[2023-03-16 10:20:34,632] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:20:34,633] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:20:34,633] [INFO] DQC Reference Directory: /var/lib/cwl/stg05d6d4f1-e9c8-4eb8-9380-9aa79323033a/dqc_reference
[2023-03-16 10:20:35,902] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:20:35,902] [INFO] Task started: Prodigal
[2023-03-16 10:20:35,902] [INFO] Running command: cat /var/lib/cwl/stgfa665dd9-c4e7-4974-b125-8c37604cd26d/OceanDNA-b41314.fa | prodigal -d OceanDNA-b41314/cds.fna -a OceanDNA-b41314/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:20:57,866] [INFO] Task succeeded: Prodigal
[2023-03-16 10:20:57,866] [INFO] Task started: HMMsearch
[2023-03-16 10:20:57,866] [INFO] Running command: hmmsearch --tblout OceanDNA-b41314/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05d6d4f1-e9c8-4eb8-9380-9aa79323033a/dqc_reference/reference_markers.hmm OceanDNA-b41314/protein.faa > /dev/null
[2023-03-16 10:20:58,102] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:20:58,103] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfa665dd9-c4e7-4974-b125-8c37604cd26d/OceanDNA-b41314.fa]
[2023-03-16 10:20:58,130] [INFO] Query marker FASTA was written to OceanDNA-b41314/markers.fasta
[2023-03-16 10:20:58,131] [INFO] Task started: Blastn
[2023-03-16 10:20:58,131] [INFO] Running command: blastn -query OceanDNA-b41314/markers.fasta -db /var/lib/cwl/stg05d6d4f1-e9c8-4eb8-9380-9aa79323033a/dqc_reference/reference_markers.fasta -out OceanDNA-b41314/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:20:58,984] [INFO] Task succeeded: Blastn
[2023-03-16 10:20:58,985] [INFO] Selected 15 target genomes.
[2023-03-16 10:20:58,985] [INFO] Target genome list was writen to OceanDNA-b41314/target_genomes.txt
[2023-03-16 10:20:58,998] [INFO] Task started: fastANI
[2023-03-16 10:20:58,998] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa665dd9-c4e7-4974-b125-8c37604cd26d/OceanDNA-b41314.fa --refList OceanDNA-b41314/target_genomes.txt --output OceanDNA-b41314/fastani_result.tsv --threads 1
[2023-03-16 10:21:14,516] [INFO] Task succeeded: fastANI
[2023-03-16 10:21:14,517] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05d6d4f1-e9c8-4eb8-9380-9aa79323033a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:21:14,517] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05d6d4f1-e9c8-4eb8-9380-9aa79323033a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:21:14,530] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:21:14,530] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:21:14,530] [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 peli	strain=DSM 17833	GCA_012986145.1	592361	592361	type	True	90.4388	944	1131	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_900099645.1	592361	592361	type	True	90.3759	945	1131	95	below_threshold
Pseudomonas guineae	strain=LMG 24016	GCA_900113745.1	425504	425504	type	True	84.6689	835	1131	95	below_threshold
Pseudomonas tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	83.078	765	1131	95	below_threshold
Pseudomonas borbori	strain=DSM 17834	GCA_900115555.1	289003	289003	type	True	83.0439	732	1131	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	82.9708	781	1131	95	below_threshold
Pseudomonas cuatrocienegasensis	strain=CIP 109853	GCA_900110925.1	543360	543360	type	True	82.8279	735	1131	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	82.6014	699	1131	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	82.2752	770	1131	95	below_threshold
Pseudomonas guryensis	strain=SR9	GCA_014164785.1	2759165	2759165	type	True	82.221	696	1131	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	81.9689	783	1131	95	below_threshold
Pseudomonas ullengensis	strain=UL070	GCA_014174475.1	2759166	2759166	type	True	81.9446	696	1131	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	81.4374	657	1131	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	81.2331	661	1131	95	below_threshold
Pseudomonas kuykendallii	strain=NRRL B-59562	GCA_900106975.1	1007099	1007099	type	True	80.322	589	1131	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:21:14,531] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41314/tc_result.tsv
[2023-03-16 10:21:14,531] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:21:14,531] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:21:14,531] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05d6d4f1-e9c8-4eb8-9380-9aa79323033a/dqc_reference/checkm_data
[2023-03-16 10:21:14,532] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:21:14,538] [INFO] Task started: CheckM
[2023-03-16 10:21:14,538] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41314/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41314/checkm_input OceanDNA-b41314/checkm_result
[2023-03-16 10:22:09,048] [INFO] Task succeeded: CheckM
[2023-03-16 10:22:09,048] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.98%
Contamintation: 20.14%
Strain heterogeneity: 88.89%
--------------------------------------------------------------------------------
[2023-03-16 10:22:09,052] [INFO] ===== Completeness check finished =====
[2023-03-16 10:22:09,052] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:22:09,052] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41314/markers.fasta)
[2023-03-16 10:22:09,053] [INFO] Task started: Blastn
[2023-03-16 10:22:09,054] [INFO] Running command: blastn -query OceanDNA-b41314/markers.fasta -db /var/lib/cwl/stg05d6d4f1-e9c8-4eb8-9380-9aa79323033a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41314/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:22:10,670] [INFO] Task succeeded: Blastn
[2023-03-16 10:22:10,671] [INFO] Selected 10 target genomes.
[2023-03-16 10:22:10,671] [INFO] Target genome list was writen to OceanDNA-b41314/target_genomes_gtdb.txt
[2023-03-16 10:22:10,712] [INFO] Task started: fastANI
[2023-03-16 10:22:10,712] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa665dd9-c4e7-4974-b125-8c37604cd26d/OceanDNA-b41314.fa --refList OceanDNA-b41314/target_genomes_gtdb.txt --output OceanDNA-b41314/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:22:21,022] [INFO] Task succeeded: fastANI
[2023-03-16 10:22:21,029] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 10:22:21,029] [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
GCA_002840155.1	s__Pseudomonas_E sp002840155	96.1866	1039	1131	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_900105355.1	s__Pseudomonas_E anguilliseptica	90.6089	966	1131	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.12	96.12	0.88	0.88	2	-
GCF_900099645.1	s__Pseudomonas_E peli	90.3427	947	1131	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.85	96.04	0.90	0.85	7	-
GCA_018827205.1	s__Pseudomonas_E sp018827205	89.6622	876	1131	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.54	99.51	0.89	0.88	4	-
GCF_004920405.1	s__Pseudomonas_E leptonychotis	86.222	936	1131	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018816095.1	s__Pseudomonas_E sp018816095	85.887	746	1131	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.20	96.15	0.83	0.82	4	-
GCA_002354655.1	s__Pseudomonas_E sp002354655	84.6068	800	1131	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.84	99.84	0.95	0.95	2	-
GCA_001465025.1	s__Pseudomonas_E sp001465025	84.1205	756	1131	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.96	95.96	0.61	0.61	2	-
GCF_014164785.1	s__Pseudomonas_E sp014164785	82.2338	694	1131	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_014851905.1	s__Pseudomonas_E sp014851905	81.5485	683	1131	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 10:22:21,029] [INFO] GTDB search result was written to OceanDNA-b41314/result_gtdb.tsv
[2023-03-16 10:22:21,029] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:22:21,031] [INFO] DFAST_QC result json was written to OceanDNA-b41314/dqc_result.json
[2023-03-16 10:22:21,031] [INFO] DFAST_QC completed!
[2023-03-16 10:22:21,031] [INFO] Total running time: 0h1m46s