[2023-03-16 19:45:43,020] [INFO] DFAST_QC pipeline started.
[2023-03-16 19:45:43,020] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 19:45:43,021] [INFO] DQC Reference Directory: /var/lib/cwl/stgef7d4929-7cf4-4496-9835-d2f2f49c77bf/dqc_reference
[2023-03-16 19:45:44,158] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 19:45:44,159] [INFO] Task started: Prodigal
[2023-03-16 19:45:44,159] [INFO] Running command: cat /var/lib/cwl/stgb7bc43c9-7e7b-46f8-8ab8-2f19c8d75b2b/OceanDNA-b12496.fa | prodigal -d OceanDNA-b12496/cds.fna -a OceanDNA-b12496/protein.faa -g 11 -q > /dev/null
[2023-03-16 19:46:03,001] [INFO] Task succeeded: Prodigal
[2023-03-16 19:46:03,002] [INFO] Task started: HMMsearch
[2023-03-16 19:46:03,002] [INFO] Running command: hmmsearch --tblout OceanDNA-b12496/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef7d4929-7cf4-4496-9835-d2f2f49c77bf/dqc_reference/reference_markers.hmm OceanDNA-b12496/protein.faa > /dev/null
[2023-03-16 19:46:03,200] [INFO] Task succeeded: HMMsearch
[2023-03-16 19:46:03,201] [INFO] Found 6/6 markers.
[2023-03-16 19:46:03,219] [INFO] Query marker FASTA was written to OceanDNA-b12496/markers.fasta
[2023-03-16 19:46:03,220] [INFO] Task started: Blastn
[2023-03-16 19:46:03,220] [INFO] Running command: blastn -query OceanDNA-b12496/markers.fasta -db /var/lib/cwl/stgef7d4929-7cf4-4496-9835-d2f2f49c77bf/dqc_reference/reference_markers.fasta -out OceanDNA-b12496/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:46:03,853] [INFO] Task succeeded: Blastn
[2023-03-16 19:46:03,854] [INFO] Selected 29 target genomes.
[2023-03-16 19:46:03,854] [INFO] Target genome list was writen to OceanDNA-b12496/target_genomes.txt
[2023-03-16 19:46:03,870] [INFO] Task started: fastANI
[2023-03-16 19:46:03,871] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7bc43c9-7e7b-46f8-8ab8-2f19c8d75b2b/OceanDNA-b12496.fa --refList OceanDNA-b12496/target_genomes.txt --output OceanDNA-b12496/fastani_result.tsv --threads 1
[2023-03-16 19:46:19,668] [INFO] Task succeeded: fastANI
[2023-03-16 19:46:19,668] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef7d4929-7cf4-4496-9835-d2f2f49c77bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 19:46:19,668] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef7d4929-7cf4-4496-9835-d2f2f49c77bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 19:46:19,668] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 19:46:19,668] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 19:46:19,668] [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 19:46:19,669] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12496/tc_result.tsv
[2023-03-16 19:46:19,669] [INFO] ===== Taxonomy check completed =====
[2023-03-16 19:46:19,669] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 19:46:19,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef7d4929-7cf4-4496-9835-d2f2f49c77bf/dqc_reference/checkm_data
[2023-03-16 19:46:19,672] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 19:46:19,923] [INFO] Task started: CheckM
[2023-03-16 19:46:19,923] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12496/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12496/checkm_input OceanDNA-b12496/checkm_result
[2023-03-16 19:47:35,151] [INFO] Task succeeded: CheckM
[2023-03-16 19:47:35,152] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 19:47:35,154] [INFO] ===== Completeness check finished =====
[2023-03-16 19:47:35,154] [INFO] ===== Start GTDB Search =====
[2023-03-16 19:47:35,154] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12496/markers.fasta)
[2023-03-16 19:47:35,156] [INFO] Task started: Blastn
[2023-03-16 19:47:35,156] [INFO] Running command: blastn -query OceanDNA-b12496/markers.fasta -db /var/lib/cwl/stgef7d4929-7cf4-4496-9835-d2f2f49c77bf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12496/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:47:36,025] [INFO] Task succeeded: Blastn
[2023-03-16 19:47:36,026] [INFO] Selected 35 target genomes.
[2023-03-16 19:47:36,026] [INFO] Target genome list was writen to OceanDNA-b12496/target_genomes_gtdb.txt
[2023-03-16 19:47:36,073] [INFO] Task started: fastANI
[2023-03-16 19:47:36,073] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7bc43c9-7e7b-46f8-8ab8-2f19c8d75b2b/OceanDNA-b12496.fa --refList OceanDNA-b12496/target_genomes_gtdb.txt --output OceanDNA-b12496/fastani_result_gtdb.tsv --threads 1
[2023-03-16 19:47:58,374] [INFO] Task succeeded: fastANI
[2023-03-16 19:47:58,377] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 19:47:58,377] [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_003448535.1	s__UBA10066 sp003448535	98.9793	564	814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__UBA10066	95.0	97.80	97.80	0.81	0.81	2	conclusive
GCA_014239715.1	s__UBA10066 sp014239715	77.8412	119	814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__UBA10066	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480225.1	s__UBA10066 sp905480225	76.5461	85	814	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__UBA10066	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 19:47:58,377] [INFO] GTDB search result was written to OceanDNA-b12496/result_gtdb.tsv
[2023-03-16 19:47:58,377] [INFO] ===== GTDB Search completed =====
[2023-03-16 19:47:58,378] [INFO] DFAST_QC result json was written to OceanDNA-b12496/dqc_result.json
[2023-03-16 19:47:58,378] [INFO] DFAST_QC completed!
[2023-03-16 19:47:58,378] [INFO] Total running time: 0h2m15s