[2023-03-14 11:49:16,999] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:49:16,999] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:49:16,999] [INFO] DQC Reference Directory: /var/lib/cwl/stg797a0a0f-d445-4f0c-b732-52f23cfa0b46/dqc_reference
[2023-03-14 11:49:18,084] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:49:18,084] [INFO] Task started: Prodigal
[2023-03-14 11:49:18,084] [INFO] Running command: cat /var/lib/cwl/stg04062205-4fb1-4d75-b245-9eb345e99318/OceanDNA-b27453.fa | prodigal -d OceanDNA-b27453/cds.fna -a OceanDNA-b27453/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:49:24,979] [INFO] Task succeeded: Prodigal
[2023-03-14 11:49:24,980] [INFO] Task started: HMMsearch
[2023-03-14 11:49:24,980] [INFO] Running command: hmmsearch --tblout OceanDNA-b27453/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg797a0a0f-d445-4f0c-b732-52f23cfa0b46/dqc_reference/reference_markers.hmm OceanDNA-b27453/protein.faa > /dev/null
[2023-03-14 11:49:25,180] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:49:25,181] [INFO] Found 6/6 markers.
[2023-03-14 11:49:25,254] [INFO] Query marker FASTA was written to OceanDNA-b27453/markers.fasta
[2023-03-14 11:49:25,256] [INFO] Task started: Blastn
[2023-03-14 11:49:25,256] [INFO] Running command: blastn -query OceanDNA-b27453/markers.fasta -db /var/lib/cwl/stg797a0a0f-d445-4f0c-b732-52f23cfa0b46/dqc_reference/reference_markers.fasta -out OceanDNA-b27453/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:49:25,995] [INFO] Task succeeded: Blastn
[2023-03-14 11:49:26,022] [INFO] Selected 23 target genomes.
[2023-03-14 11:49:26,022] [INFO] Target genome list was writen to OceanDNA-b27453/target_genomes.txt
[2023-03-14 11:49:26,035] [INFO] Task started: fastANI
[2023-03-14 11:49:26,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg04062205-4fb1-4d75-b245-9eb345e99318/OceanDNA-b27453.fa --refList OceanDNA-b27453/target_genomes.txt --output OceanDNA-b27453/fastani_result.tsv --threads 1
[2023-03-14 11:49:36,072] [INFO] Task succeeded: fastANI
[2023-03-14 11:49:36,073] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg797a0a0f-d445-4f0c-b732-52f23cfa0b46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:49:36,073] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg797a0a0f-d445-4f0c-b732-52f23cfa0b46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:49:36,073] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:49:36,073] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:49:36,073] [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
--------------------------------------------------------------------------------
[2023-03-14 11:49:36,084] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27453/tc_result.tsv
[2023-03-14 11:49:36,103] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:49:36,103] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:49:36,103] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg797a0a0f-d445-4f0c-b732-52f23cfa0b46/dqc_reference/checkm_data
[2023-03-14 11:49:36,106] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:49:36,113] [INFO] Task started: CheckM
[2023-03-14 11:49:36,113] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27453/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27453/checkm_input OceanDNA-b27453/checkm_result
[2023-03-14 11:50:01,643] [INFO] Task succeeded: CheckM
[2023-03-14 11:50:01,644] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:50:01,683] [INFO] ===== Completeness check finished =====
[2023-03-14 11:50:01,683] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:50:01,684] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27453/markers.fasta)
[2023-03-14 11:50:01,685] [INFO] Task started: Blastn
[2023-03-14 11:50:01,685] [INFO] Running command: blastn -query OceanDNA-b27453/markers.fasta -db /var/lib/cwl/stg797a0a0f-d445-4f0c-b732-52f23cfa0b46/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27453/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:50:02,867] [INFO] Task succeeded: Blastn
[2023-03-14 11:50:02,877] [INFO] Selected 26 target genomes.
[2023-03-14 11:50:02,877] [INFO] Target genome list was writen to OceanDNA-b27453/target_genomes_gtdb.txt
[2023-03-14 11:50:03,164] [INFO] Task started: fastANI
[2023-03-14 11:50:03,164] [INFO] Running command: fastANI --query /var/lib/cwl/stg04062205-4fb1-4d75-b245-9eb345e99318/OceanDNA-b27453.fa --refList OceanDNA-b27453/target_genomes_gtdb.txt --output OceanDNA-b27453/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:50:09,847] [INFO] Task succeeded: fastANI
[2023-03-14 11:50:09,851] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:50:09,852] [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_002168075.1	s__TMED25 sp002168075	99.822	421	448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__TMED25;g__TMED25	95.0	98.97	97.02	0.94	0.90	4	conclusive
GCA_002699615.1	s__TMED25 sp002699615	77.1278	70	448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__TMED25;g__TMED25	95.0	97.16	95.98	0.85	0.81	4	-
GCA_002704755.1	s__TMED25 sp002704755	76.8272	107	448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__TMED25;g__TMED25	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016780665.1	s__TMED25 sp016780665	76.4938	70	448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__TMED25;g__TMED25	95.0	99.95	99.95	0.98	0.98	2	-
GCA_902632055.1	s__TMED25 sp902632055	76.3775	72	448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__TMED25;g__TMED25	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018651345.1	s__CAJIYR01 sp018651345	76.2023	54	448	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales_B;f__TMED25;g__CAJIYR01	95.0	99.71	99.71	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-14 11:50:09,857] [INFO] GTDB search result was written to OceanDNA-b27453/result_gtdb.tsv
[2023-03-14 11:50:09,859] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:50:09,862] [INFO] DFAST_QC result json was written to OceanDNA-b27453/dqc_result.json
[2023-03-14 11:50:09,862] [INFO] DFAST_QC completed!
[2023-03-14 11:50:09,863] [INFO] Total running time: 0h0m53s