[2023-03-15 13:20:51,598] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:20:51,598] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:20:51,598] [INFO] DQC Reference Directory: /var/lib/cwl/stg38633578-f707-4559-b765-57299a1acca6/dqc_reference
[2023-03-15 13:20:52,746] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:20:52,746] [INFO] Task started: Prodigal
[2023-03-15 13:20:52,746] [INFO] Running command: cat /var/lib/cwl/stg4081aedd-38ab-4a18-8074-83ec3ce81c48/OceanDNA-b35108.fa | prodigal -d OceanDNA-b35108/cds.fna -a OceanDNA-b35108/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:21:06,860] [INFO] Task succeeded: Prodigal
[2023-03-15 13:21:06,860] [INFO] Task started: HMMsearch
[2023-03-15 13:21:06,860] [INFO] Running command: hmmsearch --tblout OceanDNA-b35108/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38633578-f707-4559-b765-57299a1acca6/dqc_reference/reference_markers.hmm OceanDNA-b35108/protein.faa > /dev/null
[2023-03-15 13:21:07,069] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:21:07,070] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4081aedd-38ab-4a18-8074-83ec3ce81c48/OceanDNA-b35108.fa]
[2023-03-15 13:21:07,093] [INFO] Query marker FASTA was written to OceanDNA-b35108/markers.fasta
[2023-03-15 13:21:07,094] [INFO] Task started: Blastn
[2023-03-15 13:21:07,094] [INFO] Running command: blastn -query OceanDNA-b35108/markers.fasta -db /var/lib/cwl/stg38633578-f707-4559-b765-57299a1acca6/dqc_reference/reference_markers.fasta -out OceanDNA-b35108/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:21:07,616] [INFO] Task succeeded: Blastn
[2023-03-15 13:21:07,618] [INFO] Selected 24 target genomes.
[2023-03-15 13:21:07,618] [INFO] Target genome list was writen to OceanDNA-b35108/target_genomes.txt
[2023-03-15 13:21:07,634] [INFO] Task started: fastANI
[2023-03-15 13:21:07,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg4081aedd-38ab-4a18-8074-83ec3ce81c48/OceanDNA-b35108.fa --refList OceanDNA-b35108/target_genomes.txt --output OceanDNA-b35108/fastani_result.tsv --threads 1
[2023-03-15 13:21:23,684] [INFO] Task succeeded: fastANI
[2023-03-15 13:21:23,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38633578-f707-4559-b765-57299a1acca6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:21:23,684] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38633578-f707-4559-b765-57299a1acca6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:21:23,689] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 13:21:23,689] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 13:21:23,689] [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
Psychrosphaera aestuarii	strain=PSC101	GCA_017948405.1	1266052	1266052	type	True	77.2949	89	874	95	below_threshold
Psychrosphaera saromensis	strain=SA4-48	GCA_002954545.1	716813	716813	type	True	77.2772	151	874	95	below_threshold
Psychrosphaera ytuae	strain=MTZ26	GCA_017638545.1	2820710	2820710	type	True	77.2726	85	874	95	below_threshold
Psychrosphaera saromensis	strain=KCTC 23240	GCA_014652155.1	716813	716813	type	True	77.2419	152	874	95	below_threshold
Pseudoalteromonas prydzensis	strain=DSM 14232	GCA_001661495.1	182141	182141	type	True	75.8493	50	874	95	below_threshold
Pseudoalteromonas prydzensis	strain=ACAM 620	GCA_014925355.1	182141	182141	type	True	75.8321	52	874	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:21:23,690] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35108/tc_result.tsv
[2023-03-15 13:21:23,691] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:21:23,691] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:21:23,691] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38633578-f707-4559-b765-57299a1acca6/dqc_reference/checkm_data
[2023-03-15 13:21:23,692] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:21:23,705] [INFO] Task started: CheckM
[2023-03-15 13:21:23,705] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35108/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35108/checkm_input OceanDNA-b35108/checkm_result
[2023-03-15 13:22:03,083] [INFO] Task succeeded: CheckM
[2023-03-15 13:22:03,083] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 13:22:03,086] [INFO] ===== Completeness check finished =====
[2023-03-15 13:22:03,087] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:22:03,087] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35108/markers.fasta)
[2023-03-15 13:22:03,088] [INFO] Task started: Blastn
[2023-03-15 13:22:03,088] [INFO] Running command: blastn -query OceanDNA-b35108/markers.fasta -db /var/lib/cwl/stg38633578-f707-4559-b765-57299a1acca6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35108/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:22:03,792] [INFO] Task succeeded: Blastn
[2023-03-15 13:22:03,794] [INFO] Selected 24 target genomes.
[2023-03-15 13:22:03,794] [INFO] Target genome list was writen to OceanDNA-b35108/target_genomes_gtdb.txt
[2023-03-15 13:22:03,813] [INFO] Task started: fastANI
[2023-03-15 13:22:03,813] [INFO] Running command: fastANI --query /var/lib/cwl/stg4081aedd-38ab-4a18-8074-83ec3ce81c48/OceanDNA-b35108.fa --refList OceanDNA-b35108/target_genomes_gtdb.txt --output OceanDNA-b35108/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:22:19,239] [INFO] Task succeeded: fastANI
[2023-03-15 13:22:19,245] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 13:22:19,245] [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_013373245.1	s__Psychrosphaera sp013373245	77.4997	136	874	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009728465.1	s__Psychrosphaera haliotis	77.4003	101	874	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017948405.1	s__Psychrosphaera aestuarii	77.2949	89	874	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954545.1	s__Psychrosphaera saromensis	77.2772	151	874	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017638545.1	s__Psychrosphaera sp017638545	77.2726	85	874	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860345.1	s__Psychrosphaera sp018860345	77.0891	167	874	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Psychrosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656435.1	s__Thalassotalea_C marina	75.8551	52	874	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001399975.1	s__Pseudoalteromonas sp001399975	75.7983	51	874	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:22:19,246] [INFO] GTDB search result was written to OceanDNA-b35108/result_gtdb.tsv
[2023-03-15 13:22:19,247] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:22:19,249] [INFO] DFAST_QC result json was written to OceanDNA-b35108/dqc_result.json
[2023-03-15 13:22:19,249] [INFO] DFAST_QC completed!
[2023-03-15 13:22:19,249] [INFO] Total running time: 0h1m28s