[2024-01-25 17:35:35,513] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:35:35,515] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:35:35,515] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e93987d-0ca9-48e2-8411-e7962a1cfb8a/dqc_reference
[2024-01-25 17:35:36,695] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:35:36,696] [INFO] Task started: Prodigal
[2024-01-25 17:35:36,696] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb714505-853f-4cc7-be26-e3506303d459/GCF_015712105.2_536_genomic.fna.gz | prodigal -d GCF_015712105.2_536_genomic.fna/cds.fna -a GCF_015712105.2_536_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:35:51,783] [INFO] Task succeeded: Prodigal
[2024-01-25 17:35:51,783] [INFO] Task started: HMMsearch
[2024-01-25 17:35:51,783] [INFO] Running command: hmmsearch --tblout GCF_015712105.2_536_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e93987d-0ca9-48e2-8411-e7962a1cfb8a/dqc_reference/reference_markers.hmm GCF_015712105.2_536_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:35:52,114] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:35:52,116] [INFO] Found 6/6 markers.
[2024-01-25 17:35:52,169] [INFO] Query marker FASTA was written to GCF_015712105.2_536_genomic.fna/markers.fasta
[2024-01-25 17:35:52,169] [INFO] Task started: Blastn
[2024-01-25 17:35:52,169] [INFO] Running command: blastn -query GCF_015712105.2_536_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e93987d-0ca9-48e2-8411-e7962a1cfb8a/dqc_reference/reference_markers.fasta -out GCF_015712105.2_536_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:53,077] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:53,080] [INFO] Selected 23 target genomes.
[2024-01-25 17:35:53,081] [INFO] Target genome list was writen to GCF_015712105.2_536_genomic.fna/target_genomes.txt
[2024-01-25 17:35:53,088] [INFO] Task started: fastANI
[2024-01-25 17:35:53,088] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb714505-853f-4cc7-be26-e3506303d459/GCF_015712105.2_536_genomic.fna.gz --refList GCF_015712105.2_536_genomic.fna/target_genomes.txt --output GCF_015712105.2_536_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:36:22,207] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:22,208] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e93987d-0ca9-48e2-8411-e7962a1cfb8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:36:22,209] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e93987d-0ca9-48e2-8411-e7962a1cfb8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:36:22,222] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:36:22,222] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:36:22,222] [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 toyotomiensis	strain=DSM 26169	GCA_002741095.1	554344	554344	type	True	92.4656	1458	1770	95	below_threshold
Pseudomonas chengduensis	strain=MBR	GCA_017905455.1	489632	489632	type	True	92.458	1434	1770	95	below_threshold
Pseudomonas chengduensis	strain=DSM 26382	GCA_012986985.1	489632	489632	type	True	92.4567	1458	1770	95	below_threshold
Pseudomonas chengduensis	strain=DSM 26382	GCA_900102635.1	489632	489632	type	True	92.4356	1448	1770	95	below_threshold
Pseudomonas toyotomiensis	strain=JCM 15604	GCA_900115695.1	554344	554344	type	True	92.3924	1461	1770	95	below_threshold
Pseudomonas sihuiensis	strain=KCTC 32246	GCA_900106015.1	1274359	1274359	type	True	92.2342	1446	1770	95	below_threshold
Pseudomonas alcaliphila	strain=NBRC 102411	GCA_002091495.1	101564	101564	type	True	91.7435	1456	1770	95	below_threshold
Pseudomonas alcaliphila	strain=JCM 10630	GCA_900101755.1	101564	101564	type	True	91.6963	1466	1770	95	below_threshold
Pseudomonas oleovorans subsp. oleovorans	strain=NBRC 13583	GCA_002091815.1	1218129	301	type	True	90.7194	1181	1770	95	below_threshold
Pseudomonas oleovorans subsp. oleovorans	strain=DSM 1045	GCA_002197815.1	1218129	301	type	True	90.7127	1194	1770	95	below_threshold
Pseudomonas composti	strain=CCUG 59231	GCA_900115475.1	658457	658457	type	True	89.7449	1390	1770	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	89.0011	1332	1770	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	88.4598	1330	1770	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	88.2014	1326	1770	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	81.935	875	1770	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	81.8459	868	1770	95	below_threshold
Pseudomonas muyukensis	strain=COW39	GCA_019139535.1	2842357	2842357	type	True	80.9646	802	1770	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	80.8874	716	1770	95	below_threshold
Pseudomonas plecoglossicida	strain=DSM 15088	GCA_000688275.1	70775	70775	suspected-type	True	80.7788	735	1770	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	80.6114	754	1770	95	below_threshold
Pseudomonas monteilii	strain=NBRC 103158	GCA_000730605.1	76759	76759	type	True	80.5938	692	1770	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	80.5897	728	1770	95	below_threshold
Pseudomonas monteilii	strain=DSM 14164	GCA_000621245.1	76759	76759	type	True	80.5137	719	1770	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:36:22,224] [INFO] DFAST Taxonomy check result was written to GCF_015712105.2_536_genomic.fna/tc_result.tsv
[2024-01-25 17:36:22,225] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:36:22,225] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:36:22,225] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e93987d-0ca9-48e2-8411-e7962a1cfb8a/dqc_reference/checkm_data
[2024-01-25 17:36:22,226] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:36:22,275] [INFO] Task started: CheckM
[2024-01-25 17:36:22,276] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015712105.2_536_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015712105.2_536_genomic.fna/checkm_input GCF_015712105.2_536_genomic.fna/checkm_result
[2024-01-25 17:37:06,959] [INFO] Task succeeded: CheckM
[2024-01-25 17:37:06,960] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:37:06,986] [INFO] ===== Completeness check finished =====
[2024-01-25 17:37:06,986] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:37:06,986] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015712105.2_536_genomic.fna/markers.fasta)
[2024-01-25 17:37:06,987] [INFO] Task started: Blastn
[2024-01-25 17:37:06,987] [INFO] Running command: blastn -query GCF_015712105.2_536_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e93987d-0ca9-48e2-8411-e7962a1cfb8a/dqc_reference/reference_markers_gtdb.fasta -out GCF_015712105.2_536_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:37:08,662] [INFO] Task succeeded: Blastn
[2024-01-25 17:37:08,665] [INFO] Selected 20 target genomes.
[2024-01-25 17:37:08,665] [INFO] Target genome list was writen to GCF_015712105.2_536_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:37:08,694] [INFO] Task started: fastANI
[2024-01-25 17:37:08,694] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb714505-853f-4cc7-be26-e3506303d459/GCF_015712105.2_536_genomic.fna.gz --refList GCF_015712105.2_536_genomic.fna/target_genomes_gtdb.txt --output GCF_015712105.2_536_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:37:34,244] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:34,256] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:37:34,256] [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_902506495.1	s__Pseudomonas_E sp902506495	95.9575	1539	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.72	95.94	0.90	0.87	3	conclusive
GCF_015712065.1	s__Pseudomonas_E chengduensis_A	92.6111	1472	1770	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	92.4356	1448	1770	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_001941865.1	s__Pseudomonas_E alcaliphila_B	92.4195	1414	1770	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	92.3955	1452	1770	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	92.3924	1461	1770	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_900106015.1	s__Pseudomonas_E sihuiensis	92.2342	1446	1770	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_900101755.1	s__Pseudomonas_E alcaliphila	91.6963	1466	1770	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_002197815.1	s__Pseudomonas_E oleovorans	90.7043	1195	1770	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	90.6488	1202	1770	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_900115475.1	s__Pseudomonas_E composti	89.7628	1388	1770	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_000016565.1	s__Pseudomonas_E mendocina_A	88.3512	1329	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.76	97.37	0.90	0.88	7	-
GCA_002452115.1	s__Pseudomonas nitroreducens_B	81.3879	818	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002091635.1	s__Pseudomonas_M indica	81.3739	961	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_M	95.0	99.16	98.73	0.94	0.91	4	-
GCF_900110885.1	s__Azotobacter beijerinckii	80.8052	647	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	97.34	96.47	0.86	0.85	5	-
GCF_004339665.1	s__Azotobacter chroococcum	80.7918	680	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	97.27	96.18	0.89	0.83	10	-
GCF_000802155.2	s__Pseudomonas_E frederiksbergensis_A	80.0331	688	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.21	99.12	0.93	0.92	4	-
GCF_013386165.1	s__Pseudomonas_E gingeri_C	79.8936	740	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.61	98.31	0.93	0.92	4	-
GCF_000263715.2	s__Pseudomonas_E synxantha_A	79.7023	631	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.66	97.33	0.90	0.88	8	-
GCF_003586265.1	s__Pseudomonas_D jilinensis	78.6492	407	1770	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.07	95.47	0.89	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:37:34,258] [INFO] GTDB search result was written to GCF_015712105.2_536_genomic.fna/result_gtdb.tsv
[2024-01-25 17:37:34,258] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:37:34,262] [INFO] DFAST_QC result json was written to GCF_015712105.2_536_genomic.fna/dqc_result.json
[2024-01-25 17:37:34,262] [INFO] DFAST_QC completed!
[2024-01-25 17:37:34,262] [INFO] Total running time: 0h1m59s