[2023-03-18 20:13:32,181] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:13:32,181] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:13:32,181] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc068696-54d2-45db-9e37-5f81a5dadba3/dqc_reference
[2023-03-18 20:13:33,403] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:13:33,430] [INFO] Task started: Prodigal
[2023-03-18 20:13:33,430] [INFO] Running command: cat /var/lib/cwl/stg0099bf84-867d-44a0-836f-9508dfced3da/OceanDNA-b5350.fa | prodigal -d OceanDNA-b5350/cds.fna -a OceanDNA-b5350/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:13:50,348] [INFO] Task succeeded: Prodigal
[2023-03-18 20:13:50,348] [INFO] Task started: HMMsearch
[2023-03-18 20:13:50,349] [INFO] Running command: hmmsearch --tblout OceanDNA-b5350/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc068696-54d2-45db-9e37-5f81a5dadba3/dqc_reference/reference_markers.hmm OceanDNA-b5350/protein.faa > /dev/null
[2023-03-18 20:13:50,562] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:13:50,563] [INFO] Found 6/6 markers.
[2023-03-18 20:13:50,579] [INFO] Query marker FASTA was written to OceanDNA-b5350/markers.fasta
[2023-03-18 20:13:50,579] [INFO] Task started: Blastn
[2023-03-18 20:13:50,579] [INFO] Running command: blastn -query OceanDNA-b5350/markers.fasta -db /var/lib/cwl/stgcc068696-54d2-45db-9e37-5f81a5dadba3/dqc_reference/reference_markers.fasta -out OceanDNA-b5350/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:13:51,164] [INFO] Task succeeded: Blastn
[2023-03-18 20:13:51,165] [INFO] Selected 23 target genomes.
[2023-03-18 20:13:51,165] [INFO] Target genome list was writen to OceanDNA-b5350/target_genomes.txt
[2023-03-18 20:13:51,177] [INFO] Task started: fastANI
[2023-03-18 20:13:51,177] [INFO] Running command: fastANI --query /var/lib/cwl/stg0099bf84-867d-44a0-836f-9508dfced3da/OceanDNA-b5350.fa --refList OceanDNA-b5350/target_genomes.txt --output OceanDNA-b5350/fastani_result.tsv --threads 1
[2023-03-18 20:14:04,605] [INFO] Task succeeded: fastANI
[2023-03-18 20:14:04,606] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc068696-54d2-45db-9e37-5f81a5dadba3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:14:04,606] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc068696-54d2-45db-9e37-5f81a5dadba3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:14:04,606] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:14:04,606] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 20:14:04,606] [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
--------------------------------------------------------------------------------
[2023-03-18 20:14:04,607] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5350/tc_result.tsv
[2023-03-18 20:14:04,607] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:14:04,607] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:14:04,607] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc068696-54d2-45db-9e37-5f81a5dadba3/dqc_reference/checkm_data
[2023-03-18 20:14:04,610] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:14:04,613] [INFO] Task started: CheckM
[2023-03-18 20:14:04,613] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5350/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5350/checkm_input OceanDNA-b5350/checkm_result
[2023-03-18 20:14:50,683] [INFO] Task succeeded: CheckM
[2023-03-18 20:14:50,683] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:14:50,758] [INFO] ===== Completeness check finished =====
[2023-03-18 20:14:50,758] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:14:50,758] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5350/markers.fasta)
[2023-03-18 20:14:50,759] [INFO] Task started: Blastn
[2023-03-18 20:14:50,759] [INFO] Running command: blastn -query OceanDNA-b5350/markers.fasta -db /var/lib/cwl/stgcc068696-54d2-45db-9e37-5f81a5dadba3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5350/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:14:51,685] [INFO] Task succeeded: Blastn
[2023-03-18 20:14:51,686] [INFO] Selected 23 target genomes.
[2023-03-18 20:14:51,686] [INFO] Target genome list was writen to OceanDNA-b5350/target_genomes_gtdb.txt
[2023-03-18 20:14:52,164] [INFO] Task started: fastANI
[2023-03-18 20:14:52,164] [INFO] Running command: fastANI --query /var/lib/cwl/stg0099bf84-867d-44a0-836f-9508dfced3da/OceanDNA-b5350.fa --refList OceanDNA-b5350/target_genomes_gtdb.txt --output OceanDNA-b5350/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:15:02,903] [INFO] Task succeeded: fastANI
[2023-03-18 20:15:02,909] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 20:15:02,909] [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_003149635.1	s__UBA4466 sp003149635	77.5547	70	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015665275.1	s__UBA4466 sp015665275	77.2392	66	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002427735.1	s__UBA4466 sp002427735	77.216	68	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215515.1	s__UBA4466 sp013215515	77.0488	67	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402525.1	s__UBA4466 sp018402525	77.0017	79	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017984635.1	s__M0103 sp017984635	76.3371	57	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016178305.1	s__CAIUKX01 sp016178305	75.927	53	733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__CAIUKX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 20:15:02,909] [INFO] GTDB search result was written to OceanDNA-b5350/result_gtdb.tsv
[2023-03-18 20:15:02,909] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:15:02,910] [INFO] DFAST_QC result json was written to OceanDNA-b5350/dqc_result.json
[2023-03-18 20:15:02,910] [INFO] DFAST_QC completed!
[2023-03-18 20:15:02,910] [INFO] Total running time: 0h1m31s