[2023-03-14 12:57:46,116] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:57:46,116] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:57:46,116] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4aff08e-6d17-42f0-a281-36ee7df5827e/dqc_reference
[2023-03-14 12:57:48,864] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:57:48,865] [INFO] Task started: Prodigal
[2023-03-14 12:57:48,866] [INFO] Running command: cat /var/lib/cwl/stg692877b3-020f-4652-b54f-f3ee963246f7/OceanDNA-b12847.fa | prodigal -d OceanDNA-b12847/cds.fna -a OceanDNA-b12847/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:58:05,278] [INFO] Task succeeded: Prodigal
[2023-03-14 12:58:05,278] [INFO] Task started: HMMsearch
[2023-03-14 12:58:05,278] [INFO] Running command: hmmsearch --tblout OceanDNA-b12847/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4aff08e-6d17-42f0-a281-36ee7df5827e/dqc_reference/reference_markers.hmm OceanDNA-b12847/protein.faa > /dev/null
[2023-03-14 12:58:05,692] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:58:05,692] [INFO] Found 6/6 markers.
[2023-03-14 12:58:05,715] [INFO] Query marker FASTA was written to OceanDNA-b12847/markers.fasta
[2023-03-14 12:58:05,720] [INFO] Task started: Blastn
[2023-03-14 12:58:05,720] [INFO] Running command: blastn -query OceanDNA-b12847/markers.fasta -db /var/lib/cwl/stgd4aff08e-6d17-42f0-a281-36ee7df5827e/dqc_reference/reference_markers.fasta -out OceanDNA-b12847/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:58:08,316] [INFO] Task succeeded: Blastn
[2023-03-14 12:58:08,317] [INFO] Selected 24 target genomes.
[2023-03-14 12:58:08,317] [INFO] Target genome list was writen to OceanDNA-b12847/target_genomes.txt
[2023-03-14 12:58:08,335] [INFO] Task started: fastANI
[2023-03-14 12:58:08,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg692877b3-020f-4652-b54f-f3ee963246f7/OceanDNA-b12847.fa --refList OceanDNA-b12847/target_genomes.txt --output OceanDNA-b12847/fastani_result.tsv --threads 1
[2023-03-14 12:58:31,938] [INFO] Task succeeded: fastANI
[2023-03-14 12:58:31,938] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4aff08e-6d17-42f0-a281-36ee7df5827e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:58:31,939] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4aff08e-6d17-42f0-a281-36ee7df5827e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:58:31,939] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:58:31,939] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:58:31,939] [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 12:58:31,939] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12847/tc_result.tsv
[2023-03-14 12:58:31,940] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:58:31,940] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:58:31,940] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4aff08e-6d17-42f0-a281-36ee7df5827e/dqc_reference/checkm_data
[2023-03-14 12:58:31,943] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:58:31,984] [INFO] Task started: CheckM
[2023-03-14 12:58:31,984] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12847/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12847/checkm_input OceanDNA-b12847/checkm_result
[2023-03-14 12:59:24,779] [INFO] Task succeeded: CheckM
[2023-03-14 12:59:24,780] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.64%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:59:24,782] [INFO] ===== Completeness check finished =====
[2023-03-14 12:59:24,783] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:59:24,783] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12847/markers.fasta)
[2023-03-14 12:59:24,784] [INFO] Task started: Blastn
[2023-03-14 12:59:24,784] [INFO] Running command: blastn -query OceanDNA-b12847/markers.fasta -db /var/lib/cwl/stgd4aff08e-6d17-42f0-a281-36ee7df5827e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12847/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:59:25,560] [INFO] Task succeeded: Blastn
[2023-03-14 12:59:25,562] [INFO] Selected 21 target genomes.
[2023-03-14 12:59:25,562] [INFO] Target genome list was writen to OceanDNA-b12847/target_genomes_gtdb.txt
[2023-03-14 12:59:25,630] [INFO] Task started: fastANI
[2023-03-14 12:59:25,630] [INFO] Running command: fastANI --query /var/lib/cwl/stg692877b3-020f-4652-b54f-f3ee963246f7/OceanDNA-b12847.fa --refList OceanDNA-b12847/target_genomes_gtdb.txt --output OceanDNA-b12847/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:59:39,066] [INFO] Task succeeded: fastANI
[2023-03-14 12:59:39,072] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:59:39,072] [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_003485825.1	s__UBA9320 sp003485825	95.2941	358	653	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003484585.1	s__UBA9320 sp003484585	78.2562	136	653	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	95.66	95.66	0.53	0.53	2	-
GCA_018700895.1	s__UBA9320 sp018700895	77.3997	114	653	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402155.1	s__UBA9320 sp018402155	77.1938	91	653	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002746305.1	s__UBA9320 sp002746305	76.9924	117	653	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017857855.1	s__UBA9320 sp003516975	76.9052	81	653	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	99.31	99.21	0.89	0.84	3	-
--------------------------------------------------------------------------------
[2023-03-14 12:59:39,073] [INFO] GTDB search result was written to OceanDNA-b12847/result_gtdb.tsv
[2023-03-14 12:59:39,073] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:59:39,074] [INFO] DFAST_QC result json was written to OceanDNA-b12847/dqc_result.json
[2023-03-14 12:59:39,074] [INFO] DFAST_QC completed!
[2023-03-14 12:59:39,074] [INFO] Total running time: 0h1m53s