[2023-03-16 04:20:43,515] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:20:43,515] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:20:43,515] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb010b63-ad41-4446-a672-ed04c7290687/dqc_reference
[2023-03-16 04:20:44,608] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:20:44,609] [INFO] Task started: Prodigal
[2023-03-16 04:20:44,609] [INFO] Running command: cat /var/lib/cwl/stg9e785257-274d-413e-8c22-26845beec19d/OceanDNA-b41303.fa | prodigal -d OceanDNA-b41303/cds.fna -a OceanDNA-b41303/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:21:11,671] [INFO] Task succeeded: Prodigal
[2023-03-16 04:21:11,671] [INFO] Task started: HMMsearch
[2023-03-16 04:21:11,671] [INFO] Running command: hmmsearch --tblout OceanDNA-b41303/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb010b63-ad41-4446-a672-ed04c7290687/dqc_reference/reference_markers.hmm OceanDNA-b41303/protein.faa > /dev/null
[2023-03-16 04:21:11,887] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:21:11,888] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9e785257-274d-413e-8c22-26845beec19d/OceanDNA-b41303.fa]
[2023-03-16 04:21:11,910] [INFO] Query marker FASTA was written to OceanDNA-b41303/markers.fasta
[2023-03-16 04:21:11,911] [INFO] Task started: Blastn
[2023-03-16 04:21:11,911] [INFO] Running command: blastn -query OceanDNA-b41303/markers.fasta -db /var/lib/cwl/stgfb010b63-ad41-4446-a672-ed04c7290687/dqc_reference/reference_markers.fasta -out OceanDNA-b41303/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:21:12,717] [INFO] Task succeeded: Blastn
[2023-03-16 04:21:12,718] [INFO] Selected 18 target genomes.
[2023-03-16 04:21:12,718] [INFO] Target genome list was writen to OceanDNA-b41303/target_genomes.txt
[2023-03-16 04:21:12,729] [INFO] Task started: fastANI
[2023-03-16 04:21:12,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e785257-274d-413e-8c22-26845beec19d/OceanDNA-b41303.fa --refList OceanDNA-b41303/target_genomes.txt --output OceanDNA-b41303/fastani_result.tsv --threads 1
[2023-03-16 04:21:38,988] [INFO] Task succeeded: fastANI
[2023-03-16 04:21:38,988] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb010b63-ad41-4446-a672-ed04c7290687/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:21:38,988] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb010b63-ad41-4446-a672-ed04c7290687/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:21:38,998] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:21:38,998] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:21:38,999] [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 koreensis	strain=JCM 14769	GCA_014646955.1	198620	198620	suspected-type	True	92.1223	1233	1409	95	below_threshold
Pseudomonas koreensis	strain=DSM 16610	GCA_012986595.1	198620	198620	suspected-type	True	92.1009	1241	1409	95	below_threshold
Pseudomonas koreensis	strain=CCUG 51519	GCA_008801535.1	198620	198620	suspected-type	True	92.0649	1238	1409	95	below_threshold
Pseudomonas monsensis	strain=PGSB 8459	GCA_014268495.2	2745509	2745509	type	True	90.0275	1192	1409	95	below_threshold
Pseudomonas neuropathica	strain=P155	GCA_015461835.1	2730425	2730425	type	True	89.1928	1195	1409	95	below_threshold
Pseudomonas germanica	strain=FIT28	GCA_019614655.1	2815720	2815720	type	True	89.0804	1217	1409	95	below_threshold
Pseudomonas crudilactis	strain=UCMA 17988	GCA_013433315.1	2697028	2697028	type	True	88.9919	1209	1409	95	below_threshold
Pseudomonas kribbensis	strain=46-2	GCA_003352185.1	1628086	1628086	type	True	88.8503	1185	1409	95	below_threshold
Pseudomonas allokribbensis	strain=IzPS23	GCA_014863605.1	2774460	2774460	type	True	88.7965	1201	1409	95	below_threshold
Pseudomonas sputi	strain=BML-PP014	GCA_021603585.1	2892325	2892325	type	True	88.7674	1156	1409	95	below_threshold
Pseudomonas pharyngis	strain=BML-PP036	GCA_021602345.1	2892333	2892333	type	True	88.7534	1198	1409	95	below_threshold
Pseudomonas atacamensis	strain=M7D1	GCA_004801935.1	2565368	2565368	type	True	88.5262	1131	1409	95	below_threshold
Pseudomonas siliginis	strain=SWRI31	GCA_019145195.1	2842346	2842346	type	True	88.4289	1068	1409	95	below_threshold
Pseudomonas iranensis	strain=SWRI54	GCA_014268585.2	2745503	2745503	type	True	88.4188	1140	1409	95	below_threshold
Pseudomonas triticicola	strain=SWRI88	GCA_019145375.1	2842345	2842345	type	True	88.4148	1107	1409	95	below_threshold
Pseudomonas granadensis	strain=LMG 27940	GCA_900105485.1	1421430	1421430	suspected-type	True	87.922	1162	1409	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	83.2728	979	1409	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	83.0426	959	1409	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:21:38,999] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41303/tc_result.tsv
[2023-03-16 04:21:38,999] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:21:38,999] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:21:38,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb010b63-ad41-4446-a672-ed04c7290687/dqc_reference/checkm_data
[2023-03-16 04:21:39,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:21:39,288] [INFO] Task started: CheckM
[2023-03-16 04:21:39,288] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41303/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41303/checkm_input OceanDNA-b41303/checkm_result
[2023-03-16 04:22:46,410] [INFO] Task succeeded: CheckM
[2023-03-16 04:22:46,411] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:22:46,414] [INFO] ===== Completeness check finished =====
[2023-03-16 04:22:46,414] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:22:46,414] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41303/markers.fasta)
[2023-03-16 04:22:46,414] [INFO] Task started: Blastn
[2023-03-16 04:22:46,414] [INFO] Running command: blastn -query OceanDNA-b41303/markers.fasta -db /var/lib/cwl/stgfb010b63-ad41-4446-a672-ed04c7290687/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41303/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:22:47,852] [INFO] Task succeeded: Blastn
[2023-03-16 04:22:47,853] [INFO] Selected 15 target genomes.
[2023-03-16 04:22:47,853] [INFO] Target genome list was writen to OceanDNA-b41303/target_genomes_gtdb.txt
[2023-03-16 04:22:47,882] [INFO] Task started: fastANI
[2023-03-16 04:22:47,882] [INFO] Running command: fastANI --query /var/lib/cwl/stg9e785257-274d-413e-8c22-26845beec19d/OceanDNA-b41303.fa --refList OceanDNA-b41303/target_genomes_gtdb.txt --output OceanDNA-b41303/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:23:09,919] [INFO] Task succeeded: fastANI
[2023-03-16 04:23:09,928] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:23:09,928] [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_000631985.1	s__Pseudomonas_E sp000631985	99.1485	1321	1409	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004683905.1	s__Pseudomonas_E putida_A	94.6357	1301	1409	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.80	95.08	0.93	0.90	22	-
GCF_000282275.2	s__Pseudomonas_E sp000282275	94.3793	1250	1409	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_000292795.1	s__Pseudomonas_E fluorescens_H	93.37	1251	1409	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.99	97.99	0.94	0.93	3	-
GCF_002287825.1	s__Pseudomonas_E koreensis_B	93.3091	1258	1409	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.58	96.55	0.92	0.86	13	-
GCF_003061005.1	s__Pseudomonas_E sp003061005	92.4707	1183	1409	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_012986595.1	s__Pseudomonas_E koreensis	92.1009	1241	1409	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.85	97.85	0.96	0.91	8	-
GCF_003999415.1	s__Pseudomonas_E koreensis_E	92.0677	1220	1409	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.57	98.57	0.92	0.92	2	-
GCF_002878485.1	s__Pseudomonas_E sp002878485	91.8648	1227	1409	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_000633255.1	s__Pseudomonas_E sp000633255	91.4905	1233	1409	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_004801935.1	s__Pseudomonas_E atacamensis	88.5186	1132	1409	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.5366	97.08	95.72	0.92	0.89	59	-
GCF_001605965.1	s__Pseudomonas_E koreensis_C	88.4871	1144	1409	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.5366	98.03	96.36	0.95	0.90	10	-
GCF_000817895.1	s__Pseudomonas_E fluorescens_AO	88.2264	1132	1409	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.16	98.16	0.95	0.95	2	-
GCF_900105805.1	s__Pseudomonas_E moraviensis_A	88.1988	1129	1409	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.79	98.30	0.96	0.94	7	-
GCF_002836515.1	s__Pseudomonas_E sp002836515	87.922	1104	1409	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:23:09,928] [INFO] GTDB search result was written to OceanDNA-b41303/result_gtdb.tsv
[2023-03-16 04:23:09,928] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:23:09,930] [INFO] DFAST_QC result json was written to OceanDNA-b41303/dqc_result.json
[2023-03-16 04:23:09,930] [INFO] DFAST_QC completed!
[2023-03-16 04:23:09,930] [INFO] Total running time: 0h2m26s