[2023-03-15 12:44:24,471] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:44:24,471] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:44:24,471] [INFO] DQC Reference Directory: /var/lib/cwl/stg10ab20d6-208a-418c-8634-b31aba234e1b/dqc_reference
[2023-03-15 12:44:26,205] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:44:26,206] [INFO] Task started: Prodigal
[2023-03-15 12:44:26,206] [INFO] Running command: cat /var/lib/cwl/stg9867fd94-d713-469b-b34f-4451880b1245/OceanDNA-b20744.fa | prodigal -d OceanDNA-b20744/cds.fna -a OceanDNA-b20744/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:44:29,450] [INFO] Task succeeded: Prodigal
[2023-03-15 12:44:29,450] [INFO] Task started: HMMsearch
[2023-03-15 12:44:29,451] [INFO] Running command: hmmsearch --tblout OceanDNA-b20744/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10ab20d6-208a-418c-8634-b31aba234e1b/dqc_reference/reference_markers.hmm OceanDNA-b20744/protein.faa > /dev/null
[2023-03-15 12:44:29,648] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:44:29,649] [INFO] Found 6/6 markers.
[2023-03-15 12:44:29,660] [INFO] Query marker FASTA was written to OceanDNA-b20744/markers.fasta
[2023-03-15 12:44:29,660] [INFO] Task started: Blastn
[2023-03-15 12:44:29,660] [INFO] Running command: blastn -query OceanDNA-b20744/markers.fasta -db /var/lib/cwl/stg10ab20d6-208a-418c-8634-b31aba234e1b/dqc_reference/reference_markers.fasta -out OceanDNA-b20744/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:44:30,698] [INFO] Task succeeded: Blastn
[2023-03-15 12:44:30,699] [INFO] Selected 25 target genomes.
[2023-03-15 12:44:30,699] [INFO] Target genome list was writen to OceanDNA-b20744/target_genomes.txt
[2023-03-15 12:44:30,713] [INFO] Task started: fastANI
[2023-03-15 12:44:30,713] [INFO] Running command: fastANI --query /var/lib/cwl/stg9867fd94-d713-469b-b34f-4451880b1245/OceanDNA-b20744.fa --refList OceanDNA-b20744/target_genomes.txt --output OceanDNA-b20744/fastani_result.tsv --threads 1
[2023-03-15 12:44:40,327] [INFO] Task succeeded: fastANI
[2023-03-15 12:44:40,327] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10ab20d6-208a-418c-8634-b31aba234e1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:44:40,327] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10ab20d6-208a-418c-8634-b31aba234e1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:44:40,328] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:44:40,328] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 12:44:40,328] [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
--------------------------------------------------------------------------------
[2023-03-15 12:44:40,328] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20744/tc_result.tsv
[2023-03-15 12:44:40,328] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:44:40,328] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:44:40,328] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10ab20d6-208a-418c-8634-b31aba234e1b/dqc_reference/checkm_data
[2023-03-15 12:44:40,331] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:44:40,334] [INFO] Task started: CheckM
[2023-03-15 12:44:40,334] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20744/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20744/checkm_input OceanDNA-b20744/checkm_result
[2023-03-15 12:44:55,358] [INFO] Task succeeded: CheckM
[2023-03-15 12:44:55,358] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.16%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 12:44:55,360] [INFO] ===== Completeness check finished =====
[2023-03-15 12:44:55,360] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:44:55,360] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20744/markers.fasta)
[2023-03-15 12:44:55,360] [INFO] Task started: Blastn
[2023-03-15 12:44:55,360] [INFO] Running command: blastn -query OceanDNA-b20744/markers.fasta -db /var/lib/cwl/stg10ab20d6-208a-418c-8634-b31aba234e1b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20744/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:44:56,148] [INFO] Task succeeded: Blastn
[2023-03-15 12:44:56,149] [INFO] Selected 21 target genomes.
[2023-03-15 12:44:56,149] [INFO] Target genome list was writen to OceanDNA-b20744/target_genomes_gtdb.txt
[2023-03-15 12:44:56,206] [INFO] Task started: fastANI
[2023-03-15 12:44:56,206] [INFO] Running command: fastANI --query /var/lib/cwl/stg9867fd94-d713-469b-b34f-4451880b1245/OceanDNA-b20744.fa --refList OceanDNA-b20744/target_genomes_gtdb.txt --output OceanDNA-b20744/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:45:02,765] [INFO] Task succeeded: fastANI
[2023-03-15 12:45:02,770] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 12:45:02,770] [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_002701185.1	s__TMED6 sp002701185	98.0281	129	157	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED6;g__TMED6	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002711465.1	s__TMED6 sp002711465	81.3112	94	157	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED6;g__TMED6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002710085.1	s__TMED6 sp002710085	79.3576	54	157	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED6;g__TMED6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239355.1	s__TMED6 sp014239355	79.2616	83	157	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED6;g__TMED6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167465.1	s__TMED6 sp002167465	78.9208	81	157	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__TMED6;g__TMED6	95.0	98.36	98.36	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-03-15 12:45:02,770] [INFO] GTDB search result was written to OceanDNA-b20744/result_gtdb.tsv
[2023-03-15 12:45:02,770] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:45:02,771] [INFO] DFAST_QC result json was written to OceanDNA-b20744/dqc_result.json
[2023-03-15 12:45:02,771] [INFO] DFAST_QC completed!
[2023-03-15 12:45:02,771] [INFO] Total running time: 0h0m38s