[2023-03-17 13:01:52,512] [INFO] DFAST_QC pipeline started.
[2023-03-17 13:01:52,513] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 13:01:52,513] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9f17495-fc83-40cf-955e-914b8be05566/dqc_reference
[2023-03-17 13:01:55,104] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 13:01:55,104] [INFO] Task started: Prodigal
[2023-03-17 13:01:55,104] [INFO] Running command: cat /var/lib/cwl/stg43171223-b2f1-4a8f-a342-b39bb905b8ab/OceanDNA-b42605.fa | prodigal -d OceanDNA-b42605/cds.fna -a OceanDNA-b42605/protein.faa -g 11 -q > /dev/null
[2023-03-17 13:02:00,152] [INFO] Task succeeded: Prodigal
[2023-03-17 13:02:00,152] [INFO] Task started: HMMsearch
[2023-03-17 13:02:00,152] [INFO] Running command: hmmsearch --tblout OceanDNA-b42605/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9f17495-fc83-40cf-955e-914b8be05566/dqc_reference/reference_markers.hmm OceanDNA-b42605/protein.faa > /dev/null
[2023-03-17 13:02:00,311] [INFO] Task succeeded: HMMsearch
[2023-03-17 13:02:00,311] [INFO] Found 6/6 markers.
[2023-03-17 13:02:00,321] [INFO] Query marker FASTA was written to OceanDNA-b42605/markers.fasta
[2023-03-17 13:02:00,321] [INFO] Task started: Blastn
[2023-03-17 13:02:00,321] [INFO] Running command: blastn -query OceanDNA-b42605/markers.fasta -db /var/lib/cwl/stgf9f17495-fc83-40cf-955e-914b8be05566/dqc_reference/reference_markers.fasta -out OceanDNA-b42605/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:02:02,874] [INFO] Task succeeded: Blastn
[2023-03-17 13:02:02,874] [INFO] Selected 17 target genomes.
[2023-03-17 13:02:02,874] [INFO] Target genome list was writen to OceanDNA-b42605/target_genomes.txt
[2023-03-17 13:02:02,885] [INFO] Task started: fastANI
[2023-03-17 13:02:02,885] [INFO] Running command: fastANI --query /var/lib/cwl/stg43171223-b2f1-4a8f-a342-b39bb905b8ab/OceanDNA-b42605.fa --refList OceanDNA-b42605/target_genomes.txt --output OceanDNA-b42605/fastani_result.tsv --threads 1
[2023-03-17 13:02:10,114] [INFO] Task succeeded: fastANI
[2023-03-17 13:02:10,114] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9f17495-fc83-40cf-955e-914b8be05566/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 13:02:10,114] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9f17495-fc83-40cf-955e-914b8be05566/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 13:02:10,114] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 13:02:10,114] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 13:02:10,115] [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
--------------------------------------------------------------------------------
[2023-03-17 13:02:10,115] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42605/tc_result.tsv
[2023-03-17 13:02:10,115] [INFO] ===== Taxonomy check completed =====
[2023-03-17 13:02:10,115] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 13:02:10,115] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9f17495-fc83-40cf-955e-914b8be05566/dqc_reference/checkm_data
[2023-03-17 13:02:10,118] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 13:02:10,120] [INFO] Task started: CheckM
[2023-03-17 13:02:10,120] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42605/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42605/checkm_input OceanDNA-b42605/checkm_result
[2023-03-17 13:02:35,521] [INFO] Task succeeded: CheckM
[2023-03-17 13:02:35,521] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.52%
Contamintation: 1.50%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-17 13:02:35,522] [INFO] ===== Completeness check finished =====
[2023-03-17 13:02:35,523] [INFO] ===== Start GTDB Search =====
[2023-03-17 13:02:35,523] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42605/markers.fasta)
[2023-03-17 13:02:35,523] [INFO] Task started: Blastn
[2023-03-17 13:02:35,523] [INFO] Running command: blastn -query OceanDNA-b42605/markers.fasta -db /var/lib/cwl/stgf9f17495-fc83-40cf-955e-914b8be05566/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42605/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 13:02:36,618] [INFO] Task succeeded: Blastn
[2023-03-17 13:02:36,618] [INFO] Selected 25 target genomes.
[2023-03-17 13:02:36,619] [INFO] Target genome list was writen to OceanDNA-b42605/target_genomes_gtdb.txt
[2023-03-17 13:02:37,093] [INFO] Task started: fastANI
[2023-03-17 13:02:37,093] [INFO] Running command: fastANI --query /var/lib/cwl/stg43171223-b2f1-4a8f-a342-b39bb905b8ab/OceanDNA-b42605.fa --refList OceanDNA-b42605/target_genomes_gtdb.txt --output OceanDNA-b42605/fastani_result_gtdb.tsv --threads 1
[2023-03-17 13:02:44,318] [INFO] Task succeeded: fastANI
[2023-03-17 13:02:44,322] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 13:02:44,322] [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_002707915.1	s__GCA-2707915 sp002707915	98.2995	235	304	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	97.24	96.30	0.83	0.75	4	conclusive
GCA_902594545.1	s__GCA-2707915 sp902594545	77.52	98	304	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	99.77	99.77	0.82	0.82	2	-
GCA_902620785.1	s__GCA-2707915 sp902620785	77.2348	88	304	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	95.48	95.02	0.87	0.85	6	-
GCA_902604855.1	s__GCA-2707915 sp902604855	77.1541	81	304	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902517565.1	s__GCA-2707915 sp902517565	76.8596	69	304	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004214065.1	s__GCA-2707915 sp004214065	76.6198	72	304	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	97.49	97.45	0.77	0.70	3	-
--------------------------------------------------------------------------------
[2023-03-17 13:02:44,323] [INFO] GTDB search result was written to OceanDNA-b42605/result_gtdb.tsv
[2023-03-17 13:02:44,323] [INFO] ===== GTDB Search completed =====
[2023-03-17 13:02:44,323] [INFO] DFAST_QC result json was written to OceanDNA-b42605/dqc_result.json
[2023-03-17 13:02:44,324] [INFO] DFAST_QC completed!
[2023-03-17 13:02:44,324] [INFO] Total running time: 0h0m52s