[2024-01-24 14:22:33,552] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:33,553] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:33,553] [INFO] DQC Reference Directory: /var/lib/cwl/stg67469902-1e2b-4623-bd88-0250427ff923/dqc_reference
[2024-01-24 14:22:34,818] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:34,819] [INFO] Task started: Prodigal
[2024-01-24 14:22:34,819] [INFO] Running command: gunzip -c /var/lib/cwl/stg73416b0d-231c-4c04-bff3-7bbf40813396/GCF_012986985.1_ASM1298698v1_genomic.fna.gz | prodigal -d GCF_012986985.1_ASM1298698v1_genomic.fna/cds.fna -a GCF_012986985.1_ASM1298698v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:51,568] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:51,569] [INFO] Task started: HMMsearch
[2024-01-24 14:22:51,569] [INFO] Running command: hmmsearch --tblout GCF_012986985.1_ASM1298698v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67469902-1e2b-4623-bd88-0250427ff923/dqc_reference/reference_markers.hmm GCF_012986985.1_ASM1298698v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:51,900] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:51,901] [INFO] Found 6/6 markers.
[2024-01-24 14:22:51,956] [INFO] Query marker FASTA was written to GCF_012986985.1_ASM1298698v1_genomic.fna/markers.fasta
[2024-01-24 14:22:51,956] [INFO] Task started: Blastn
[2024-01-24 14:22:51,957] [INFO] Running command: blastn -query GCF_012986985.1_ASM1298698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67469902-1e2b-4623-bd88-0250427ff923/dqc_reference/reference_markers.fasta -out GCF_012986985.1_ASM1298698v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:52,997] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:53,000] [INFO] Selected 13 target genomes.
[2024-01-24 14:22:53,001] [INFO] Target genome list was writen to GCF_012986985.1_ASM1298698v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:53,008] [INFO] Task started: fastANI
[2024-01-24 14:22:53,008] [INFO] Running command: fastANI --query /var/lib/cwl/stg73416b0d-231c-4c04-bff3-7bbf40813396/GCF_012986985.1_ASM1298698v1_genomic.fna.gz --refList GCF_012986985.1_ASM1298698v1_genomic.fna/target_genomes.txt --output GCF_012986985.1_ASM1298698v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:10,600] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:10,600] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67469902-1e2b-4623-bd88-0250427ff923/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:10,601] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67469902-1e2b-4623-bd88-0250427ff923/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:10,614] [INFO] Found 13 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 14:23:10,614] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:23:10,614] [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 chengduensis	strain=DSM 26382	GCA_012986985.1	489632	489632	type	True	100.0	1786	1788	95	inconclusive
Pseudomonas chengduensis	strain=DSM 26382	GCA_900102635.1	489632	489632	type	True	99.985	1771	1788	95	inconclusive
Pseudomonas chengduensis	strain=MBR	GCA_017905455.1	489632	489632	type	True	99.9753	1760	1788	95	inconclusive
Pseudomonas sihuiensis	strain=KCTC 32246	GCA_900106015.1	1274359	1274359	type	True	96.7588	1507	1788	95	inconclusive
Pseudomonas toyotomiensis	strain=DSM 26169	GCA_002741095.1	554344	554344	type	True	94.9533	1479	1788	95	below_threshold
Pseudomonas toyotomiensis	strain=JCM 15604	GCA_900115695.1	554344	554344	type	True	94.923	1494	1788	95	below_threshold
Pseudomonas oleovorans subsp. oleovorans	strain=NBRC 13583	GCA_002091815.1	1218129	301	type	True	93.5942	1189	1788	95	below_threshold
Pseudomonas sediminis	strain=PI11	GCA_002741105.1	1691904	1691904	type	True	91.7005	1414	1788	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	89.8299	1365	1788	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	89.2533	1303	1788	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	89.201	1332	1788	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	82.3044	902	1788	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	82.0495	909	1788	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:10,616] [INFO] DFAST Taxonomy check result was written to GCF_012986985.1_ASM1298698v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:10,623] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:10,624] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:10,624] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67469902-1e2b-4623-bd88-0250427ff923/dqc_reference/checkm_data
[2024-01-24 14:23:10,625] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:10,687] [INFO] Task started: CheckM
[2024-01-24 14:23:10,687] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012986985.1_ASM1298698v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012986985.1_ASM1298698v1_genomic.fna/checkm_input GCF_012986985.1_ASM1298698v1_genomic.fna/checkm_result
[2024-01-24 14:24:03,395] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:03,400] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:03,455] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:03,455] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:03,455] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012986985.1_ASM1298698v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:03,456] [INFO] Task started: Blastn
[2024-01-24 14:24:03,456] [INFO] Running command: blastn -query GCF_012986985.1_ASM1298698v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67469902-1e2b-4623-bd88-0250427ff923/dqc_reference/reference_markers_gtdb.fasta -out GCF_012986985.1_ASM1298698v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:05,565] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:05,569] [INFO] Selected 11 target genomes.
[2024-01-24 14:24:05,569] [INFO] Target genome list was writen to GCF_012986985.1_ASM1298698v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:05,578] [INFO] Task started: fastANI
[2024-01-24 14:24:05,579] [INFO] Running command: fastANI --query /var/lib/cwl/stg73416b0d-231c-4c04-bff3-7bbf40813396/GCF_012986985.1_ASM1298698v1_genomic.fna.gz --refList GCF_012986985.1_ASM1298698v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012986985.1_ASM1298698v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:21,827] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:21,842] [INFO] Found 11 fastANI hits (3 hits with ANI > circumscription radius)
[2024-01-24 14:24:21,842] [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_900102635.1	s__Pseudomonas_E chengduensis	99.985	1771	1788	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.7402	99.23	98.24	0.94	0.89	5	inconclusive
GCF_900106015.1	s__Pseudomonas_E sihuiensis	96.7588	1507	1788	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	96.7402	N/A	N/A	N/A	N/A	1	inconclusive
GCF_015712065.1	s__Pseudomonas_E chengduensis_A	96.7072	1532	1788	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_001941865.1	s__Pseudomonas_E alcaliphila_B	95.7859	1450	1788	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.7502	96.52	96.24	0.87	0.86	3	inconclusive
GCF_002803095.1	s__Pseudomonas_E sp002803095	95.6019	1473	1788	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	94.923	1494	1788	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	93.5999	1197	1788	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_003052605.1	s__Pseudomonas_E indoloxydans	93.5656	1216	1788	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	92.7829	1451	1788	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_002741105.1	s__Pseudomonas_E sediminis	91.7005	1414	1788	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.01	95.51	0.89	0.85	6	-
GCF_007049795.1	s__Pseudomonas_E mendocina_D	91.3438	1290	1788	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.17	96.47	0.87	0.84	6	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:21,844] [INFO] GTDB search result was written to GCF_012986985.1_ASM1298698v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:21,845] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:21,848] [INFO] DFAST_QC result json was written to GCF_012986985.1_ASM1298698v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:21,849] [INFO] DFAST_QC completed!
[2024-01-24 14:24:21,849] [INFO] Total running time: 0h1m48s