[2023-03-15 05:53:02,372] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:53:02,373] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:53:02,373] [INFO] DQC Reference Directory: /var/lib/cwl/stga6d8284d-4bb5-4702-9754-cf27547be9d4/dqc_reference
[2023-03-15 05:53:03,512] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:53:03,512] [INFO] Task started: Prodigal
[2023-03-15 05:53:03,512] [INFO] Running command: cat /var/lib/cwl/stg62052399-511f-44bd-ac75-2881da955a04/OceanDNA-b24139.fa | prodigal -d OceanDNA-b24139/cds.fna -a OceanDNA-b24139/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:53:08,618] [INFO] Task succeeded: Prodigal
[2023-03-15 05:53:08,618] [INFO] Task started: HMMsearch
[2023-03-15 05:53:08,619] [INFO] Running command: hmmsearch --tblout OceanDNA-b24139/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6d8284d-4bb5-4702-9754-cf27547be9d4/dqc_reference/reference_markers.hmm OceanDNA-b24139/protein.faa > /dev/null
[2023-03-15 05:53:08,756] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:53:08,756] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg62052399-511f-44bd-ac75-2881da955a04/OceanDNA-b24139.fa]
[2023-03-15 05:53:08,777] [INFO] Query marker FASTA was written to OceanDNA-b24139/markers.fasta
[2023-03-15 05:53:08,779] [INFO] Task started: Blastn
[2023-03-15 05:53:08,779] [INFO] Running command: blastn -query OceanDNA-b24139/markers.fasta -db /var/lib/cwl/stga6d8284d-4bb5-4702-9754-cf27547be9d4/dqc_reference/reference_markers.fasta -out OceanDNA-b24139/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:53:09,344] [INFO] Task succeeded: Blastn
[2023-03-15 05:53:09,348] [INFO] Selected 9 target genomes.
[2023-03-15 05:53:09,348] [INFO] Target genome list was writen to OceanDNA-b24139/target_genomes.txt
[2023-03-15 05:53:09,358] [INFO] Task started: fastANI
[2023-03-15 05:53:09,358] [INFO] Running command: fastANI --query /var/lib/cwl/stg62052399-511f-44bd-ac75-2881da955a04/OceanDNA-b24139.fa --refList OceanDNA-b24139/target_genomes.txt --output OceanDNA-b24139/fastani_result.tsv --threads 1
[2023-03-15 05:53:15,146] [INFO] Task succeeded: fastANI
[2023-03-15 05:53:15,146] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6d8284d-4bb5-4702-9754-cf27547be9d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:53:15,146] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6d8284d-4bb5-4702-9754-cf27547be9d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:53:15,146] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:53:15,146] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 05:53:15,146] [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 05:53:15,148] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24139/tc_result.tsv
[2023-03-15 05:53:15,148] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:53:15,148] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:53:15,148] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6d8284d-4bb5-4702-9754-cf27547be9d4/dqc_reference/checkm_data
[2023-03-15 05:53:15,151] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:53:15,155] [INFO] Task started: CheckM
[2023-03-15 05:53:15,155] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24139/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24139/checkm_input OceanDNA-b24139/checkm_result
[2023-03-15 05:53:33,959] [INFO] Task succeeded: CheckM
[2023-03-15 05:53:33,960] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 44.41%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:53:33,965] [INFO] ===== Completeness check finished =====
[2023-03-15 05:53:33,965] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:53:33,966] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24139/markers.fasta)
[2023-03-15 05:53:33,967] [INFO] Task started: Blastn
[2023-03-15 05:53:33,967] [INFO] Running command: blastn -query OceanDNA-b24139/markers.fasta -db /var/lib/cwl/stga6d8284d-4bb5-4702-9754-cf27547be9d4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24139/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:53:34,670] [INFO] Task succeeded: Blastn
[2023-03-15 05:53:34,673] [INFO] Selected 14 target genomes.
[2023-03-15 05:53:34,673] [INFO] Target genome list was writen to OceanDNA-b24139/target_genomes_gtdb.txt
[2023-03-15 05:53:34,688] [INFO] Task started: fastANI
[2023-03-15 05:53:34,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg62052399-511f-44bd-ac75-2881da955a04/OceanDNA-b24139.fa --refList OceanDNA-b24139/target_genomes_gtdb.txt --output OceanDNA-b24139/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:53:41,835] [INFO] Task succeeded: fastANI
[2023-03-15 05:53:41,838] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 05:53:41,838] [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_002689465.1	s__UBA830 sp002689465	99.9155	241	283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_905181725.1	s__UBA830 sp905181725	78.3224	126	283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479125.1	s__UBA830 sp905479125	78.1516	92	283	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	98.22	98.19	0.84	0.83	3	-
--------------------------------------------------------------------------------
[2023-03-15 05:53:41,840] [INFO] GTDB search result was written to OceanDNA-b24139/result_gtdb.tsv
[2023-03-15 05:53:41,842] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:53:41,844] [INFO] DFAST_QC result json was written to OceanDNA-b24139/dqc_result.json
[2023-03-15 05:53:41,844] [INFO] DFAST_QC completed!
[2023-03-15 05:53:41,844] [INFO] Total running time: 0h0m39s