[2023-03-17 10:08:39,074] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:08:39,074] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:08:39,074] [INFO] DQC Reference Directory: /var/lib/cwl/stgee96eda6-246a-4d26-b7a4-d00c03b19c63/dqc_reference
[2023-03-17 10:08:40,197] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:08:40,198] [INFO] Task started: Prodigal
[2023-03-17 10:08:40,198] [INFO] Running command: cat /var/lib/cwl/stg8ab3ee10-8b72-4a02-b828-0986f3bc21b9/OceanDNA-a32.fa | prodigal -d OceanDNA-a32/cds.fna -a OceanDNA-a32/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:08:47,521] [INFO] Task succeeded: Prodigal
[2023-03-17 10:08:47,522] [INFO] Task started: HMMsearch
[2023-03-17 10:08:47,522] [INFO] Running command: hmmsearch --tblout OceanDNA-a32/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee96eda6-246a-4d26-b7a4-d00c03b19c63/dqc_reference/reference_markers.hmm OceanDNA-a32/protein.faa > /dev/null
[2023-03-17 10:08:47,657] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:08:47,658] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg8ab3ee10-8b72-4a02-b828-0986f3bc21b9/OceanDNA-a32.fa]
[2023-03-17 10:08:47,669] [INFO] Query marker FASTA was written to OceanDNA-a32/markers.fasta
[2023-03-17 10:08:47,670] [INFO] Task started: Blastn
[2023-03-17 10:08:47,670] [INFO] Running command: blastn -query OceanDNA-a32/markers.fasta -db /var/lib/cwl/stgee96eda6-246a-4d26-b7a4-d00c03b19c63/dqc_reference/reference_markers.fasta -out OceanDNA-a32/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:08:48,091] [INFO] Task succeeded: Blastn
[2023-03-17 10:08:48,092] [INFO] Selected 4 target genomes.
[2023-03-17 10:08:48,092] [INFO] Target genome list was writen to OceanDNA-a32/target_genomes.txt
[2023-03-17 10:08:48,095] [INFO] Task started: fastANI
[2023-03-17 10:08:48,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ab3ee10-8b72-4a02-b828-0986f3bc21b9/OceanDNA-a32.fa --refList OceanDNA-a32/target_genomes.txt --output OceanDNA-a32/fastani_result.tsv --threads 1
[2023-03-17 10:08:48,973] [INFO] Task succeeded: fastANI
[2023-03-17 10:08:48,974] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee96eda6-246a-4d26-b7a4-d00c03b19c63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:08:48,974] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee96eda6-246a-4d26-b7a4-d00c03b19c63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:08:48,977] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:08:48,977] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 10:08:48,977] [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
Nitrosopumilus oxyclinae	strain=HCE1	GCA_013407165.1	1959104	1959104	type	True	77.0856	130	461	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 10:08:48,977] [INFO] DFAST Taxonomy check result was written to OceanDNA-a32/tc_result.tsv
[2023-03-17 10:08:48,977] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:08:48,977] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:08:48,978] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee96eda6-246a-4d26-b7a4-d00c03b19c63/dqc_reference/checkm_data
[2023-03-17 10:08:48,978] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:08:48,981] [INFO] Task started: CheckM
[2023-03-17 10:08:48,981] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a32/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a32/checkm_input OceanDNA-a32/checkm_result
[2023-03-17 10:09:12,968] [INFO] Task succeeded: CheckM
[2023-03-17 10:09:12,968] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.08%
Contamintation: 0.93%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-17 10:09:12,970] [INFO] ===== Completeness check finished =====
[2023-03-17 10:09:12,970] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:09:12,970] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a32/markers.fasta)
[2023-03-17 10:09:12,971] [INFO] Task started: Blastn
[2023-03-17 10:09:12,972] [INFO] Running command: blastn -query OceanDNA-a32/markers.fasta -db /var/lib/cwl/stgee96eda6-246a-4d26-b7a4-d00c03b19c63/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a32/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:09:13,359] [INFO] Task succeeded: Blastn
[2023-03-17 10:09:13,360] [INFO] Selected 5 target genomes.
[2023-03-17 10:09:13,360] [INFO] Target genome list was writen to OceanDNA-a32/target_genomes_gtdb.txt
[2023-03-17 10:09:13,364] [INFO] Task started: fastANI
[2023-03-17 10:09:13,364] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ab3ee10-8b72-4a02-b828-0986f3bc21b9/OceanDNA-a32.fa --refList OceanDNA-a32/target_genomes_gtdb.txt --output OceanDNA-a32/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:09:14,911] [INFO] Task succeeded: fastANI
[2023-03-17 10:09:14,915] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 10:09:14,915] [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
GCF_014078545.1	s__PXYB01 sp014078545	87.1558	397	461	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__PXYB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003352285.1	s__PXYB01 sp003352285	87.1096	419	461	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__PXYB01	95.0	99.99	99.99	0.99	0.99	4	-
GCA_905616385.1	s__Nitrosopumilus sp905616385	77.0322	70	461	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	97.32	96.75	0.55	0.53	3	-
GCA_013215285.1	s__Nitrosopumilus sp013215285	76.8546	123	461	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002737455.1	s__Nitrosopumilus sp002737455	76.7246	98	461	d__Archaea;p__Thermoproteota;c__Nitrososphaeria;o__Nitrososphaerales;f__Nitrosopumilaceae;g__Nitrosopumilus	95.0	98.95	98.72	0.92	0.87	8	-
--------------------------------------------------------------------------------
[2023-03-17 10:09:14,915] [INFO] GTDB search result was written to OceanDNA-a32/result_gtdb.tsv
[2023-03-17 10:09:14,916] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:09:14,916] [INFO] DFAST_QC result json was written to OceanDNA-a32/dqc_result.json
[2023-03-17 10:09:14,916] [INFO] DFAST_QC completed!
[2023-03-17 10:09:14,916] [INFO] Total running time: 0h0m36s