[2023-03-18 23:44:06,306] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:44:06,306] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:44:06,306] [INFO] DQC Reference Directory: /var/lib/cwl/stg71ffe70b-01a8-4f71-8dae-da6d37e1cee6/dqc_reference
[2023-03-18 23:44:07,410] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:44:07,411] [INFO] Task started: Prodigal
[2023-03-18 23:44:07,411] [INFO] Running command: cat /var/lib/cwl/stg3aee0e16-710f-4257-97f3-bb0d16d87203/OceanDNA-b41223.fa | prodigal -d OceanDNA-b41223/cds.fna -a OceanDNA-b41223/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:44:20,907] [INFO] Task succeeded: Prodigal
[2023-03-18 23:44:20,907] [INFO] Task started: HMMsearch
[2023-03-18 23:44:20,907] [INFO] Running command: hmmsearch --tblout OceanDNA-b41223/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71ffe70b-01a8-4f71-8dae-da6d37e1cee6/dqc_reference/reference_markers.hmm OceanDNA-b41223/protein.faa > /dev/null
[2023-03-18 23:44:21,096] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:44:21,097] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3aee0e16-710f-4257-97f3-bb0d16d87203/OceanDNA-b41223.fa]
[2023-03-18 23:44:21,119] [INFO] Query marker FASTA was written to OceanDNA-b41223/markers.fasta
[2023-03-18 23:44:21,120] [INFO] Task started: Blastn
[2023-03-18 23:44:21,120] [INFO] Running command: blastn -query OceanDNA-b41223/markers.fasta -db /var/lib/cwl/stg71ffe70b-01a8-4f71-8dae-da6d37e1cee6/dqc_reference/reference_markers.fasta -out OceanDNA-b41223/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:44:21,981] [INFO] Task succeeded: Blastn
[2023-03-18 23:44:21,982] [INFO] Selected 11 target genomes.
[2023-03-18 23:44:21,982] [INFO] Target genome list was writen to OceanDNA-b41223/target_genomes.txt
[2023-03-18 23:44:21,991] [INFO] Task started: fastANI
[2023-03-18 23:44:21,991] [INFO] Running command: fastANI --query /var/lib/cwl/stg3aee0e16-710f-4257-97f3-bb0d16d87203/OceanDNA-b41223.fa --refList OceanDNA-b41223/target_genomes.txt --output OceanDNA-b41223/fastani_result.tsv --threads 1
[2023-03-18 23:44:31,042] [INFO] Task succeeded: fastANI
[2023-03-18 23:44:31,043] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71ffe70b-01a8-4f71-8dae-da6d37e1cee6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:44:31,043] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71ffe70b-01a8-4f71-8dae-da6d37e1cee6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:44:31,051] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:44:31,051] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:44:31,051] [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	88.7024	517	600	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_900099645.1	592361	592361	type	True	88.6789	521	600	95	below_threshold
Pseudomonas guineae	strain=LMG 24016	GCA_900113745.1	425504	425504	type	True	85.008	499	600	95	below_threshold
Pseudomonas borbori	strain=DSM 17834	GCA_900115555.1	289003	289003	type	True	82.3951	421	600	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	82.3643	435	600	95	below_threshold
Pseudomonas tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	82.1309	449	600	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	81.741	413	600	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	81.3684	437	600	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	81.2805	431	600	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	80.7133	363	600	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	80.495	361	600	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:44:31,051] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41223/tc_result.tsv
[2023-03-18 23:44:31,051] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:44:31,051] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:44:31,051] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71ffe70b-01a8-4f71-8dae-da6d37e1cee6/dqc_reference/checkm_data
[2023-03-18 23:44:31,052] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:44:31,057] [INFO] Task started: CheckM
[2023-03-18 23:44:31,057] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41223/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41223/checkm_input OceanDNA-b41223/checkm_result
[2023-03-18 23:45:08,438] [INFO] Task succeeded: CheckM
[2023-03-18 23:45:08,439] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:45:08,451] [INFO] ===== Completeness check finished =====
[2023-03-18 23:45:08,451] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:45:08,452] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41223/markers.fasta)
[2023-03-18 23:45:08,453] [INFO] Task started: Blastn
[2023-03-18 23:45:08,453] [INFO] Running command: blastn -query OceanDNA-b41223/markers.fasta -db /var/lib/cwl/stg71ffe70b-01a8-4f71-8dae-da6d37e1cee6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41223/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:45:09,976] [INFO] Task succeeded: Blastn
[2023-03-18 23:45:09,980] [INFO] Selected 11 target genomes.
[2023-03-18 23:45:09,980] [INFO] Target genome list was writen to OceanDNA-b41223/target_genomes_gtdb.txt
[2023-03-18 23:45:09,988] [INFO] Task started: fastANI
[2023-03-18 23:45:09,988] [INFO] Running command: fastANI --query /var/lib/cwl/stg3aee0e16-710f-4257-97f3-bb0d16d87203/OceanDNA-b41223.fa --refList OceanDNA-b41223/target_genomes_gtdb.txt --output OceanDNA-b41223/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:45:18,651] [INFO] Task succeeded: fastANI
[2023-03-18 23:45:18,658] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:45:18,658] [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_018827205.1	s__Pseudomonas_E sp018827205	96.5457	522	600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.54	99.51	0.89	0.88	4	conclusive
GCA_002840155.1	s__Pseudomonas_E sp002840155	89.9158	559	600	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_900105355.1	s__Pseudomonas_E anguilliseptica	89.4917	543	600	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	88.6696	522	600	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_018816095.1	s__Pseudomonas_E sp018816095	86.4721	449	600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.20	96.15	0.83	0.82	4	-
GCF_003060885.1	s__Pseudomonas_E sp003060885	86.0982	508	600	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_002354655.1	s__Pseudomonas_E sp002354655	83.5331	453	600	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	83.5273	432	600	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_009763245.1	s__Pseudomonas_E sp009763245	82.9923	431	600	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_009799925.1	s__Pseudomonas_E sp009799925	81.516	394	600	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	81.1339	364	600	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:45:18,660] [INFO] GTDB search result was written to OceanDNA-b41223/result_gtdb.tsv
[2023-03-18 23:45:18,661] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:45:18,664] [INFO] DFAST_QC result json was written to OceanDNA-b41223/dqc_result.json
[2023-03-18 23:45:18,665] [INFO] DFAST_QC completed!
[2023-03-18 23:45:18,665] [INFO] Total running time: 0h1m12s