[2023-03-19 02:40:15,838] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:40:15,838] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:40:15,838] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf29e2a5-9168-4612-956d-3863633bf3eb/dqc_reference
[2023-03-19 02:40:17,560] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:40:17,563] [INFO] Task started: Prodigal
[2023-03-19 02:40:17,563] [INFO] Running command: cat /var/lib/cwl/stg334c1b32-fa02-44ce-bcc2-7ebb14172c85/OceanDNA-b11078.fa | prodigal -d OceanDNA-b11078/cds.fna -a OceanDNA-b11078/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:40:27,460] [INFO] Task succeeded: Prodigal
[2023-03-19 02:40:27,461] [INFO] Task started: HMMsearch
[2023-03-19 02:40:27,461] [INFO] Running command: hmmsearch --tblout OceanDNA-b11078/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf29e2a5-9168-4612-956d-3863633bf3eb/dqc_reference/reference_markers.hmm OceanDNA-b11078/protein.faa > /dev/null
[2023-03-19 02:40:27,655] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:40:27,656] [INFO] Found 6/6 markers.
[2023-03-19 02:40:27,666] [INFO] Query marker FASTA was written to OceanDNA-b11078/markers.fasta
[2023-03-19 02:40:27,668] [INFO] Task started: Blastn
[2023-03-19 02:40:27,668] [INFO] Running command: blastn -query OceanDNA-b11078/markers.fasta -db /var/lib/cwl/stgdf29e2a5-9168-4612-956d-3863633bf3eb/dqc_reference/reference_markers.fasta -out OceanDNA-b11078/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:40:28,202] [INFO] Task succeeded: Blastn
[2023-03-19 02:40:28,204] [INFO] Selected 33 target genomes.
[2023-03-19 02:40:28,204] [INFO] Target genome list was writen to OceanDNA-b11078/target_genomes.txt
[2023-03-19 02:40:28,227] [INFO] Task started: fastANI
[2023-03-19 02:40:28,227] [INFO] Running command: fastANI --query /var/lib/cwl/stg334c1b32-fa02-44ce-bcc2-7ebb14172c85/OceanDNA-b11078.fa --refList OceanDNA-b11078/target_genomes.txt --output OceanDNA-b11078/fastani_result.tsv --threads 1
[2023-03-19 02:40:45,718] [INFO] Task succeeded: fastANI
[2023-03-19 02:40:45,719] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf29e2a5-9168-4612-956d-3863633bf3eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:40:45,719] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf29e2a5-9168-4612-956d-3863633bf3eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:40:45,719] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:40:45,719] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:40:45,719] [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 02:40:45,721] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11078/tc_result.tsv
[2023-03-19 02:40:45,723] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:40:45,723] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:40:45,723] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf29e2a5-9168-4612-956d-3863633bf3eb/dqc_reference/checkm_data
[2023-03-19 02:40:45,725] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:40:45,767] [INFO] Task started: CheckM
[2023-03-19 02:40:45,767] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11078/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11078/checkm_input OceanDNA-b11078/checkm_result
[2023-03-19 02:41:15,175] [INFO] Task succeeded: CheckM
[2023-03-19 02:41:15,176] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:41:15,208] [INFO] ===== Completeness check finished =====
[2023-03-19 02:41:15,209] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:41:15,209] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11078/markers.fasta)
[2023-03-19 02:41:15,210] [INFO] Task started: Blastn
[2023-03-19 02:41:15,210] [INFO] Running command: blastn -query OceanDNA-b11078/markers.fasta -db /var/lib/cwl/stgdf29e2a5-9168-4612-956d-3863633bf3eb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11078/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:41:15,965] [INFO] Task succeeded: Blastn
[2023-03-19 02:41:15,974] [INFO] Selected 9 target genomes.
[2023-03-19 02:41:15,975] [INFO] Target genome list was writen to OceanDNA-b11078/target_genomes_gtdb.txt
[2023-03-19 02:41:15,984] [INFO] Task started: fastANI
[2023-03-19 02:41:15,984] [INFO] Running command: fastANI --query /var/lib/cwl/stg334c1b32-fa02-44ce-bcc2-7ebb14172c85/OceanDNA-b11078.fa --refList OceanDNA-b11078/target_genomes_gtdb.txt --output OceanDNA-b11078/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:41:19,244] [INFO] Task succeeded: fastANI
[2023-03-19 02:41:19,249] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:41:19,249] [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_009937085.1	s__UBA7446 sp009937085	89.5449	326	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331305.1	s__UBA7446 sp002470745	83.2182	307	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	99.36	99.14	0.86	0.83	3	-
GCA_017856205.1	s__UBA7446 sp017856205	80.4697	259	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002478685.1	s__UBA7446 sp002478685	79.9876	256	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	99.74	99.74	0.91	0.91	3	-
GCA_009886265.1	s__UBA7446 sp009886265	78.8616	132	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862645.1	s__UBA7446 sp002862645	77.6995	113	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	95.15	95.15	0.79	0.79	2	-
GCA_002698745.1	s__UBA7446 sp002698745	77.3546	79	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7446	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:41:19,252] [INFO] GTDB search result was written to OceanDNA-b11078/result_gtdb.tsv
[2023-03-19 02:41:19,258] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:41:19,262] [INFO] DFAST_QC result json was written to OceanDNA-b11078/dqc_result.json
[2023-03-19 02:41:19,262] [INFO] DFAST_QC completed!
[2023-03-19 02:41:19,262] [INFO] Total running time: 0h1m3s