[2023-03-19 01:33:27,244] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:33:27,245] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:33:27,245] [INFO] DQC Reference Directory: /var/lib/cwl/stg38f17117-feff-4ea1-9006-ad127dbb14fd/dqc_reference
[2023-03-19 01:33:28,339] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:33:28,339] [INFO] Task started: Prodigal
[2023-03-19 01:33:28,339] [INFO] Running command: cat /var/lib/cwl/stg3c8887d4-73f1-4a6c-8ec0-96c812bca3fa/OceanDNA-b41259.fa | prodigal -d OceanDNA-b41259/cds.fna -a OceanDNA-b41259/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:33:51,696] [INFO] Task succeeded: Prodigal
[2023-03-19 01:33:51,696] [INFO] Task started: HMMsearch
[2023-03-19 01:33:51,696] [INFO] Running command: hmmsearch --tblout OceanDNA-b41259/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38f17117-feff-4ea1-9006-ad127dbb14fd/dqc_reference/reference_markers.hmm OceanDNA-b41259/protein.faa > /dev/null
[2023-03-19 01:33:51,924] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:33:51,925] [INFO] Found 6/6 markers.
[2023-03-19 01:33:51,950] [INFO] Query marker FASTA was written to OceanDNA-b41259/markers.fasta
[2023-03-19 01:33:51,952] [INFO] Task started: Blastn
[2023-03-19 01:33:51,952] [INFO] Running command: blastn -query OceanDNA-b41259/markers.fasta -db /var/lib/cwl/stg38f17117-feff-4ea1-9006-ad127dbb14fd/dqc_reference/reference_markers.fasta -out OceanDNA-b41259/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:33:52,787] [INFO] Task succeeded: Blastn
[2023-03-19 01:33:52,787] [INFO] Selected 14 target genomes.
[2023-03-19 01:33:52,788] [INFO] Target genome list was writen to OceanDNA-b41259/target_genomes.txt
[2023-03-19 01:33:52,796] [INFO] Task started: fastANI
[2023-03-19 01:33:52,796] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c8887d4-73f1-4a6c-8ec0-96c812bca3fa/OceanDNA-b41259.fa --refList OceanDNA-b41259/target_genomes.txt --output OceanDNA-b41259/fastani_result.tsv --threads 1
[2023-03-19 01:34:09,419] [INFO] Task succeeded: fastANI
[2023-03-19 01:34:09,420] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38f17117-feff-4ea1-9006-ad127dbb14fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:34:09,420] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38f17117-feff-4ea1-9006-ad127dbb14fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:34:09,429] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2023-03-19 01:34:09,429] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-19 01:34:09,429] [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 brenneri	strain=DSM 15294	GCA_007858285.1	129817	129817	type	True	97.7354	1082	1209	95	conclusive
Pseudomonas brenneri	strain=JCM 13307	GCA_014646715.1	129817	129817	type	True	97.7214	1080	1209	95	conclusive
Pseudomonas proteolytica	strain=DSM 15321	GCA_007858275.1	219574	219574	type	True	92.8698	1038	1209	95	below_threshold
Pseudomonas proteolytica	strain=CCUG 51515T	GCA_008692865.1	219574	219574	type	True	92.7893	1039	1209	95	below_threshold
Pseudomonas gessardii	strain=DSM 17152	GCA_001983165.1	78544	78544	type	True	92.3627	1041	1209	95	below_threshold
Pseudomonas gessardii	strain=DSM 17152	GCA_009671285.1	78544	78544	type	True	92.3627	1041	1209	95	below_threshold
Pseudomonas gessardii		GCA_900625085.1	78544	78544	type	True	92.3324	1030	1209	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	87.4239	961	1209	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	87.4188	954	1209	95	below_threshold
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	87.2525	929	1209	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	87.0575	935	1209	95	below_threshold
Pseudomonas fluorescens	strain=NCTC10038	GCA_900475215.1	294	294	suspected-type	True	86.8625	947	1209	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	86.7851	865	1209	95	below_threshold
Pseudomonas trivialis	strain=DSM 14937	GCA_001439805.1	200450	200450	type	True	86.4086	864	1209	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:34:09,429] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41259/tc_result.tsv
[2023-03-19 01:34:09,430] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:34:09,430] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:34:09,430] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38f17117-feff-4ea1-9006-ad127dbb14fd/dqc_reference/checkm_data
[2023-03-19 01:34:09,430] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:34:09,436] [INFO] Task started: CheckM
[2023-03-19 01:34:09,436] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41259/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41259/checkm_input OceanDNA-b41259/checkm_result
[2023-03-19 01:35:07,805] [INFO] Task succeeded: CheckM
[2023-03-19 01:35:07,806] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.56%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:35:07,808] [INFO] ===== Completeness check finished =====
[2023-03-19 01:35:07,809] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:35:07,809] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41259/markers.fasta)
[2023-03-19 01:35:07,810] [INFO] Task started: Blastn
[2023-03-19 01:35:07,810] [INFO] Running command: blastn -query OceanDNA-b41259/markers.fasta -db /var/lib/cwl/stg38f17117-feff-4ea1-9006-ad127dbb14fd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41259/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:35:09,357] [INFO] Task succeeded: Blastn
[2023-03-19 01:35:09,358] [INFO] Selected 9 target genomes.
[2023-03-19 01:35:09,358] [INFO] Target genome list was writen to OceanDNA-b41259/target_genomes_gtdb.txt
[2023-03-19 01:35:09,369] [INFO] Task started: fastANI
[2023-03-19 01:35:09,369] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c8887d4-73f1-4a6c-8ec0-96c812bca3fa/OceanDNA-b41259.fa --refList OceanDNA-b41259/target_genomes_gtdb.txt --output OceanDNA-b41259/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:35:20,825] [INFO] Task succeeded: fastANI
[2023-03-19 01:35:20,831] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 01:35:20,832] [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_007858285.1	s__Pseudomonas_E brenneri	97.7354	1082	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.23	97.33	0.94	0.88	10	conclusive
GCF_007858275.1	s__Pseudomonas_E proteolytica	92.8693	1038	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.69	98.38	0.90	0.86	19	-
GCF_001983165.1	s__Pseudomonas_E gessardii	92.375	1040	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.96	98.08	0.94	0.88	9	-
GCF_016925675.1	s__Pseudomonas_E sp012985665	92.3261	1035	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.30	97.44	0.92	0.88	4	-
GCF_012985465.1	s__Pseudomonas_E sp012985465	92.2076	1054	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.03	98.94	0.91	0.90	5	-
GCF_003626995.1	s__Pseudomonas_E fluorescens_BA	91.8921	1036	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.95	98.57	0.93	0.88	19	-
GCF_000730425.1	s__Pseudomonas_E fluorescens_X	91.5997	1020	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.75	99.75	0.93	0.93	2	-
GCF_013386765.1	s__Pseudomonas_E yamanorum_A	87.8192	951	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.70	98.16	0.94	0.91	5	-
GCF_000346755.1	s__Pseudomonas_E sp000346755	87.5599	939	1209	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:35:20,832] [INFO] GTDB search result was written to OceanDNA-b41259/result_gtdb.tsv
[2023-03-19 01:35:20,832] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:35:20,833] [INFO] DFAST_QC result json was written to OceanDNA-b41259/dqc_result.json
[2023-03-19 01:35:20,833] [INFO] DFAST_QC completed!
[2023-03-19 01:35:20,834] [INFO] Total running time: 0h1m54s