[2023-03-16 07:15:38,934] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:15:38,934] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:15:38,934] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b4c2519-10ea-40a9-8ad6-196fc29f7c28/dqc_reference
[2023-03-16 07:15:40,018] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:15:40,018] [INFO] Task started: Prodigal
[2023-03-16 07:15:40,019] [INFO] Running command: cat /var/lib/cwl/stg751f9681-9fbc-4e91-a282-461bf114a8e7/OceanDNA-b12642.fa | prodigal -d OceanDNA-b12642/cds.fna -a OceanDNA-b12642/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:15:56,417] [INFO] Task succeeded: Prodigal
[2023-03-16 07:15:56,418] [INFO] Task started: HMMsearch
[2023-03-16 07:15:56,418] [INFO] Running command: hmmsearch --tblout OceanDNA-b12642/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b4c2519-10ea-40a9-8ad6-196fc29f7c28/dqc_reference/reference_markers.hmm OceanDNA-b12642/protein.faa > /dev/null
[2023-03-16 07:15:56,607] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:15:56,607] [INFO] Found 6/6 markers.
[2023-03-16 07:15:56,627] [INFO] Query marker FASTA was written to OceanDNA-b12642/markers.fasta
[2023-03-16 07:15:56,628] [INFO] Task started: Blastn
[2023-03-16 07:15:56,628] [INFO] Running command: blastn -query OceanDNA-b12642/markers.fasta -db /var/lib/cwl/stg7b4c2519-10ea-40a9-8ad6-196fc29f7c28/dqc_reference/reference_markers.fasta -out OceanDNA-b12642/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:15:57,158] [INFO] Task succeeded: Blastn
[2023-03-16 07:15:57,159] [INFO] Selected 32 target genomes.
[2023-03-16 07:15:57,159] [INFO] Target genome list was writen to OceanDNA-b12642/target_genomes.txt
[2023-03-16 07:15:57,179] [INFO] Task started: fastANI
[2023-03-16 07:15:57,179] [INFO] Running command: fastANI --query /var/lib/cwl/stg751f9681-9fbc-4e91-a282-461bf114a8e7/OceanDNA-b12642.fa --refList OceanDNA-b12642/target_genomes.txt --output OceanDNA-b12642/fastani_result.tsv --threads 1
[2023-03-16 07:16:13,010] [INFO] Task succeeded: fastANI
[2023-03-16 07:16:13,010] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b4c2519-10ea-40a9-8ad6-196fc29f7c28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:16:13,010] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b4c2519-10ea-40a9-8ad6-196fc29f7c28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:16:13,010] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:16:13,010] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 07:16:13,010] [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
--------------------------------------------------------------------------------
[2023-03-16 07:16:13,011] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12642/tc_result.tsv
[2023-03-16 07:16:13,011] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:16:13,011] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:16:13,011] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b4c2519-10ea-40a9-8ad6-196fc29f7c28/dqc_reference/checkm_data
[2023-03-16 07:16:13,014] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:16:13,018] [INFO] Task started: CheckM
[2023-03-16 07:16:13,018] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12642/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12642/checkm_input OceanDNA-b12642/checkm_result
[2023-03-16 07:16:56,950] [INFO] Task succeeded: CheckM
[2023-03-16 07:16:56,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.39%
Contamintation: 2.78%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 07:16:56,953] [INFO] ===== Completeness check finished =====
[2023-03-16 07:16:56,953] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:16:56,953] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12642/markers.fasta)
[2023-03-16 07:16:56,954] [INFO] Task started: Blastn
[2023-03-16 07:16:56,955] [INFO] Running command: blastn -query OceanDNA-b12642/markers.fasta -db /var/lib/cwl/stg7b4c2519-10ea-40a9-8ad6-196fc29f7c28/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12642/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:16:57,683] [INFO] Task succeeded: Blastn
[2023-03-16 07:16:57,684] [INFO] Selected 25 target genomes.
[2023-03-16 07:16:57,685] [INFO] Target genome list was writen to OceanDNA-b12642/target_genomes_gtdb.txt
[2023-03-16 07:16:57,729] [INFO] Task started: fastANI
[2023-03-16 07:16:57,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg751f9681-9fbc-4e91-a282-461bf114a8e7/OceanDNA-b12642.fa --refList OceanDNA-b12642/target_genomes_gtdb.txt --output OceanDNA-b12642/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:17:09,702] [INFO] Task succeeded: fastANI
[2023-03-16 07:17:09,706] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:17:09,706] [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_905182175.1	s__NORP294 sp905182175	90.651	721	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__NORP294	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018608405.1	s__NORP294 sp018608405	77.7475	238	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__NORP294	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479325.1	s__NORP294 sp905479325	77.6724	226	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__NORP294	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763995.1	s__NORP294 sp016763995	77.2149	124	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__NORP294	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002415785.1	s__UBA5081 sp002415785	76.1877	53	808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Vicingaceae;g__UBA5081	95.0	99.97	99.97	0.98	0.96	4	-
--------------------------------------------------------------------------------
[2023-03-16 07:17:09,707] [INFO] GTDB search result was written to OceanDNA-b12642/result_gtdb.tsv
[2023-03-16 07:17:09,707] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:17:09,708] [INFO] DFAST_QC result json was written to OceanDNA-b12642/dqc_result.json
[2023-03-16 07:17:09,708] [INFO] DFAST_QC completed!
[2023-03-16 07:17:09,708] [INFO] Total running time: 0h1m31s