[2023-03-14 12:19:39,492] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:19:39,492] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:19:39,493] [INFO] DQC Reference Directory: /var/lib/cwl/stg19c2b11a-a6d6-4d9a-b8f7-a8cbc3bfa964/dqc_reference
[2023-03-14 12:19:40,596] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:19:40,596] [INFO] Task started: Prodigal
[2023-03-14 12:19:40,596] [INFO] Running command: cat /var/lib/cwl/stg84f7427e-6bcc-497f-90e6-0147b963844e/OceanDNA-b25512.fa | prodigal -d OceanDNA-b25512/cds.fna -a OceanDNA-b25512/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:19:45,851] [INFO] Task succeeded: Prodigal
[2023-03-14 12:19:45,851] [INFO] Task started: HMMsearch
[2023-03-14 12:19:45,851] [INFO] Running command: hmmsearch --tblout OceanDNA-b25512/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg19c2b11a-a6d6-4d9a-b8f7-a8cbc3bfa964/dqc_reference/reference_markers.hmm OceanDNA-b25512/protein.faa > /dev/null
[2023-03-14 12:19:46,012] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:19:46,012] [INFO] Found 6/6 markers.
[2023-03-14 12:19:46,026] [INFO] Query marker FASTA was written to OceanDNA-b25512/markers.fasta
[2023-03-14 12:19:46,027] [INFO] Task started: Blastn
[2023-03-14 12:19:46,027] [INFO] Running command: blastn -query OceanDNA-b25512/markers.fasta -db /var/lib/cwl/stg19c2b11a-a6d6-4d9a-b8f7-a8cbc3bfa964/dqc_reference/reference_markers.fasta -out OceanDNA-b25512/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:19:46,551] [INFO] Task succeeded: Blastn
[2023-03-14 12:19:46,556] [INFO] Selected 19 target genomes.
[2023-03-14 12:19:46,557] [INFO] Target genome list was writen to OceanDNA-b25512/target_genomes.txt
[2023-03-14 12:19:46,570] [INFO] Task started: fastANI
[2023-03-14 12:19:46,571] [INFO] Running command: fastANI --query /var/lib/cwl/stg84f7427e-6bcc-497f-90e6-0147b963844e/OceanDNA-b25512.fa --refList OceanDNA-b25512/target_genomes.txt --output OceanDNA-b25512/fastani_result.tsv --threads 1
[2023-03-14 12:19:53,647] [INFO] Task succeeded: fastANI
[2023-03-14 12:19:53,647] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg19c2b11a-a6d6-4d9a-b8f7-a8cbc3bfa964/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:19:53,647] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg19c2b11a-a6d6-4d9a-b8f7-a8cbc3bfa964/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:19:53,648] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:19:53,648] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:19:53,648] [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 12:19:53,649] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25512/tc_result.tsv
[2023-03-14 12:19:53,650] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:19:53,650] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:19:53,650] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg19c2b11a-a6d6-4d9a-b8f7-a8cbc3bfa964/dqc_reference/checkm_data
[2023-03-14 12:19:53,653] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:19:53,664] [INFO] Task started: CheckM
[2023-03-14 12:19:53,664] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25512/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25512/checkm_input OceanDNA-b25512/checkm_result
[2023-03-14 12:20:12,930] [INFO] Task succeeded: CheckM
[2023-03-14 12:20:12,931] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.70%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 12:20:13,014] [INFO] ===== Completeness check finished =====
[2023-03-14 12:20:13,014] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:20:13,014] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25512/markers.fasta)
[2023-03-14 12:20:13,015] [INFO] Task started: Blastn
[2023-03-14 12:20:13,015] [INFO] Running command: blastn -query OceanDNA-b25512/markers.fasta -db /var/lib/cwl/stg19c2b11a-a6d6-4d9a-b8f7-a8cbc3bfa964/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25512/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:20:13,885] [INFO] Task succeeded: Blastn
[2023-03-14 12:20:13,889] [INFO] Selected 17 target genomes.
[2023-03-14 12:20:13,889] [INFO] Target genome list was writen to OceanDNA-b25512/target_genomes_gtdb.txt
[2023-03-14 12:20:13,910] [INFO] Task started: fastANI
[2023-03-14 12:20:13,911] [INFO] Running command: fastANI --query /var/lib/cwl/stg84f7427e-6bcc-497f-90e6-0147b963844e/OceanDNA-b25512.fa --refList OceanDNA-b25512/target_genomes_gtdb.txt --output OceanDNA-b25512/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:20:17,309] [INFO] Task succeeded: fastANI
[2023-03-14 12:20:17,314] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:20:17,314] [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	99.0342	203	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__HIMB114	95.0	99.62	99.25	0.83	0.70	3	conclusive
GCA_000163555.2	s__HIMB114 sp000163555	92.5419	241	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__HIMB114	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008638005.1	s__HIMB114 sp008638005	79.2421	141	279	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	79.2395	150	279	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	78.4537	149	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__HIMB114	95.0	97.17	97.17	0.86	0.86	2	-
GCA_003209195.1	s__HIMB114 sp003209195	78.2561	116	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__HIMB114	95.0	99.64	99.28	0.95	0.90	3	-
GCA_018402735.1	s__IMCC9063 sp000750175	76.1049	54	279	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__IMCC9063	95.0	99.21	99.21	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-03-14 12:20:17,315] [INFO] GTDB search result was written to OceanDNA-b25512/result_gtdb.tsv
[2023-03-14 12:20:17,316] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:20:17,319] [INFO] DFAST_QC result json was written to OceanDNA-b25512/dqc_result.json
[2023-03-14 12:20:17,319] [INFO] DFAST_QC completed!
[2023-03-14 12:20:17,319] [INFO] Total running time: 0h0m38s