[2024-01-24 14:30:47,251] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:47,253] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:47,253] [INFO] DQC Reference Directory: /var/lib/cwl/stg9082b2cc-9c09-4683-85bc-385ccf07a146/dqc_reference
[2024-01-24 14:30:48,484] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:48,485] [INFO] Task started: Prodigal
[2024-01-24 14:30:48,485] [INFO] Running command: gunzip -c /var/lib/cwl/stgee522416-c75c-45d6-98db-b37648bf809b/GCF_002741105.1_ASM274110v1_genomic.fna.gz | prodigal -d GCF_002741105.1_ASM274110v1_genomic.fna/cds.fna -a GCF_002741105.1_ASM274110v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:03,596] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:03,597] [INFO] Task started: HMMsearch
[2024-01-24 14:31:03,597] [INFO] Running command: hmmsearch --tblout GCF_002741105.1_ASM274110v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9082b2cc-9c09-4683-85bc-385ccf07a146/dqc_reference/reference_markers.hmm GCF_002741105.1_ASM274110v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:03,935] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:03,936] [INFO] Found 6/6 markers.
[2024-01-24 14:31:03,982] [INFO] Query marker FASTA was written to GCF_002741105.1_ASM274110v1_genomic.fna/markers.fasta
[2024-01-24 14:31:03,983] [INFO] Task started: Blastn
[2024-01-24 14:31:03,983] [INFO] Running command: blastn -query GCF_002741105.1_ASM274110v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9082b2cc-9c09-4683-85bc-385ccf07a146/dqc_reference/reference_markers.fasta -out GCF_002741105.1_ASM274110v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:05,087] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:05,091] [INFO] Selected 17 target genomes.
[2024-01-24 14:31:05,091] [INFO] Target genome list was writen to GCF_002741105.1_ASM274110v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:05,100] [INFO] Task started: fastANI
[2024-01-24 14:31:05,100] [INFO] Running command: fastANI --query /var/lib/cwl/stgee522416-c75c-45d6-98db-b37648bf809b/GCF_002741105.1_ASM274110v1_genomic.fna.gz --refList GCF_002741105.1_ASM274110v1_genomic.fna/target_genomes.txt --output GCF_002741105.1_ASM274110v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:26,716] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:26,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9082b2cc-9c09-4683-85bc-385ccf07a146/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:26,717] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9082b2cc-9c09-4683-85bc-385ccf07a146/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:26,731] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:26,731] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:26,731] [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 sediminis	strain=PI11	GCA_002741105.1	1691904	1691904	type	True	100.0	1618	1619	95	conclusive
Pseudomonas chengduensis	strain=DSM 26382	GCA_012986985.1	489632	489632	type	True	91.7167	1408	1619	95	below_threshold
Pseudomonas chengduensis	strain=DSM 26382	GCA_900102635.1	489632	489632	type	True	91.6844	1417	1619	95	below_threshold
Pseudomonas chengduensis	strain=MBR	GCA_017905455.1	489632	489632	type	True	91.6689	1410	1619	95	below_threshold
Pseudomonas sihuiensis	strain=KCTC 32246	GCA_900106015.1	1274359	1274359	type	True	91.5843	1420	1619	95	below_threshold
Pseudomonas toyotomiensis	strain=DSM 26169	GCA_002741095.1	554344	554344	type	True	91.2906	1441	1619	95	below_threshold
Pseudomonas toyotomiensis	strain=JCM 15604	GCA_900115695.1	554344	554344	type	True	91.2516	1443	1619	95	below_threshold
Pseudomonas oleovorans subsp. oleovorans	strain=DSM 1045	GCA_002197815.1	1218129	301	type	True	91.0882	1171	1619	95	below_threshold
Pseudomonas oleovorans subsp. oleovorans	strain=NBRC 13583	GCA_002091815.1	1218129	301	type	True	91.0597	1174	1619	95	below_threshold
Pseudomonas oleovorans	strain=NCTC10692	GCA_900455615.1	301	301	type	True	91.0332	1198	1619	95	below_threshold
Pseudomonas alcaliphila	strain=NBRC 102411	GCA_002091495.1	101564	101564	type	True	90.4263	1388	1619	95	below_threshold
Pseudomonas alcaliphila	strain=JCM 10630	GCA_900101755.1	101564	101564	type	True	90.3831	1395	1619	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	88.9741	1334	1619	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	88.6888	1289	1619	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	88.0401	1298	1619	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	81.9462	881	1619	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	81.8831	899	1619	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:26,733] [INFO] DFAST Taxonomy check result was written to GCF_002741105.1_ASM274110v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:26,733] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:26,734] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:26,734] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9082b2cc-9c09-4683-85bc-385ccf07a146/dqc_reference/checkm_data
[2024-01-24 14:31:26,735] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:26,783] [INFO] Task started: CheckM
[2024-01-24 14:31:26,783] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002741105.1_ASM274110v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002741105.1_ASM274110v1_genomic.fna/checkm_input GCF_002741105.1_ASM274110v1_genomic.fna/checkm_result
[2024-01-24 14:32:13,935] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:13,937] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:13,972] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:13,972] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:13,973] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002741105.1_ASM274110v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:13,973] [INFO] Task started: Blastn
[2024-01-24 14:32:13,973] [INFO] Running command: blastn -query GCF_002741105.1_ASM274110v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9082b2cc-9c09-4683-85bc-385ccf07a146/dqc_reference/reference_markers_gtdb.fasta -out GCF_002741105.1_ASM274110v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:16,048] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:16,057] [INFO] Selected 14 target genomes.
[2024-01-24 14:32:16,057] [INFO] Target genome list was writen to GCF_002741105.1_ASM274110v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:16,069] [INFO] Task started: fastANI
[2024-01-24 14:32:16,070] [INFO] Running command: fastANI --query /var/lib/cwl/stgee522416-c75c-45d6-98db-b37648bf809b/GCF_002741105.1_ASM274110v1_genomic.fna.gz --refList GCF_002741105.1_ASM274110v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002741105.1_ASM274110v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:34,774] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:34,787] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:34,787] [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_002741105.1	s__Pseudomonas_E sediminis	100.0	1618	1619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.01	95.51	0.89	0.85	6	conclusive
GCF_007049795.1	s__Pseudomonas_E mendocina_D	94.8188	1302	1619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.17	96.47	0.87	0.84	6	-
GCF_015712065.1	s__Pseudomonas_E chengduensis_A	91.6937	1461	1619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.7107	97.25	97.17	0.91	0.89	9	-
GCF_900102635.1	s__Pseudomonas_E chengduensis	91.6738	1418	1619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.7402	99.23	98.24	0.94	0.89	5	-
GCF_900106015.1	s__Pseudomonas_E sihuiensis	91.5843	1420	1619	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_001941865.1	s__Pseudomonas_E alcaliphila_B	91.2918	1393	1619	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_002803095.1	s__Pseudomonas_E sp002803095	91.266	1411	1619	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_900115695.1	s__Pseudomonas_E toyotomiensis	91.2548	1442	1619	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_002197815.1	s__Pseudomonas_E oleovorans	91.1025	1170	1619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.52	97.92	96.68	0.87	0.80	18	-
GCF_900115475.1	s__Pseudomonas_E composti	90.7749	1442	1619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.90	97.79	0.91	0.90	5	-
GCF_003052605.1	s__Pseudomonas_E indoloxydans	90.7556	1148	1619	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_902506495.1	s__Pseudomonas_E sp902506495	90.5951	1397	1619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.72	95.94	0.90	0.87	3	-
GCF_900101755.1	s__Pseudomonas_E alcaliphila	90.3831	1395	1619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.74	97.49	0.95	0.92	3	-
GCF_900636545.1	s__Pseudomonas_E mendocina	89.5094	1394	1619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.91	97.19	0.93	0.89	14	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:34,789] [INFO] GTDB search result was written to GCF_002741105.1_ASM274110v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:34,789] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:34,797] [INFO] DFAST_QC result json was written to GCF_002741105.1_ASM274110v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:34,797] [INFO] DFAST_QC completed!
[2024-01-24 14:32:34,797] [INFO] Total running time: 0h1m48s