[2023-03-15 15:20:28,456] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:20:28,456] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:20:28,456] [INFO] DQC Reference Directory: /var/lib/cwl/stg68fab30e-e7ec-41dc-a54c-6f7502783955/dqc_reference
[2023-03-15 15:20:29,560] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:20:29,561] [INFO] Task started: Prodigal
[2023-03-15 15:20:29,561] [INFO] Running command: cat /var/lib/cwl/stgda2150b6-ceb8-448f-8440-88ae0fb4a233/OceanDNA-b5565.fa | prodigal -d OceanDNA-b5565/cds.fna -a OceanDNA-b5565/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:20:43,564] [INFO] Task succeeded: Prodigal
[2023-03-15 15:20:43,564] [INFO] Task started: HMMsearch
[2023-03-15 15:20:43,564] [INFO] Running command: hmmsearch --tblout OceanDNA-b5565/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68fab30e-e7ec-41dc-a54c-6f7502783955/dqc_reference/reference_markers.hmm OceanDNA-b5565/protein.faa > /dev/null
[2023-03-15 15:20:43,744] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:20:43,745] [INFO] Found 6/6 markers.
[2023-03-15 15:20:43,761] [INFO] Query marker FASTA was written to OceanDNA-b5565/markers.fasta
[2023-03-15 15:20:43,762] [INFO] Task started: Blastn
[2023-03-15 15:20:43,762] [INFO] Running command: blastn -query OceanDNA-b5565/markers.fasta -db /var/lib/cwl/stg68fab30e-e7ec-41dc-a54c-6f7502783955/dqc_reference/reference_markers.fasta -out OceanDNA-b5565/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:20:44,330] [INFO] Task succeeded: Blastn
[2023-03-15 15:20:44,332] [INFO] Selected 29 target genomes.
[2023-03-15 15:20:44,332] [INFO] Target genome list was writen to OceanDNA-b5565/target_genomes.txt
[2023-03-15 15:20:44,346] [INFO] Task started: fastANI
[2023-03-15 15:20:44,346] [INFO] Running command: fastANI --query /var/lib/cwl/stgda2150b6-ceb8-448f-8440-88ae0fb4a233/OceanDNA-b5565.fa --refList OceanDNA-b5565/target_genomes.txt --output OceanDNA-b5565/fastani_result.tsv --threads 1
[2023-03-15 15:21:01,536] [INFO] Task succeeded: fastANI
[2023-03-15 15:21:01,536] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68fab30e-e7ec-41dc-a54c-6f7502783955/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:21:01,537] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68fab30e-e7ec-41dc-a54c-6f7502783955/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:21:01,537] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:21:01,537] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 15:21:01,537] [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 15:21:01,537] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5565/tc_result.tsv
[2023-03-15 15:21:01,538] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:21:01,539] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:21:01,539] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68fab30e-e7ec-41dc-a54c-6f7502783955/dqc_reference/checkm_data
[2023-03-15 15:21:01,542] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:21:01,545] [INFO] Task started: CheckM
[2023-03-15 15:21:01,545] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5565/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5565/checkm_input OceanDNA-b5565/checkm_result
[2023-03-15 15:21:40,661] [INFO] Task succeeded: CheckM
[2023-03-15 15:21:40,661] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:21:40,687] [INFO] ===== Completeness check finished =====
[2023-03-15 15:21:40,687] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:21:40,688] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5565/markers.fasta)
[2023-03-15 15:21:40,689] [INFO] Task started: Blastn
[2023-03-15 15:21:40,689] [INFO] Running command: blastn -query OceanDNA-b5565/markers.fasta -db /var/lib/cwl/stg68fab30e-e7ec-41dc-a54c-6f7502783955/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5565/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:21:41,526] [INFO] Task succeeded: Blastn
[2023-03-15 15:21:41,537] [INFO] Selected 20 target genomes.
[2023-03-15 15:21:41,537] [INFO] Target genome list was writen to OceanDNA-b5565/target_genomes_gtdb.txt
[2023-03-15 15:21:41,604] [INFO] Task started: fastANI
[2023-03-15 15:21:41,604] [INFO] Running command: fastANI --query /var/lib/cwl/stgda2150b6-ceb8-448f-8440-88ae0fb4a233/OceanDNA-b5565.fa --refList OceanDNA-b5565/target_genomes_gtdb.txt --output OceanDNA-b5565/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:21:51,691] [INFO] Task succeeded: fastANI
[2023-03-15 15:21:51,695] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 15:21:51,695] [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_002293185.1	s__UBA952 sp002293185	94.5519	553	587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004295165.1	s__UBA952 sp004295165	79.4643	217	587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872115.1	s__UBA952 sp016872115	78.9358	282	587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002478565.1	s__UBA952 sp002478565	78.278	239	587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	99.96	99.96	0.95	0.95	2	-
GCA_903860985.1	s__UBA952 sp903860985	76.7908	63	587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	99.77	99.68	0.93	0.92	3	-
GCA_903935095.1	s__UBA952 sp903935095	76.7363	65	587	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	99.97	99.95	0.99	0.98	5	-
--------------------------------------------------------------------------------
[2023-03-15 15:21:51,698] [INFO] GTDB search result was written to OceanDNA-b5565/result_gtdb.tsv
[2023-03-15 15:21:51,702] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:21:51,707] [INFO] DFAST_QC result json was written to OceanDNA-b5565/dqc_result.json
[2023-03-15 15:21:51,708] [INFO] DFAST_QC completed!
[2023-03-15 15:21:51,708] [INFO] Total running time: 0h1m23s