[2023-03-19 00:48:24,528] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:48:24,528] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:48:24,528] [INFO] DQC Reference Directory: /var/lib/cwl/stga9f05161-0dbe-469e-b6d0-5483ed7e69ed/dqc_reference
[2023-03-19 00:48:26,000] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:48:26,001] [INFO] Task started: Prodigal
[2023-03-19 00:48:26,001] [INFO] Running command: cat /var/lib/cwl/stgb90bc2f3-4fd9-4398-acd8-d61ea51eca18/OceanDNA-b25483.fa | prodigal -d OceanDNA-b25483/cds.fna -a OceanDNA-b25483/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:48:29,474] [INFO] Task succeeded: Prodigal
[2023-03-19 00:48:29,474] [INFO] Task started: HMMsearch
[2023-03-19 00:48:29,474] [INFO] Running command: hmmsearch --tblout OceanDNA-b25483/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9f05161-0dbe-469e-b6d0-5483ed7e69ed/dqc_reference/reference_markers.hmm OceanDNA-b25483/protein.faa > /dev/null
[2023-03-19 00:48:29,613] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:48:29,613] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb90bc2f3-4fd9-4398-acd8-d61ea51eca18/OceanDNA-b25483.fa]
[2023-03-19 00:48:29,622] [INFO] Query marker FASTA was written to OceanDNA-b25483/markers.fasta
[2023-03-19 00:48:29,623] [INFO] Task started: Blastn
[2023-03-19 00:48:29,624] [INFO] Running command: blastn -query OceanDNA-b25483/markers.fasta -db /var/lib/cwl/stga9f05161-0dbe-469e-b6d0-5483ed7e69ed/dqc_reference/reference_markers.fasta -out OceanDNA-b25483/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:48:30,200] [INFO] Task succeeded: Blastn
[2023-03-19 00:48:30,202] [INFO] Selected 13 target genomes.
[2023-03-19 00:48:30,202] [INFO] Target genome list was writen to OceanDNA-b25483/target_genomes.txt
[2023-03-19 00:48:30,211] [INFO] Task started: fastANI
[2023-03-19 00:48:30,211] [INFO] Running command: fastANI --query /var/lib/cwl/stgb90bc2f3-4fd9-4398-acd8-d61ea51eca18/OceanDNA-b25483.fa --refList OceanDNA-b25483/target_genomes.txt --output OceanDNA-b25483/fastani_result.tsv --threads 1
[2023-03-19 00:48:35,470] [INFO] Task succeeded: fastANI
[2023-03-19 00:48:35,470] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9f05161-0dbe-469e-b6d0-5483ed7e69ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:48:35,470] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9f05161-0dbe-469e-b6d0-5483ed7e69ed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:48:35,470] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:48:35,470] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:48:35,471] [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
--------------------------------------------------------------------------------
[2023-03-19 00:48:35,471] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25483/tc_result.tsv
[2023-03-19 00:48:35,471] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:48:35,471] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:48:35,471] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9f05161-0dbe-469e-b6d0-5483ed7e69ed/dqc_reference/checkm_data
[2023-03-19 00:48:35,482] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:48:35,484] [INFO] Task started: CheckM
[2023-03-19 00:48:35,484] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25483/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25483/checkm_input OceanDNA-b25483/checkm_result
[2023-03-19 00:48:51,431] [INFO] Task succeeded: CheckM
[2023-03-19 00:48:51,431] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.60%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:48:51,433] [INFO] ===== Completeness check finished =====
[2023-03-19 00:48:51,434] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:48:51,434] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25483/markers.fasta)
[2023-03-19 00:48:51,435] [INFO] Task started: Blastn
[2023-03-19 00:48:51,436] [INFO] Running command: blastn -query OceanDNA-b25483/markers.fasta -db /var/lib/cwl/stga9f05161-0dbe-469e-b6d0-5483ed7e69ed/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25483/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:48:52,231] [INFO] Task succeeded: Blastn
[2023-03-19 00:48:52,232] [INFO] Selected 13 target genomes.
[2023-03-19 00:48:52,232] [INFO] Target genome list was writen to OceanDNA-b25483/target_genomes_gtdb.txt
[2023-03-19 00:48:52,241] [INFO] Task started: fastANI
[2023-03-19 00:48:52,241] [INFO] Running command: fastANI --query /var/lib/cwl/stgb90bc2f3-4fd9-4398-acd8-d61ea51eca18/OceanDNA-b25483.fa --refList OceanDNA-b25483/target_genomes_gtdb.txt --output OceanDNA-b25483/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:48:54,243] [INFO] Task succeeded: fastANI
[2023-03-19 00:48:54,247] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 00:48:54,247] [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_002171085.1	s__HIMB114 sp002171085	80.841	86	159	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__HIMB114	95.0	99.62	99.25	0.83	0.70	3	-
GCA_000163555.2	s__HIMB114 sp000163555	80.584	114	159	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__HIMB114	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902524955.1	s__HIMB114 sp902524955	78.8574	98	159	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__HIMB114	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002684895.1	s__HIMB114 sp002684895	78.7575	85	159	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__HIMB114	95.0	97.17	97.17	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-03-19 00:48:54,249] [INFO] GTDB search result was written to OceanDNA-b25483/result_gtdb.tsv
[2023-03-19 00:48:54,252] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:48:54,255] [INFO] DFAST_QC result json was written to OceanDNA-b25483/dqc_result.json
[2023-03-19 00:48:54,255] [INFO] DFAST_QC completed!
[2023-03-19 00:48:54,255] [INFO] Total running time: 0h0m30s