[2023-03-16 09:47:30,766] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:47:30,767] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:47:30,767] [INFO] DQC Reference Directory: /var/lib/cwl/stg59b63abd-ea54-4eb6-8a36-75c4281c3f02/dqc_reference
[2023-03-16 09:47:31,881] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:47:31,881] [INFO] Task started: Prodigal
[2023-03-16 09:47:31,881] [INFO] Running command: cat /var/lib/cwl/stg5a7be4a8-f1da-46fd-90c6-a861f6a2bbf0/OceanDNA-b41242.fa | prodigal -d OceanDNA-b41242/cds.fna -a OceanDNA-b41242/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:48:01,722] [INFO] Task succeeded: Prodigal
[2023-03-16 09:48:01,722] [INFO] Task started: HMMsearch
[2023-03-16 09:48:01,722] [INFO] Running command: hmmsearch --tblout OceanDNA-b41242/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59b63abd-ea54-4eb6-8a36-75c4281c3f02/dqc_reference/reference_markers.hmm OceanDNA-b41242/protein.faa > /dev/null
[2023-03-16 09:48:01,969] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:48:01,970] [INFO] Found 6/6 markers.
[2023-03-16 09:48:02,000] [INFO] Query marker FASTA was written to OceanDNA-b41242/markers.fasta
[2023-03-16 09:48:02,001] [INFO] Task started: Blastn
[2023-03-16 09:48:02,001] [INFO] Running command: blastn -query OceanDNA-b41242/markers.fasta -db /var/lib/cwl/stg59b63abd-ea54-4eb6-8a36-75c4281c3f02/dqc_reference/reference_markers.fasta -out OceanDNA-b41242/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:48:02,969] [INFO] Task succeeded: Blastn
[2023-03-16 09:48:02,972] [INFO] Selected 17 target genomes.
[2023-03-16 09:48:02,972] [INFO] Target genome list was writen to OceanDNA-b41242/target_genomes.txt
[2023-03-16 09:48:03,054] [INFO] Task started: fastANI
[2023-03-16 09:48:03,054] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a7be4a8-f1da-46fd-90c6-a861f6a2bbf0/OceanDNA-b41242.fa --refList OceanDNA-b41242/target_genomes.txt --output OceanDNA-b41242/fastani_result.tsv --threads 1
[2023-03-16 09:48:25,023] [INFO] Task succeeded: fastANI
[2023-03-16 09:48:25,023] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59b63abd-ea54-4eb6-8a36-75c4281c3f02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:48:25,024] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59b63abd-ea54-4eb6-8a36-75c4281c3f02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:48:25,034] [INFO] Found 17 fastANI hits (4 hits with ANI > threshold)
[2023-03-16 09:48:25,034] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-03-16 09:48:25,034] [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	95.9229	1352	1589	95	inconclusive
Pseudomonas chengduensis	strain=MBR	GCA_017905455.1	489632	489632	type	True	95.8761	1349	1589	95	inconclusive
Pseudomonas chengduensis	strain=DSM 26382	GCA_900102635.1	489632	489632	type	True	95.8483	1357	1589	95	inconclusive
Pseudomonas sihuiensis	strain=KCTC 32246	GCA_900106015.1	1274359	1274359	type	True	95.4008	1374	1589	95	inconclusive
Pseudomonas toyotomiensis	strain=JCM 15604	GCA_900115695.1	554344	554344	type	True	94.6194	1367	1589	95	below_threshold
Pseudomonas toyotomiensis	strain=DSM 26169	GCA_002741095.1	554344	554344	type	True	94.5952	1361	1589	95	below_threshold
Pseudomonas oleovorans subsp. oleovorans	strain=DSM 1045	GCA_002197815.1	1218129	301	type	True	94.219	1160	1589	95	below_threshold
Pseudomonas oleovorans	strain=NCTC10692	GCA_900455615.1	301	301	type	True	94.2112	1192	1589	95	below_threshold
Pseudomonas oleovorans subsp. oleovorans	strain=NBRC 13583	GCA_002091815.1	1218129	301	type	True	94.1618	1169	1589	95	below_threshold
Pseudomonas alcaliphila	strain=NBRC 102411	GCA_002091495.1	101564	101564	type	True	92.1985	1307	1589	95	below_threshold
Pseudomonas alcaliphila	strain=JCM 10630	GCA_900101755.1	101564	101564	type	True	92.1408	1311	1589	95	below_threshold
Pseudomonas sediminis	strain=PI11	GCA_002741105.1	1691904	1691904	type	True	91.319	1308	1589	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	89.585	1283	1589	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	88.9304	1191	1589	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	88.8711	1239	1589	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	83.343	914	1589	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	82.2658	856	1589	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:48:25,034] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41242/tc_result.tsv
[2023-03-16 09:48:25,034] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:48:25,034] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:48:25,034] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59b63abd-ea54-4eb6-8a36-75c4281c3f02/dqc_reference/checkm_data
[2023-03-16 09:48:25,035] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:48:25,060] [INFO] Task started: CheckM
[2023-03-16 09:48:25,060] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41242/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41242/checkm_input OceanDNA-b41242/checkm_result
[2023-03-16 09:49:37,718] [INFO] Task succeeded: CheckM
[2023-03-16 09:49:37,718] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.59%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:49:37,721] [INFO] ===== Completeness check finished =====
[2023-03-16 09:49:37,722] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:49:37,722] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41242/markers.fasta)
[2023-03-16 09:49:37,723] [INFO] Task started: Blastn
[2023-03-16 09:49:37,723] [INFO] Running command: blastn -query OceanDNA-b41242/markers.fasta -db /var/lib/cwl/stg59b63abd-ea54-4eb6-8a36-75c4281c3f02/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41242/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:49:39,545] [INFO] Task succeeded: Blastn
[2023-03-16 09:49:39,546] [INFO] Selected 11 target genomes.
[2023-03-16 09:49:39,546] [INFO] Target genome list was writen to OceanDNA-b41242/target_genomes_gtdb.txt
[2023-03-16 09:49:39,556] [INFO] Task started: fastANI
[2023-03-16 09:49:39,556] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a7be4a8-f1da-46fd-90c6-a861f6a2bbf0/OceanDNA-b41242.fa --refList OceanDNA-b41242/target_genomes_gtdb.txt --output OceanDNA-b41242/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:49:54,751] [INFO] Task succeeded: fastANI
[2023-03-16 09:49:54,758] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 09:49:54,758] [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_001941865.1	s__Pseudomonas_E alcaliphila_B	96.906	1424	1589	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.7502	96.52	96.24	0.87	0.86	3	conclusive
GCF_900102635.1	s__Pseudomonas_E chengduensis	95.8325	1358	1589	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_015712065.1	s__Pseudomonas_E chengduensis_A	95.7856	1411	1589	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_900106015.1	s__Pseudomonas_E sihuiensis	95.3645	1377	1589	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_002803095.1	s__Pseudomonas_E sp002803095	95.2152	1356	1589	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	94.6046	1368	1589	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	94.2357	1159	1589	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	94.0701	1150	1589	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	92.7718	1326	1589	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	92.1408	1311	1589	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_008041835.1	s__Pseudomonas_E sp002282595	90.5265	1062	1589	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.53	95.53	0.75	0.75	2	-
--------------------------------------------------------------------------------
[2023-03-16 09:49:54,758] [INFO] GTDB search result was written to OceanDNA-b41242/result_gtdb.tsv
[2023-03-16 09:49:54,758] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:49:54,760] [INFO] DFAST_QC result json was written to OceanDNA-b41242/dqc_result.json
[2023-03-16 09:49:54,760] [INFO] DFAST_QC completed!
[2023-03-16 09:49:54,760] [INFO] Total running time: 0h2m24s