[2023-03-14 12:03:55,351] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:03:55,358] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:03:55,358] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb37f367-a97b-412d-b324-e300fcaed07a/dqc_reference
[2023-03-14 12:03:56,863] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:03:56,864] [INFO] Task started: Prodigal
[2023-03-14 12:03:56,864] [INFO] Running command: cat /var/lib/cwl/stge0200bfd-9baf-4d65-b06f-6f84b96186cf/OceanDNA-b41998.fa | prodigal -d OceanDNA-b41998/cds.fna -a OceanDNA-b41998/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:03:59,775] [INFO] Task succeeded: Prodigal
[2023-03-14 12:03:59,775] [INFO] Task started: HMMsearch
[2023-03-14 12:03:59,775] [INFO] Running command: hmmsearch --tblout OceanDNA-b41998/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb37f367-a97b-412d-b324-e300fcaed07a/dqc_reference/reference_markers.hmm OceanDNA-b41998/protein.faa > /dev/null
[2023-03-14 12:03:59,963] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:03:59,964] [WARNING] Found 3/6 markers. [/var/lib/cwl/stge0200bfd-9baf-4d65-b06f-6f84b96186cf/OceanDNA-b41998.fa]
[2023-03-14 12:04:00,010] [INFO] Query marker FASTA was written to OceanDNA-b41998/markers.fasta
[2023-03-14 12:04:00,012] [INFO] Task started: Blastn
[2023-03-14 12:04:00,012] [INFO] Running command: blastn -query OceanDNA-b41998/markers.fasta -db /var/lib/cwl/stgbb37f367-a97b-412d-b324-e300fcaed07a/dqc_reference/reference_markers.fasta -out OceanDNA-b41998/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:04:02,666] [INFO] Task succeeded: Blastn
[2023-03-14 12:04:02,678] [INFO] Selected 5 target genomes.
[2023-03-14 12:04:02,678] [INFO] Target genome list was writen to OceanDNA-b41998/target_genomes.txt
[2023-03-14 12:04:02,683] [INFO] Task started: fastANI
[2023-03-14 12:04:02,683] [INFO] Running command: fastANI --query /var/lib/cwl/stge0200bfd-9baf-4d65-b06f-6f84b96186cf/OceanDNA-b41998.fa --refList OceanDNA-b41998/target_genomes.txt --output OceanDNA-b41998/fastani_result.tsv --threads 1
[2023-03-14 12:04:04,361] [INFO] Task succeeded: fastANI
[2023-03-14 12:04:04,361] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb37f367-a97b-412d-b324-e300fcaed07a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:04:04,361] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb37f367-a97b-412d-b324-e300fcaed07a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:04:04,361] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:04:04,361] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:04:04,362] [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 12:04:04,365] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41998/tc_result.tsv
[2023-03-14 12:04:04,369] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:04:04,370] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:04:04,370] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb37f367-a97b-412d-b324-e300fcaed07a/dqc_reference/checkm_data
[2023-03-14 12:04:04,435] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:04:04,439] [INFO] Task started: CheckM
[2023-03-14 12:04:04,439] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41998/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41998/checkm_input OceanDNA-b41998/checkm_result
[2023-03-14 12:04:24,367] [INFO] Task succeeded: CheckM
[2023-03-14 12:04:24,368] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 36.05%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:04:24,411] [INFO] ===== Completeness check finished =====
[2023-03-14 12:04:24,411] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:04:24,411] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41998/markers.fasta)
[2023-03-14 12:04:24,413] [INFO] Task started: Blastn
[2023-03-14 12:04:24,414] [INFO] Running command: blastn -query OceanDNA-b41998/markers.fasta -db /var/lib/cwl/stgbb37f367-a97b-412d-b324-e300fcaed07a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41998/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:04:25,320] [INFO] Task succeeded: Blastn
[2023-03-14 12:04:25,351] [INFO] Selected 11 target genomes.
[2023-03-14 12:04:25,351] [INFO] Target genome list was writen to OceanDNA-b41998/target_genomes_gtdb.txt
[2023-03-14 12:04:25,475] [INFO] Task started: fastANI
[2023-03-14 12:04:25,475] [INFO] Running command: fastANI --query /var/lib/cwl/stge0200bfd-9baf-4d65-b06f-6f84b96186cf/OceanDNA-b41998.fa --refList OceanDNA-b41998/target_genomes_gtdb.txt --output OceanDNA-b41998/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:04:27,564] [INFO] Task succeeded: fastANI
[2023-03-14 12:04:27,567] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:04:27,568] [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_905182885.1	s__SCGC-AAA076-P13 sp905182885	82.8459	137	183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000384935.1	s__SCGC-AAA076-P13 sp000384935	77.2435	51	183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018607365.1	s__SCGC-AAA076-P13 sp018607365	76.9084	50	183	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:04:27,576] [INFO] GTDB search result was written to OceanDNA-b41998/result_gtdb.tsv
[2023-03-14 12:04:27,586] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:04:27,591] [INFO] DFAST_QC result json was written to OceanDNA-b41998/dqc_result.json
[2023-03-14 12:04:27,591] [INFO] DFAST_QC completed!
[2023-03-14 12:04:27,591] [INFO] Total running time: 0h0m32s