[2023-03-17 00:17:04,491] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:17:04,491] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:17:04,491] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a6a26bc-aad8-4c3a-bdf0-b10a2745e15e/dqc_reference
[2023-03-17 00:17:05,590] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:17:05,590] [INFO] Task started: Prodigal
[2023-03-17 00:17:05,590] [INFO] Running command: cat /var/lib/cwl/stg11d2915a-a31f-4884-9faf-1eee227cd5a7/OceanDNA-b42461.fa | prodigal -d OceanDNA-b42461/cds.fna -a OceanDNA-b42461/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:17:09,014] [INFO] Task succeeded: Prodigal
[2023-03-17 00:17:09,015] [INFO] Task started: HMMsearch
[2023-03-17 00:17:09,015] [INFO] Running command: hmmsearch --tblout OceanDNA-b42461/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a6a26bc-aad8-4c3a-bdf0-b10a2745e15e/dqc_reference/reference_markers.hmm OceanDNA-b42461/protein.faa > /dev/null
[2023-03-17 00:17:09,154] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:17:09,154] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg11d2915a-a31f-4884-9faf-1eee227cd5a7/OceanDNA-b42461.fa]
[2023-03-17 00:17:09,164] [INFO] Query marker FASTA was written to OceanDNA-b42461/markers.fasta
[2023-03-17 00:17:09,164] [INFO] Task started: Blastn
[2023-03-17 00:17:09,164] [INFO] Running command: blastn -query OceanDNA-b42461/markers.fasta -db /var/lib/cwl/stg4a6a26bc-aad8-4c3a-bdf0-b10a2745e15e/dqc_reference/reference_markers.fasta -out OceanDNA-b42461/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:17:09,600] [INFO] Task succeeded: Blastn
[2023-03-17 00:17:09,601] [INFO] Selected 19 target genomes.
[2023-03-17 00:17:09,601] [INFO] Target genome list was writen to OceanDNA-b42461/target_genomes.txt
[2023-03-17 00:17:09,612] [INFO] Task started: fastANI
[2023-03-17 00:17:09,612] [INFO] Running command: fastANI --query /var/lib/cwl/stg11d2915a-a31f-4884-9faf-1eee227cd5a7/OceanDNA-b42461.fa --refList OceanDNA-b42461/target_genomes.txt --output OceanDNA-b42461/fastani_result.tsv --threads 1
[2023-03-17 00:17:18,310] [INFO] Task succeeded: fastANI
[2023-03-17 00:17:18,311] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a6a26bc-aad8-4c3a-bdf0-b10a2745e15e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:17:18,311] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a6a26bc-aad8-4c3a-bdf0-b10a2745e15e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:17:18,311] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:17:18,311] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 00:17:18,311] [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
--------------------------------------------------------------------------------
[2023-03-17 00:17:18,311] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42461/tc_result.tsv
[2023-03-17 00:17:18,311] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:17:18,311] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:17:18,312] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a6a26bc-aad8-4c3a-bdf0-b10a2745e15e/dqc_reference/checkm_data
[2023-03-17 00:17:18,314] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:17:18,397] [INFO] Task started: CheckM
[2023-03-17 00:17:18,398] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42461/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42461/checkm_input OceanDNA-b42461/checkm_result
[2023-03-17 00:17:33,897] [INFO] Task succeeded: CheckM
[2023-03-17 00:17:33,897] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.79%
Contamintation: 0.98%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 00:17:33,956] [INFO] ===== Completeness check finished =====
[2023-03-17 00:17:33,956] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:17:33,956] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42461/markers.fasta)
[2023-03-17 00:17:33,957] [INFO] Task started: Blastn
[2023-03-17 00:17:33,957] [INFO] Running command: blastn -query OceanDNA-b42461/markers.fasta -db /var/lib/cwl/stg4a6a26bc-aad8-4c3a-bdf0-b10a2745e15e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42461/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:17:34,419] [INFO] Task succeeded: Blastn
[2023-03-17 00:17:34,420] [INFO] Selected 20 target genomes.
[2023-03-17 00:17:34,420] [INFO] Target genome list was writen to OceanDNA-b42461/target_genomes_gtdb.txt
[2023-03-17 00:17:34,521] [INFO] Task started: fastANI
[2023-03-17 00:17:34,522] [INFO] Running command: fastANI --query /var/lib/cwl/stg11d2915a-a31f-4884-9faf-1eee227cd5a7/OceanDNA-b42461.fa --refList OceanDNA-b42461/target_genomes_gtdb.txt --output OceanDNA-b42461/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:17:39,421] [INFO] Task succeeded: fastANI
[2023-03-17 00:17:39,424] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 00:17:39,424] [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_902630715.1	s__GCA-2707915 sp902630715	96.8992	112	152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003212335.1	s__GCA-2707915 sp003212335	77.7758	50	152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__SAR86;g__GCA-2707915	95.0	96.12	95.05	0.82	0.77	11	-
--------------------------------------------------------------------------------
[2023-03-17 00:17:39,428] [INFO] GTDB search result was written to OceanDNA-b42461/result_gtdb.tsv
[2023-03-17 00:17:39,432] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:17:39,434] [INFO] DFAST_QC result json was written to OceanDNA-b42461/dqc_result.json
[2023-03-17 00:17:39,434] [INFO] DFAST_QC completed!
[2023-03-17 00:17:39,434] [INFO] Total running time: 0h0m35s