[2023-03-18 01:26:26,331] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:26:26,331] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:26:26,331] [INFO] DQC Reference Directory: /var/lib/cwl/stgefaec379-5305-4c36-8323-f911f75ceceb/dqc_reference
[2023-03-18 01:26:27,459] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:26:27,459] [INFO] Task started: Prodigal
[2023-03-18 01:26:27,460] [INFO] Running command: cat /var/lib/cwl/stg69d1c1a3-f92f-4527-a244-7c33dbe71afd/OceanDNA-b26238.fa | prodigal -d OceanDNA-b26238/cds.fna -a OceanDNA-b26238/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:26:37,796] [INFO] Task succeeded: Prodigal
[2023-03-18 01:26:37,796] [INFO] Task started: HMMsearch
[2023-03-18 01:26:37,796] [INFO] Running command: hmmsearch --tblout OceanDNA-b26238/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefaec379-5305-4c36-8323-f911f75ceceb/dqc_reference/reference_markers.hmm OceanDNA-b26238/protein.faa > /dev/null
[2023-03-18 01:26:38,004] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:26:38,005] [INFO] Found 6/6 markers.
[2023-03-18 01:26:38,026] [INFO] Query marker FASTA was written to OceanDNA-b26238/markers.fasta
[2023-03-18 01:26:38,027] [INFO] Task started: Blastn
[2023-03-18 01:26:38,027] [INFO] Running command: blastn -query OceanDNA-b26238/markers.fasta -db /var/lib/cwl/stgefaec379-5305-4c36-8323-f911f75ceceb/dqc_reference/reference_markers.fasta -out OceanDNA-b26238/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:26:38,673] [INFO] Task succeeded: Blastn
[2023-03-18 01:26:38,674] [INFO] Selected 26 target genomes.
[2023-03-18 01:26:38,674] [INFO] Target genome list was writen to OceanDNA-b26238/target_genomes.txt
[2023-03-18 01:26:38,729] [INFO] Task started: fastANI
[2023-03-18 01:26:38,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg69d1c1a3-f92f-4527-a244-7c33dbe71afd/OceanDNA-b26238.fa --refList OceanDNA-b26238/target_genomes.txt --output OceanDNA-b26238/fastani_result.tsv --threads 1
[2023-03-18 01:26:56,078] [INFO] Task succeeded: fastANI
[2023-03-18 01:26:56,078] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefaec379-5305-4c36-8323-f911f75ceceb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:26:56,078] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefaec379-5305-4c36-8323-f911f75ceceb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:26:56,079] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:26:56,079] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 01:26:56,079] [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
--------------------------------------------------------------------------------
[2023-03-18 01:26:56,079] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26238/tc_result.tsv
[2023-03-18 01:26:56,079] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:26:56,079] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:26:56,079] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefaec379-5305-4c36-8323-f911f75ceceb/dqc_reference/checkm_data
[2023-03-18 01:26:56,082] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:26:56,086] [INFO] Task started: CheckM
[2023-03-18 01:26:56,086] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26238/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26238/checkm_input OceanDNA-b26238/checkm_result
[2023-03-18 01:27:25,993] [INFO] Task succeeded: CheckM
[2023-03-18 01:27:25,994] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.30%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-03-18 01:27:25,997] [INFO] ===== Completeness check finished =====
[2023-03-18 01:27:25,997] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:27:25,997] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26238/markers.fasta)
[2023-03-18 01:27:25,998] [INFO] Task started: Blastn
[2023-03-18 01:27:25,998] [INFO] Running command: blastn -query OceanDNA-b26238/markers.fasta -db /var/lib/cwl/stgefaec379-5305-4c36-8323-f911f75ceceb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26238/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:27:27,076] [INFO] Task succeeded: Blastn
[2023-03-18 01:27:27,077] [INFO] Selected 10 target genomes.
[2023-03-18 01:27:27,077] [INFO] Target genome list was writen to OceanDNA-b26238/target_genomes_gtdb.txt
[2023-03-18 01:27:27,084] [INFO] Task started: fastANI
[2023-03-18 01:27:27,084] [INFO] Running command: fastANI --query /var/lib/cwl/stg69d1c1a3-f92f-4527-a244-7c33dbe71afd/OceanDNA-b26238.fa --refList OceanDNA-b26238/target_genomes_gtdb.txt --output OceanDNA-b26238/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:27:30,386] [INFO] Task succeeded: fastANI
[2023-03-18 01:27:30,392] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:27:30,392] [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_905182545.1	s__UBA3439 sp905182545	92.7586	409	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017859295.1	s__UBA3439 sp017859295	92.4354	357	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	98.52	98.52	0.78	0.78	2	-
GCA_016778825.1	s__UBA3439 sp016778825	92.3053	236	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002378605.1	s__UBA3439 sp002378605	90.3956	369	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	99.28	99.28	0.80	0.80	2	-
GCA_009919335.1	s__UBA3439 sp009919335	80.2959	268	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	98.81	98.81	0.76	0.76	2	-
GCA_016778895.1	s__UBA3439 sp016778895	79.5318	300	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	99.63	99.63	0.87	0.87	2	-
GCA_016780525.1	s__UBA3439 sp016780525	77.5447	96	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	99.22	99.22	0.71	0.71	2	-
GCA_902583715.1	s__UBA3439 sp902583715	77.2033	55	485	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__Puniceispirillaceae;g__UBA3439	95.0	95.85	95.85	0.55	0.55	2	-
--------------------------------------------------------------------------------
[2023-03-18 01:27:30,392] [INFO] GTDB search result was written to OceanDNA-b26238/result_gtdb.tsv
[2023-03-18 01:27:30,392] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:27:30,393] [INFO] DFAST_QC result json was written to OceanDNA-b26238/dqc_result.json
[2023-03-18 01:27:30,394] [INFO] DFAST_QC completed!
[2023-03-18 01:27:30,394] [INFO] Total running time: 0h1m4s