[2023-03-19 04:55:39,417] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:55:39,417] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:55:39,417] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6852cc3-02f4-4edd-86a0-c3db1839b317/dqc_reference
[2023-03-19 04:55:40,560] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:55:40,561] [INFO] Task started: Prodigal
[2023-03-19 04:55:40,561] [INFO] Running command: cat /var/lib/cwl/stg95f89564-0e67-4d5c-a5ea-fba361a146e0/OceanDNA-b4143.fa | prodigal -d OceanDNA-b4143/cds.fna -a OceanDNA-b4143/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:56:07,612] [INFO] Task succeeded: Prodigal
[2023-03-19 04:56:07,612] [INFO] Task started: HMMsearch
[2023-03-19 04:56:07,612] [INFO] Running command: hmmsearch --tblout OceanDNA-b4143/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6852cc3-02f4-4edd-86a0-c3db1839b317/dqc_reference/reference_markers.hmm OceanDNA-b4143/protein.faa > /dev/null
[2023-03-19 04:56:07,837] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:56:07,838] [INFO] Found 6/6 markers.
[2023-03-19 04:56:07,877] [INFO] Query marker FASTA was written to OceanDNA-b4143/markers.fasta
[2023-03-19 04:56:07,880] [INFO] Task started: Blastn
[2023-03-19 04:56:07,880] [INFO] Running command: blastn -query OceanDNA-b4143/markers.fasta -db /var/lib/cwl/stgc6852cc3-02f4-4edd-86a0-c3db1839b317/dqc_reference/reference_markers.fasta -out OceanDNA-b4143/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:56:08,448] [INFO] Task succeeded: Blastn
[2023-03-19 04:56:08,452] [INFO] Selected 22 target genomes.
[2023-03-19 04:56:08,452] [INFO] Target genome list was writen to OceanDNA-b4143/target_genomes.txt
[2023-03-19 04:56:08,467] [INFO] Task started: fastANI
[2023-03-19 04:56:08,467] [INFO] Running command: fastANI --query /var/lib/cwl/stg95f89564-0e67-4d5c-a5ea-fba361a146e0/OceanDNA-b4143.fa --refList OceanDNA-b4143/target_genomes.txt --output OceanDNA-b4143/fastani_result.tsv --threads 1
[2023-03-19 04:56:23,135] [INFO] Task succeeded: fastANI
[2023-03-19 04:56:23,136] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6852cc3-02f4-4edd-86a0-c3db1839b317/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:56:23,136] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6852cc3-02f4-4edd-86a0-c3db1839b317/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:56:23,140] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:56:23,140] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 04:56:23,140] [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
Roseivirga pacifica	strain=DSM 100771	GCA_003633845.1	1267423	1267423	type	True	76.3071	51	823	95	below_threshold
Roseivirga pacifica	strain=CGMCC 1.12402	GCA_900111145.1	1267423	1267423	type	True	76.2737	52	823	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 04:56:23,141] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4143/tc_result.tsv
[2023-03-19 04:56:23,146] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:56:23,146] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:56:23,147] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6852cc3-02f4-4edd-86a0-c3db1839b317/dqc_reference/checkm_data
[2023-03-19 04:56:23,147] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:56:23,157] [INFO] Task started: CheckM
[2023-03-19 04:56:23,157] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4143/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4143/checkm_input OceanDNA-b4143/checkm_result
[2023-03-19 04:57:33,912] [INFO] Task succeeded: CheckM
[2023-03-19 04:57:33,913] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.08%
Contamintation: 4.69%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 04:57:33,952] [INFO] ===== Completeness check finished =====
[2023-03-19 04:57:33,952] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:57:33,953] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4143/markers.fasta)
[2023-03-19 04:57:33,954] [INFO] Task started: Blastn
[2023-03-19 04:57:33,954] [INFO] Running command: blastn -query OceanDNA-b4143/markers.fasta -db /var/lib/cwl/stgc6852cc3-02f4-4edd-86a0-c3db1839b317/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4143/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:57:34,839] [INFO] Task succeeded: Blastn
[2023-03-19 04:57:34,847] [INFO] Selected 31 target genomes.
[2023-03-19 04:57:34,847] [INFO] Target genome list was writen to OceanDNA-b4143/target_genomes_gtdb.txt
[2023-03-19 04:57:34,880] [INFO] Task started: fastANI
[2023-03-19 04:57:34,880] [INFO] Running command: fastANI --query /var/lib/cwl/stg95f89564-0e67-4d5c-a5ea-fba361a146e0/OceanDNA-b4143.fa --refList OceanDNA-b4143/target_genomes_gtdb.txt --output OceanDNA-b4143/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:57:57,922] [INFO] Task succeeded: fastANI
[2023-03-19 04:57:57,926] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:57:57,926] [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_002427745.1	s__Roseivirga sp002427745	76.8656	121	823	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Roseivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111145.1	s__Fabibacter pacificus	76.2737	52	823	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013373005.1	s__Fabibacter sp013373005	75.9273	50	823	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017592825.1	s__Fabibacter sp017592825	75.6067	50	823	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fabibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 04:57:57,928] [INFO] GTDB search result was written to OceanDNA-b4143/result_gtdb.tsv
[2023-03-19 04:57:57,930] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:57:57,934] [INFO] DFAST_QC result json was written to OceanDNA-b4143/dqc_result.json
[2023-03-19 04:57:57,934] [INFO] DFAST_QC completed!
[2023-03-19 04:57:57,934] [INFO] Total running time: 0h2m19s