Pseudomonas alcaligenes	strain=NBRC 14159	GCA_000467105.1	43263	43263	type	True	88.2182	1108	1781	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	84.4874	912	1781	95	below_threshold
Pseudomonas tohonis	strain=TUM18999	GCA_012767755.2	2725477	2725477	type	True	84.4754	1126	1781	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	84.3342	1012	1781	95	below_threshold
Pseudomonas delhiensis	strain=RLD-1	GCA_900187975.1	366289	366289	type	True	84.1321	1083	1781	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	84.1073	1073	1781	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	84.1062	1074	1781	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	83.8426	1024	1781	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	83.677	983	1781	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	83.6528	936	1781	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	83.3666	807	1781	95	below_threshold
Pseudomonas alcaliphila	strain=NBRC 102411	GCA_002091495.1	101564	101564	type	True	83.2563	938	1781	95	below_threshold
Pseudomonas alcaliphila	strain=JCM 10630	GCA_900101755.1	101564	101564	type	True	83.1793	950	1781	95	below_threshold
Pseudomonas sihuiensis	strain=KCTC 32246	GCA_900106015.1	1274359	1274359	type	True	83.1278	971	1781	95	below_threshold
Pseudomonas composti	strain=CCUG 59231	GCA_900115475.1	658457	658457	type	True	82.8758	980	1781	95	below_threshold
Stutzerimonas azotifigens	strain=DSM 17556	GCA_000425625.1	291995	291995	type	True	82.6688	834	1781	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	82.6653	991	1781	95	below_threshold
Pseudomonas aeruginosa	strain=CCUG 551	GCA_008801675.1	287	287	type	True	82.6415	996	1781	95	below_threshold
Pseudomonas indica	strain=JCM 21544	GCA_900100285.1	137658	137658	type	True	82.6166	974	1781	95	below_threshold
Pseudomonas indica	strain=NBRC 103045	GCA_002091635.1	137658	137658	type	True	82.6159	973	1781	95	below_threshold
Azotobacter chroococcum subsp. isscasi	strain=P205	GCA_004327895.1	2528971	353	type	True	82.5058	763	1781	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	82.4915	1016	1781	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:54,096] [INFO] DFAST Taxonomy check result was written to GCF_019655855.2_ASM1965585v2_genomic.fna/tc_result.tsv
[2024-01-24 10:57:54,097] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:54,097] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:54,097] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5c38a94-a0a9-47a1-90ad-877fced6bd50/dqc_reference/checkm_data
[2024-01-24 10:57:54,098] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:54,147] [INFO] Task started: CheckM
[2024-01-24 10:57:54,147] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019655855.2_ASM1965585v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019655855.2_ASM1965585v2_genomic.fna/checkm_input GCF_019655855.2_ASM1965585v2_genomic.fna/checkm_result
[2024-01-24 10:58:40,273] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:40,275] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:40,296] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:40,297] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:40,297] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019655855.2_ASM1965585v2_genomic.fna/markers.fasta)
[2024-01-24 10:58:40,297] [INFO] Task started: Blastn
[2024-01-24 10:58:40,298] [INFO] Running command: blastn -query GCF_019655855.2_ASM1965585v2_genomic.fna/markers.fasta -db /var/lib/cwl/stge5c38a94-a0a9-47a1-90ad-877fced6bd50/dqc_reference/reference_markers_gtdb.fasta -out GCF_019655855.2_ASM1965585v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:42,443] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:42,447] [INFO] Selected 13 target genomes.
[2024-01-24 10:58:42,447] [INFO] Target genome list was writen to GCF_019655855.2_ASM1965585v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:42,501] [INFO] Task started: fastANI
[2024-01-24 10:58:42,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ece4c15-a76f-42d0-9255-943512cee8f9/GCF_019655855.2_ASM1965585v2_genomic.fna.gz --refList GCF_019655855.2_ASM1965585v2_genomic.fna/target_genomes_gtdb.txt --output GCF_019655855.2_ASM1965585v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:59,412] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:59,426] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:59,426] [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
GCA_002483005.1	s__Pseudomonas_E sp002483005	95.7766	783	1781	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_005508865.1	s__Pseudomonas_E sp005508865	89.1534	1154	1781	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_003205495.1	s__Pseudomonas_E alcaligenes_B	88.8433	1012	1781	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_014851565.1	s__Pseudomonas_E sp014851565	88.7646	1136	1781	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_000761545.1	s__Pseudomonas_E sp000761545	88.4745	1128	1781	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_000467105.1	s__Pseudomonas_E alcaligenes	88.2633	1105	1781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.23	96.43	0.89	0.81	8	-
GCF_900156545.1	s__Pseudomonas_E alcaligenes_A	87.7409	1050	1781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.95	95.95	0.92	0.92	2	-
GCF_014851865.1	s__Pseudomonas_E sp014851865	87.7212	1296	1781	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_014490745.1	s__Pseudomonas_E alcaligenes_C	86.8929	1098	1781	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_003696305.1	s__Pseudomonas_E sp003696305	85.2242	980	1781	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_012767755.2	s__Pseudomonas_F sp003234055	84.5152	1121	1781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	96.89	96.11	0.89	0.88	3	-
GCF_000474255.1	s__Pseudomonas_F alcaligenes_A	84.2099	1103	1781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	98.08	97.69	0.89	0.89	3	-
GCF_013393345.1	s__Pseudomonas_F resinovorans_C	82.5639	982	1781	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	95.04	95.04	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:59,428] [INFO] GTDB search result was written to GCF_019655855.2_ASM1965585v2_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:59,428] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:59,432] [INFO] DFAST_QC result json was written to GCF_019655855.2_ASM1965585v2_genomic.fna/dqc_result.json
[2024-01-24 10:58:59,432] [INFO] DFAST_QC completed!
[2024-01-24 10:58:59,433] [INFO] Total running time: 0h1m53s