[2023-03-16 10:46:24,392] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:46:24,392] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:46:24,392] [INFO] DQC Reference Directory: /var/lib/cwl/stg6fb2f25a-275c-4293-9070-df8d0fa2cce4/dqc_reference
[2023-03-16 10:46:25,725] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:46:25,725] [INFO] Task started: Prodigal
[2023-03-16 10:46:25,725] [INFO] Running command: cat /var/lib/cwl/stgae9489ae-1a2e-4581-8736-3e48a218c4a8/OceanDNA-b41695.fa | prodigal -d OceanDNA-b41695/cds.fna -a OceanDNA-b41695/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:46:32,625] [INFO] Task succeeded: Prodigal
[2023-03-16 10:46:32,625] [INFO] Task started: HMMsearch
[2023-03-16 10:46:32,625] [INFO] Running command: hmmsearch --tblout OceanDNA-b41695/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6fb2f25a-275c-4293-9070-df8d0fa2cce4/dqc_reference/reference_markers.hmm OceanDNA-b41695/protein.faa > /dev/null
[2023-03-16 10:46:33,013] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:46:33,014] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgae9489ae-1a2e-4581-8736-3e48a218c4a8/OceanDNA-b41695.fa]
[2023-03-16 10:46:33,021] [INFO] Query marker FASTA was written to OceanDNA-b41695/markers.fasta
[2023-03-16 10:46:33,023] [INFO] Task started: Blastn
[2023-03-16 10:46:33,023] [INFO] Running command: blastn -query OceanDNA-b41695/markers.fasta -db /var/lib/cwl/stg6fb2f25a-275c-4293-9070-df8d0fa2cce4/dqc_reference/reference_markers.fasta -out OceanDNA-b41695/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:46:34,520] [INFO] Task succeeded: Blastn
[2023-03-16 10:46:34,521] [INFO] Selected 16 target genomes.
[2023-03-16 10:46:34,521] [INFO] Target genome list was writen to OceanDNA-b41695/target_genomes.txt
[2023-03-16 10:46:34,598] [INFO] Task started: fastANI
[2023-03-16 10:46:34,598] [INFO] Running command: fastANI --query /var/lib/cwl/stgae9489ae-1a2e-4581-8736-3e48a218c4a8/OceanDNA-b41695.fa --refList OceanDNA-b41695/target_genomes.txt --output OceanDNA-b41695/fastani_result.tsv --threads 1
[2023-03-16 10:46:46,975] [INFO] Task succeeded: fastANI
[2023-03-16 10:46:46,976] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6fb2f25a-275c-4293-9070-df8d0fa2cce4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:46:46,976] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6fb2f25a-275c-4293-9070-df8d0fa2cce4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:46:46,976] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:46:46,976] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 10:46:46,976] [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
--------------------------------------------------------------------------------
[2023-03-16 10:46:46,976] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41695/tc_result.tsv
[2023-03-16 10:46:46,976] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:46:46,977] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:46:46,977] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6fb2f25a-275c-4293-9070-df8d0fa2cce4/dqc_reference/checkm_data
[2023-03-16 10:46:46,987] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:46:46,989] [INFO] Task started: CheckM
[2023-03-16 10:46:46,989] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41695/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41695/checkm_input OceanDNA-b41695/checkm_result
[2023-03-16 10:47:07,963] [INFO] Task succeeded: CheckM
[2023-03-16 10:47:07,964] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 3.54%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 10:47:07,965] [INFO] ===== Completeness check finished =====
[2023-03-16 10:47:07,965] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:47:07,965] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41695/markers.fasta)
[2023-03-16 10:47:07,967] [INFO] Task started: Blastn
[2023-03-16 10:47:07,967] [INFO] Running command: blastn -query OceanDNA-b41695/markers.fasta -db /var/lib/cwl/stg6fb2f25a-275c-4293-9070-df8d0fa2cce4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41695/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:47:09,078] [INFO] Task succeeded: Blastn
[2023-03-16 10:47:09,079] [INFO] Selected 22 target genomes.
[2023-03-16 10:47:09,079] [INFO] Target genome list was writen to OceanDNA-b41695/target_genomes_gtdb.txt
[2023-03-16 10:47:09,183] [INFO] Task started: fastANI
[2023-03-16 10:47:09,183] [INFO] Running command: fastANI --query /var/lib/cwl/stgae9489ae-1a2e-4581-8736-3e48a218c4a8/OceanDNA-b41695.fa --refList OceanDNA-b41695/target_genomes_gtdb.txt --output OceanDNA-b41695/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:47:15,361] [INFO] Task succeeded: fastANI
[2023-03-16 10:47:15,365] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:47:15,365] [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_902629465.1	s__MEDG-81 sp902629465	77.7034	67	312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902561325.1	s__MEDG-81 sp902561325	77.5129	89	312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	98.13	98.13	0.81	0.81	2	-
GCA_003213595.1	s__MEDG-81 sp003213595	77.4652	93	312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	99.82	99.63	0.96	0.91	3	-
GCA_902595715.1	s__MEDG-81 sp902595715	77.4249	87	312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331625.1	s__MEDG-81 sp003331625	77.3693	80	312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	96.72	96.66	0.81	0.79	3	-
GCA_902540995.1	s__MEDG-81 sp902540995	76.9282	78	312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__AG-339-G14;g__MEDG-81	95.0	98.42	98.42	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-03-16 10:47:15,366] [INFO] GTDB search result was written to OceanDNA-b41695/result_gtdb.tsv
[2023-03-16 10:47:15,366] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:47:15,366] [INFO] DFAST_QC result json was written to OceanDNA-b41695/dqc_result.json
[2023-03-16 10:47:15,366] [INFO] DFAST_QC completed!
[2023-03-16 10:47:15,366] [INFO] Total running time: 0h0m51s