[2023-03-17 07:01:49,036] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:01:49,036] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:01:49,036] [INFO] DQC Reference Directory: /var/lib/cwl/stg18895fc4-9fe8-42e3-af42-e3aefc8a7625/dqc_reference
[2023-03-17 07:01:50,171] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:01:50,171] [INFO] Task started: Prodigal
[2023-03-17 07:01:50,171] [INFO] Running command: cat /var/lib/cwl/stg7009b42b-f00d-42c6-898f-7d6b73aea7f1/OceanDNA-b44542.fa | prodigal -d OceanDNA-b44542/cds.fna -a OceanDNA-b44542/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:01:55,845] [INFO] Task succeeded: Prodigal
[2023-03-17 07:01:55,845] [INFO] Task started: HMMsearch
[2023-03-17 07:01:55,845] [INFO] Running command: hmmsearch --tblout OceanDNA-b44542/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg18895fc4-9fe8-42e3-af42-e3aefc8a7625/dqc_reference/reference_markers.hmm OceanDNA-b44542/protein.faa > /dev/null
[2023-03-17 07:01:55,996] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:01:55,997] [INFO] Found 6/6 markers.
[2023-03-17 07:01:56,007] [INFO] Query marker FASTA was written to OceanDNA-b44542/markers.fasta
[2023-03-17 07:01:56,007] [INFO] Task started: Blastn
[2023-03-17 07:01:56,007] [INFO] Running command: blastn -query OceanDNA-b44542/markers.fasta -db /var/lib/cwl/stg18895fc4-9fe8-42e3-af42-e3aefc8a7625/dqc_reference/reference_markers.fasta -out OceanDNA-b44542/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:01:56,558] [INFO] Task succeeded: Blastn
[2023-03-17 07:01:56,558] [INFO] Selected 22 target genomes.
[2023-03-17 07:01:56,559] [INFO] Target genome list was writen to OceanDNA-b44542/target_genomes.txt
[2023-03-17 07:01:56,568] [INFO] Task started: fastANI
[2023-03-17 07:01:56,568] [INFO] Running command: fastANI --query /var/lib/cwl/stg7009b42b-f00d-42c6-898f-7d6b73aea7f1/OceanDNA-b44542.fa --refList OceanDNA-b44542/target_genomes.txt --output OceanDNA-b44542/fastani_result.tsv --threads 1
[2023-03-17 07:02:07,784] [INFO] Task succeeded: fastANI
[2023-03-17 07:02:07,784] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg18895fc4-9fe8-42e3-af42-e3aefc8a7625/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:02:07,784] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg18895fc4-9fe8-42e3-af42-e3aefc8a7625/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:02:07,784] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:02:07,784] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 07:02:07,784] [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 07:02:07,785] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44542/tc_result.tsv
[2023-03-17 07:02:07,785] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:02:07,785] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:02:07,785] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg18895fc4-9fe8-42e3-af42-e3aefc8a7625/dqc_reference/checkm_data
[2023-03-17 07:02:07,787] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:02:07,792] [INFO] Task started: CheckM
[2023-03-17 07:02:07,792] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44542/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44542/checkm_input OceanDNA-b44542/checkm_result
[2023-03-17 07:02:27,991] [INFO] Task succeeded: CheckM
[2023-03-17 07:02:27,991] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 4.17%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-17 07:02:27,993] [INFO] ===== Completeness check finished =====
[2023-03-17 07:02:27,993] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:02:27,993] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44542/markers.fasta)
[2023-03-17 07:02:27,994] [INFO] Task started: Blastn
[2023-03-17 07:02:27,994] [INFO] Running command: blastn -query OceanDNA-b44542/markers.fasta -db /var/lib/cwl/stg18895fc4-9fe8-42e3-af42-e3aefc8a7625/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44542/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:02:28,913] [INFO] Task succeeded: Blastn
[2023-03-17 07:02:28,914] [INFO] Selected 21 target genomes.
[2023-03-17 07:02:28,914] [INFO] Target genome list was writen to OceanDNA-b44542/target_genomes_gtdb.txt
[2023-03-17 07:02:29,311] [INFO] Task started: fastANI
[2023-03-17 07:02:29,311] [INFO] Running command: fastANI --query /var/lib/cwl/stg7009b42b-f00d-42c6-898f-7d6b73aea7f1/OceanDNA-b44542.fa --refList OceanDNA-b44542/target_genomes_gtdb.txt --output OceanDNA-b44542/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:02:35,127] [INFO] Task succeeded: fastANI
[2023-03-17 07:02:35,130] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 07:02:35,130] [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_002728725.1	s__SP4260 sp002728725	95.0135	238	333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__SP4260	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902517795.1	s__SP4260 sp902517795	92.9123	212	333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__SP4260	95.0	99.80	99.80	0.68	0.68	2	-
GCA_002715745.1	s__SP4260 sp002715745	89.9315	245	333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__SP4260	95.0	97.07	97.07	0.87	0.87	2	-
GCA_003331585.1	s__SP4260 sp003331585	78.4	62	333	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__SP4260	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:02:35,131] [INFO] GTDB search result was written to OceanDNA-b44542/result_gtdb.tsv
[2023-03-17 07:02:35,131] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:02:35,131] [INFO] DFAST_QC result json was written to OceanDNA-b44542/dqc_result.json
[2023-03-17 07:02:35,131] [INFO] DFAST_QC completed!
[2023-03-17 07:02:35,131] [INFO] Total running time: 0h0m46s