[2023-03-17 11:29:30,400] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:29:30,400] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:29:30,400] [INFO] DQC Reference Directory: /var/lib/cwl/stg46a5bc2b-f471-469e-b339-f6c93f298a70/dqc_reference
[2023-03-17 11:29:31,529] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:29:31,529] [INFO] Task started: Prodigal
[2023-03-17 11:29:31,529] [INFO] Running command: cat /var/lib/cwl/stgb94f909e-f0a1-4600-bf56-d38556484f83/OceanDNA-b21042.fa | prodigal -d OceanDNA-b21042/cds.fna -a OceanDNA-b21042/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:29:41,168] [INFO] Task succeeded: Prodigal
[2023-03-17 11:29:41,168] [INFO] Task started: HMMsearch
[2023-03-17 11:29:41,168] [INFO] Running command: hmmsearch --tblout OceanDNA-b21042/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46a5bc2b-f471-469e-b339-f6c93f298a70/dqc_reference/reference_markers.hmm OceanDNA-b21042/protein.faa > /dev/null
[2023-03-17 11:29:41,321] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:29:41,321] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb94f909e-f0a1-4600-bf56-d38556484f83/OceanDNA-b21042.fa]
[2023-03-17 11:29:41,339] [INFO] Query marker FASTA was written to OceanDNA-b21042/markers.fasta
[2023-03-17 11:29:41,340] [INFO] Task started: Blastn
[2023-03-17 11:29:41,340] [INFO] Running command: blastn -query OceanDNA-b21042/markers.fasta -db /var/lib/cwl/stg46a5bc2b-f471-469e-b339-f6c93f298a70/dqc_reference/reference_markers.fasta -out OceanDNA-b21042/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:29:41,907] [INFO] Task succeeded: Blastn
[2023-03-17 11:29:41,908] [INFO] Selected 20 target genomes.
[2023-03-17 11:29:41,908] [INFO] Target genome list was writen to OceanDNA-b21042/target_genomes.txt
[2023-03-17 11:29:41,936] [INFO] Task started: fastANI
[2023-03-17 11:29:41,936] [INFO] Running command: fastANI --query /var/lib/cwl/stgb94f909e-f0a1-4600-bf56-d38556484f83/OceanDNA-b21042.fa --refList OceanDNA-b21042/target_genomes.txt --output OceanDNA-b21042/fastani_result.tsv --threads 1
[2023-03-17 11:29:56,499] [INFO] Task succeeded: fastANI
[2023-03-17 11:29:56,500] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46a5bc2b-f471-469e-b339-f6c93f298a70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:29:56,500] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46a5bc2b-f471-469e-b339-f6c93f298a70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:29:56,500] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:29:56,500] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:29:56,500] [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 11:29:56,580] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21042/tc_result.tsv
[2023-03-17 11:29:56,581] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:29:56,581] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:29:56,581] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46a5bc2b-f471-469e-b339-f6c93f298a70/dqc_reference/checkm_data
[2023-03-17 11:29:56,584] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:29:56,608] [INFO] Task started: CheckM
[2023-03-17 11:29:56,608] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21042/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21042/checkm_input OceanDNA-b21042/checkm_result
[2023-03-17 11:30:24,541] [INFO] Task succeeded: CheckM
[2023-03-17 11:30:24,541] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:30:24,561] [INFO] ===== Completeness check finished =====
[2023-03-17 11:30:24,561] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:30:24,562] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21042/markers.fasta)
[2023-03-17 11:30:24,563] [INFO] Task started: Blastn
[2023-03-17 11:30:24,563] [INFO] Running command: blastn -query OceanDNA-b21042/markers.fasta -db /var/lib/cwl/stg46a5bc2b-f471-469e-b339-f6c93f298a70/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21042/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:30:25,413] [INFO] Task succeeded: Blastn
[2023-03-17 11:30:25,418] [INFO] Selected 14 target genomes.
[2023-03-17 11:30:25,418] [INFO] Target genome list was writen to OceanDNA-b21042/target_genomes_gtdb.txt
[2023-03-17 11:30:25,511] [INFO] Task started: fastANI
[2023-03-17 11:30:25,511] [INFO] Running command: fastANI --query /var/lib/cwl/stgb94f909e-f0a1-4600-bf56-d38556484f83/OceanDNA-b21042.fa --refList OceanDNA-b21042/target_genomes_gtdb.txt --output OceanDNA-b21042/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:30:34,459] [INFO] Task succeeded: fastANI
[2023-03-17 11:30:34,465] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:30:34,466] [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_002729515.1	s__GCA-2729515 sp002729515	99.7429	427	436	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__GCA-2729515	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013215605.1	s__JABSQW01 sp013215605	76.3429	73	436	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__JABSQW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576805.1	s__PR03 sp003576805	76.3261	78	436	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__PR03	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002687015.1	s__GCA-2687015 sp002687015	76.2338	84	436	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__GCA-2687015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215615.1	s__JABSQX01 sp013215615	76.1097	67	436	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__JABSQX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011055735.1	s__DSOP01 sp011055735	76.013	91	436	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__DSOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713665.1	s__JADJOR01 sp016713665	76.006	63	436	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__JADJOR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875395.1	s__VGRF01 sp016875395	75.7776	62	436	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__VGRF01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:30:34,466] [INFO] GTDB search result was written to OceanDNA-b21042/result_gtdb.tsv
[2023-03-17 11:30:34,472] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:30:34,477] [INFO] DFAST_QC result json was written to OceanDNA-b21042/dqc_result.json
[2023-03-17 11:30:34,477] [INFO] DFAST_QC completed!
[2023-03-17 11:30:34,477] [INFO] Total running time: 0h1m4s