[2023-03-17 00:45:49,099] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:45:49,100] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:45:49,100] [INFO] DQC Reference Directory: /var/lib/cwl/stge5cde872-7aa8-42e1-ab54-d09126e8a980/dqc_reference
[2023-03-17 00:45:50,192] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:45:50,192] [INFO] Task started: Prodigal
[2023-03-17 00:45:50,192] [INFO] Running command: cat /var/lib/cwl/stg4d059a27-d185-4433-b45e-5288471a5575/OceanDNA-b10937.fa | prodigal -d OceanDNA-b10937/cds.fna -a OceanDNA-b10937/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:46:00,198] [INFO] Task succeeded: Prodigal
[2023-03-17 00:46:00,198] [INFO] Task started: HMMsearch
[2023-03-17 00:46:00,198] [INFO] Running command: hmmsearch --tblout OceanDNA-b10937/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5cde872-7aa8-42e1-ab54-d09126e8a980/dqc_reference/reference_markers.hmm OceanDNA-b10937/protein.faa > /dev/null
[2023-03-17 00:46:00,379] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:46:00,379] [INFO] Found 6/6 markers.
[2023-03-17 00:46:00,389] [INFO] Query marker FASTA was written to OceanDNA-b10937/markers.fasta
[2023-03-17 00:46:00,389] [INFO] Task started: Blastn
[2023-03-17 00:46:00,389] [INFO] Running command: blastn -query OceanDNA-b10937/markers.fasta -db /var/lib/cwl/stge5cde872-7aa8-42e1-ab54-d09126e8a980/dqc_reference/reference_markers.fasta -out OceanDNA-b10937/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:46:00,925] [INFO] Task succeeded: Blastn
[2023-03-17 00:46:00,926] [INFO] Selected 28 target genomes.
[2023-03-17 00:46:00,926] [INFO] Target genome list was writen to OceanDNA-b10937/target_genomes.txt
[2023-03-17 00:46:00,982] [INFO] Task started: fastANI
[2023-03-17 00:46:00,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d059a27-d185-4433-b45e-5288471a5575/OceanDNA-b10937.fa --refList OceanDNA-b10937/target_genomes.txt --output OceanDNA-b10937/fastani_result.tsv --threads 1
[2023-03-17 00:46:16,347] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:16,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5cde872-7aa8-42e1-ab54-d09126e8a980/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:46:16,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5cde872-7aa8-42e1-ab54-d09126e8a980/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:46:16,348] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:46:16,348] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 00:46:16,348] [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 00:46:16,348] [INFO] DFAST Taxonomy check result was written to OceanDNA-b10937/tc_result.tsv
[2023-03-17 00:46:16,349] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:46:16,349] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:46:16,349] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5cde872-7aa8-42e1-ab54-d09126e8a980/dqc_reference/checkm_data
[2023-03-17 00:46:16,351] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:46:16,354] [INFO] Task started: CheckM
[2023-03-17 00:46:16,354] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b10937/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b10937/checkm_input OceanDNA-b10937/checkm_result
[2023-03-17 00:46:45,777] [INFO] Task succeeded: CheckM
[2023-03-17 00:46:45,777] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:46:45,779] [INFO] ===== Completeness check finished =====
[2023-03-17 00:46:45,779] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:46:45,779] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b10937/markers.fasta)
[2023-03-17 00:46:45,780] [INFO] Task started: Blastn
[2023-03-17 00:46:45,780] [INFO] Running command: blastn -query OceanDNA-b10937/markers.fasta -db /var/lib/cwl/stge5cde872-7aa8-42e1-ab54-d09126e8a980/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b10937/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:46:46,528] [INFO] Task succeeded: Blastn
[2023-03-17 00:46:46,529] [INFO] Selected 28 target genomes.
[2023-03-17 00:46:46,529] [INFO] Target genome list was writen to OceanDNA-b10937/target_genomes_gtdb.txt
[2023-03-17 00:46:47,027] [INFO] Task started: fastANI
[2023-03-17 00:46:47,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d059a27-d185-4433-b45e-5288471a5575/OceanDNA-b10937.fa --refList OceanDNA-b10937/target_genomes_gtdb.txt --output OceanDNA-b10937/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:46:58,446] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:58,449] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:46:58,449] [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_905478905.1	s__UBA7428 sp905478905	78.437	139	498	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	98.97	98.97	0.80	0.80	2	-
GCA_011526285.1	s__UBA7428 sp011526285	77.2207	132	498	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526275.1	s__UBA7428 sp011526275	77.0676	135	498	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181615.1	s__UBA7428 sp905181615	76.5223	57	498	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA7428	95.0	99.59	99.59	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-03-17 00:46:58,449] [INFO] GTDB search result was written to OceanDNA-b10937/result_gtdb.tsv
[2023-03-17 00:46:58,449] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:46:58,450] [INFO] DFAST_QC result json was written to OceanDNA-b10937/dqc_result.json
[2023-03-17 00:46:58,450] [INFO] DFAST_QC completed!
[2023-03-17 00:46:58,450] [INFO] Total running time: 0h1m9s