[2023-03-18 09:58:36,587] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:58:36,588] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:58:36,588] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f0bf5fe-379a-4eb6-92eb-b58e1be1f9ce/dqc_reference
[2023-03-18 09:58:38,401] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:58:38,401] [INFO] Task started: Prodigal
[2023-03-18 09:58:38,401] [INFO] Running command: cat /var/lib/cwl/stg5d7b1b54-dbce-469b-ab1a-18c7b2c96a79/OceanDNA-b28718.fa | prodigal -d OceanDNA-b28718/cds.fna -a OceanDNA-b28718/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:58:47,249] [INFO] Task succeeded: Prodigal
[2023-03-18 09:58:47,249] [INFO] Task started: HMMsearch
[2023-03-18 09:58:47,249] [INFO] Running command: hmmsearch --tblout OceanDNA-b28718/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f0bf5fe-379a-4eb6-92eb-b58e1be1f9ce/dqc_reference/reference_markers.hmm OceanDNA-b28718/protein.faa > /dev/null
[2023-03-18 09:58:47,446] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:58:47,447] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5d7b1b54-dbce-469b-ab1a-18c7b2c96a79/OceanDNA-b28718.fa]
[2023-03-18 09:58:47,461] [INFO] Query marker FASTA was written to OceanDNA-b28718/markers.fasta
[2023-03-18 09:58:47,461] [INFO] Task started: Blastn
[2023-03-18 09:58:47,461] [INFO] Running command: blastn -query OceanDNA-b28718/markers.fasta -db /var/lib/cwl/stg5f0bf5fe-379a-4eb6-92eb-b58e1be1f9ce/dqc_reference/reference_markers.fasta -out OceanDNA-b28718/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:58:47,961] [INFO] Task succeeded: Blastn
[2023-03-18 09:58:47,962] [INFO] Selected 16 target genomes.
[2023-03-18 09:58:47,962] [INFO] Target genome list was writen to OceanDNA-b28718/target_genomes.txt
[2023-03-18 09:58:47,974] [INFO] Task started: fastANI
[2023-03-18 09:58:47,974] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d7b1b54-dbce-469b-ab1a-18c7b2c96a79/OceanDNA-b28718.fa --refList OceanDNA-b28718/target_genomes.txt --output OceanDNA-b28718/fastani_result.tsv --threads 1
[2023-03-18 09:58:55,384] [INFO] Task succeeded: fastANI
[2023-03-18 09:58:55,384] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f0bf5fe-379a-4eb6-92eb-b58e1be1f9ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:58:55,384] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f0bf5fe-379a-4eb6-92eb-b58e1be1f9ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:58:55,384] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:58:55,384] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:58:55,384] [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 09:58:55,385] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28718/tc_result.tsv
[2023-03-18 09:58:55,385] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:58:55,385] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:58:55,385] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f0bf5fe-379a-4eb6-92eb-b58e1be1f9ce/dqc_reference/checkm_data
[2023-03-18 09:58:55,387] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:58:55,391] [INFO] Task started: CheckM
[2023-03-18 09:58:55,391] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28718/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28718/checkm_input OceanDNA-b28718/checkm_result
[2023-03-18 09:59:22,398] [INFO] Task succeeded: CheckM
[2023-03-18 09:59:22,399] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:59:22,400] [INFO] ===== Completeness check finished =====
[2023-03-18 09:59:22,401] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:59:22,401] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28718/markers.fasta)
[2023-03-18 09:59:22,401] [INFO] Task started: Blastn
[2023-03-18 09:59:22,401] [INFO] Running command: blastn -query OceanDNA-b28718/markers.fasta -db /var/lib/cwl/stg5f0bf5fe-379a-4eb6-92eb-b58e1be1f9ce/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28718/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:59:23,087] [INFO] Task succeeded: Blastn
[2023-03-18 09:59:23,088] [INFO] Selected 11 target genomes.
[2023-03-18 09:59:23,088] [INFO] Target genome list was writen to OceanDNA-b28718/target_genomes_gtdb.txt
[2023-03-18 09:59:23,101] [INFO] Task started: fastANI
[2023-03-18 09:59:23,101] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d7b1b54-dbce-469b-ab1a-18c7b2c96a79/OceanDNA-b28718.fa --refList OceanDNA-b28718/target_genomes_gtdb.txt --output OceanDNA-b28718/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:59:27,054] [INFO] Task succeeded: fastANI
[2023-03-18 09:59:27,059] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:59:27,059] [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_902573175.1	s__MED-G52 sp902573175	89.4474	266	550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MED-G52	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902534325.1	s__MED-G52 sp902534325	88.7068	362	550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MED-G52	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902543185.1	s__MED-G52 sp902543185	88.4557	372	550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MED-G52	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902554705.1	s__MED-G52 sp902554705	88.4157	327	550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MED-G52	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902606585.1	s__MED-G52 sp902606585	87.9223	324	550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MED-G52	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003332035.1	s__MED-G52 sp003332035	83.1657	289	550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MED-G52	95.0	96.52	96.52	0.74	0.74	2	-
GCA_902632125.1	s__MED-G52 sp902632125	82.5134	303	550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MED-G52	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012270125.1	s__MED-G52 sp001627375	79.0792	295	550	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__MED-G52	95.0	97.90	95.50	0.79	0.63	16	-
--------------------------------------------------------------------------------
[2023-03-18 09:59:27,059] [INFO] GTDB search result was written to OceanDNA-b28718/result_gtdb.tsv
[2023-03-18 09:59:27,060] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:59:27,060] [INFO] DFAST_QC result json was written to OceanDNA-b28718/dqc_result.json
[2023-03-18 09:59:27,060] [INFO] DFAST_QC completed!
[2023-03-18 09:59:27,061] [INFO] Total running time: 0h0m50s