[2023-03-16 23:05:03,947] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:05:03,947] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:05:03,947] [INFO] DQC Reference Directory: /var/lib/cwl/stg70c10355-a5ed-4fc1-b6e4-4c0418f945f5/dqc_reference
[2023-03-16 23:05:05,131] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:05:05,131] [INFO] Task started: Prodigal
[2023-03-16 23:05:05,131] [INFO] Running command: cat /var/lib/cwl/stg10000501-e2ec-40e5-aa61-e75a0d79e534/OceanDNA-b41288.fa | prodigal -d OceanDNA-b41288/cds.fna -a OceanDNA-b41288/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:05:35,729] [INFO] Task succeeded: Prodigal
[2023-03-16 23:05:35,729] [INFO] Task started: HMMsearch
[2023-03-16 23:05:35,730] [INFO] Running command: hmmsearch --tblout OceanDNA-b41288/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70c10355-a5ed-4fc1-b6e4-4c0418f945f5/dqc_reference/reference_markers.hmm OceanDNA-b41288/protein.faa > /dev/null
[2023-03-16 23:05:36,047] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:05:36,047] [INFO] Found 6/6 markers.
[2023-03-16 23:05:36,076] [INFO] Query marker FASTA was written to OceanDNA-b41288/markers.fasta
[2023-03-16 23:05:36,076] [INFO] Task started: Blastn
[2023-03-16 23:05:36,076] [INFO] Running command: blastn -query OceanDNA-b41288/markers.fasta -db /var/lib/cwl/stg70c10355-a5ed-4fc1-b6e4-4c0418f945f5/dqc_reference/reference_markers.fasta -out OceanDNA-b41288/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:05:37,099] [INFO] Task succeeded: Blastn
[2023-03-16 23:05:37,100] [INFO] Selected 17 target genomes.
[2023-03-16 23:05:37,100] [INFO] Target genome list was writen to OceanDNA-b41288/target_genomes.txt
[2023-03-16 23:05:37,107] [INFO] Task started: fastANI
[2023-03-16 23:05:37,107] [INFO] Running command: fastANI --query /var/lib/cwl/stg10000501-e2ec-40e5-aa61-e75a0d79e534/OceanDNA-b41288.fa --refList OceanDNA-b41288/target_genomes.txt --output OceanDNA-b41288/fastani_result.tsv --threads 1
[2023-03-16 23:05:56,891] [INFO] Task succeeded: fastANI
[2023-03-16 23:05:56,891] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70c10355-a5ed-4fc1-b6e4-4c0418f945f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:05:56,891] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70c10355-a5ed-4fc1-b6e4-4c0418f945f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:05:56,901] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:05:56,901] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 23:05:56,901] [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 guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	88.0508	1264	1623	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	87.7877	1232	1623	95	below_threshold
Pseudomonas chengduensis	strain=DSM 26382	GCA_012986985.1	489632	489632	type	True	87.5589	1254	1623	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	87.5458	1197	1623	95	below_threshold
Pseudomonas alcaliphila	strain=JCM 10630	GCA_900101755.1	101564	101564	type	True	87.4946	1263	1623	95	below_threshold
Pseudomonas toyotomiensis	strain=DSM 26169	GCA_002741095.1	554344	554344	type	True	87.4873	1275	1623	95	below_threshold
Pseudomonas sihuiensis	strain=KCTC 32246	GCA_900106015.1	1274359	1274359	type	True	87.4779	1265	1623	95	below_threshold
Pseudomonas chengduensis	strain=MBR	GCA_017905455.1	489632	489632	type	True	87.4705	1269	1623	95	below_threshold
Pseudomonas alcaliphila	strain=NBRC 102411	GCA_002091495.1	101564	101564	type	True	87.4627	1256	1623	95	below_threshold
Pseudomonas toyotomiensis	strain=JCM 15604	GCA_900115695.1	554344	554344	type	True	87.4579	1314	1623	95	below_threshold
Pseudomonas composti	strain=CCUG 59231	GCA_900115475.1	658457	658457	type	True	87.3881	1328	1623	95	below_threshold
Pseudomonas mendocina	strain=NCTC10897	GCA_900636545.1	300	300	suspected-type	True	87.1624	1249	1623	95	below_threshold
Pseudomonas mendocina	strain=NBRC 14162	GCA_000813265.1	300	300	suspected-type	True	87.1621	1228	1623	95	below_threshold
Pseudomonas sediminis	strain=PI11	GCA_002741105.1	1691904	1691904	type	True	87.1563	1279	1623	95	below_threshold
Pseudomonas oleovorans subsp. oleovorans	strain=NBRC 13583	GCA_002091815.1	1218129	301	type	True	87.0925	1081	1623	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	84.0585	952	1623	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	82.7571	892	1623	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 23:05:56,901] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41288/tc_result.tsv
[2023-03-16 23:05:56,901] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:05:56,902] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:05:56,902] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70c10355-a5ed-4fc1-b6e4-4c0418f945f5/dqc_reference/checkm_data
[2023-03-16 23:05:56,902] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:05:56,908] [INFO] Task started: CheckM
[2023-03-16 23:05:56,909] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41288/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41288/checkm_input OceanDNA-b41288/checkm_result
[2023-03-16 23:07:13,526] [INFO] Task succeeded: CheckM
[2023-03-16 23:07:13,527] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:07:13,530] [INFO] ===== Completeness check finished =====
[2023-03-16 23:07:13,530] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:07:13,530] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41288/markers.fasta)
[2023-03-16 23:07:13,531] [INFO] Task started: Blastn
[2023-03-16 23:07:13,531] [INFO] Running command: blastn -query OceanDNA-b41288/markers.fasta -db /var/lib/cwl/stg70c10355-a5ed-4fc1-b6e4-4c0418f945f5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41288/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:07:15,520] [INFO] Task succeeded: Blastn
[2023-03-16 23:07:15,521] [INFO] Selected 14 target genomes.
[2023-03-16 23:07:15,521] [INFO] Target genome list was writen to OceanDNA-b41288/target_genomes_gtdb.txt
[2023-03-16 23:07:15,684] [INFO] Task started: fastANI
[2023-03-16 23:07:15,684] [INFO] Running command: fastANI --query /var/lib/cwl/stg10000501-e2ec-40e5-aa61-e75a0d79e534/OceanDNA-b41288.fa --refList OceanDNA-b41288/target_genomes_gtdb.txt --output OceanDNA-b41288/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:07:32,706] [INFO] Task succeeded: fastANI
[2023-03-16 23:07:32,714] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 23:07:32,715] [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_004521985.1	s__Pseudomonas_E khazarica	98.1347	1473	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.35	98.01	0.91	0.87	12	conclusive
GCF_900104265.1	s__Pseudomonas_E guguanensis	88.0511	1264	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.13	97.13	0.85	0.85	2	-
GCF_000418555.1	s__Pseudomonas_E sp000418555	87.7639	1265	1623	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_000016565.1	s__Pseudomonas_E mendocina_A	87.7241	1251	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.76	97.37	0.90	0.88	7	-
GCF_001941865.1	s__Pseudomonas_E alcaliphila_B	87.5255	1226	1623	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_900101755.1	s__Pseudomonas_E alcaliphila	87.5031	1262	1623	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_002803095.1	s__Pseudomonas_E sp002803095	87.482	1260	1623	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_900106015.1	s__Pseudomonas_E sihuiensis	87.467	1267	1623	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_900115695.1	s__Pseudomonas_E toyotomiensis	87.4579	1314	1623	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_003696305.1	s__Pseudomonas_E sp003696305	87.4507	1132	1623	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_016008875.1	s__Pseudomonas_E sp002439135	87.4014	1203	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.91	96.75	0.87	0.85	5	-
GCF_900636545.1	s__Pseudomonas_E mendocina	87.1766	1248	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.91	97.19	0.93	0.89	14	-
GCF_008041835.1	s__Pseudomonas_E sp002282595	87.095	1064	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.53	95.53	0.75	0.75	2	-
GCF_014109765.1	s__Pseudomonas_E oleovorans_B	86.4491	1280	1623	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.92	96.88	0.93	0.92	3	-
--------------------------------------------------------------------------------
[2023-03-16 23:07:32,715] [INFO] GTDB search result was written to OceanDNA-b41288/result_gtdb.tsv
[2023-03-16 23:07:32,715] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:07:32,717] [INFO] DFAST_QC result json was written to OceanDNA-b41288/dqc_result.json
[2023-03-16 23:07:32,717] [INFO] DFAST_QC completed!
[2023-03-16 23:07:32,717] [INFO] Total running time: 0h2m29s