[2023-03-17 08:56:41,465] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:56:41,467] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:56:41,467] [INFO] DQC Reference Directory: /var/lib/cwl/stg31bdb494-c1df-41c7-b58b-9323917a1235/dqc_reference
[2023-03-17 08:56:42,669] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:56:42,669] [INFO] Task started: Prodigal
[2023-03-17 08:56:42,669] [INFO] Running command: cat /var/lib/cwl/stgd6025c89-cbc6-4ca9-95e7-f7f23ece9e2b/OceanDNA-b2519.fa | prodigal -d OceanDNA-b2519/cds.fna -a OceanDNA-b2519/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:56:46,422] [INFO] Task succeeded: Prodigal
[2023-03-17 08:56:46,423] [INFO] Task started: HMMsearch
[2023-03-17 08:56:46,423] [INFO] Running command: hmmsearch --tblout OceanDNA-b2519/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31bdb494-c1df-41c7-b58b-9323917a1235/dqc_reference/reference_markers.hmm OceanDNA-b2519/protein.faa > /dev/null
[2023-03-17 08:56:46,640] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:56:46,640] [INFO] Found 6/6 markers.
[2023-03-17 08:56:46,649] [INFO] Query marker FASTA was written to OceanDNA-b2519/markers.fasta
[2023-03-17 08:56:46,650] [INFO] Task started: Blastn
[2023-03-17 08:56:46,650] [INFO] Running command: blastn -query OceanDNA-b2519/markers.fasta -db /var/lib/cwl/stg31bdb494-c1df-41c7-b58b-9323917a1235/dqc_reference/reference_markers.fasta -out OceanDNA-b2519/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:56:47,744] [INFO] Task succeeded: Blastn
[2023-03-17 08:56:47,745] [INFO] Selected 29 target genomes.
[2023-03-17 08:56:47,745] [INFO] Target genome list was writen to OceanDNA-b2519/target_genomes.txt
[2023-03-17 08:56:47,912] [INFO] Task started: fastANI
[2023-03-17 08:56:47,913] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6025c89-cbc6-4ca9-95e7-f7f23ece9e2b/OceanDNA-b2519.fa --refList OceanDNA-b2519/target_genomes.txt --output OceanDNA-b2519/fastani_result.tsv --threads 1
[2023-03-17 08:57:02,928] [INFO] Task succeeded: fastANI
[2023-03-17 08:57:02,928] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31bdb494-c1df-41c7-b58b-9323917a1235/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:57:02,928] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31bdb494-c1df-41c7-b58b-9323917a1235/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:57:02,929] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:57:02,929] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 08:57:02,929] [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 08:57:02,929] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2519/tc_result.tsv
[2023-03-17 08:57:02,929] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:57:02,929] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:57:02,929] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31bdb494-c1df-41c7-b58b-9323917a1235/dqc_reference/checkm_data
[2023-03-17 08:57:02,932] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:57:02,934] [INFO] Task started: CheckM
[2023-03-17 08:57:02,934] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2519/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2519/checkm_input OceanDNA-b2519/checkm_result
[2023-03-17 08:57:22,114] [INFO] Task succeeded: CheckM
[2023-03-17 08:57:22,115] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.50%
Contamintation: 0.93%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 08:57:22,120] [INFO] ===== Completeness check finished =====
[2023-03-17 08:57:22,120] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:57:22,121] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2519/markers.fasta)
[2023-03-17 08:57:22,122] [INFO] Task started: Blastn
[2023-03-17 08:57:22,122] [INFO] Running command: blastn -query OceanDNA-b2519/markers.fasta -db /var/lib/cwl/stg31bdb494-c1df-41c7-b58b-9323917a1235/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2519/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:57:23,462] [INFO] Task succeeded: Blastn
[2023-03-17 08:57:23,469] [INFO] Selected 28 target genomes.
[2023-03-17 08:57:23,469] [INFO] Target genome list was writen to OceanDNA-b2519/target_genomes_gtdb.txt
[2023-03-17 08:57:24,310] [INFO] Task started: fastANI
[2023-03-17 08:57:24,311] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6025c89-cbc6-4ca9-95e7-f7f23ece9e2b/OceanDNA-b2519.fa --refList OceanDNA-b2519/target_genomes_gtdb.txt --output OceanDNA-b2519/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:57:35,001] [INFO] Task succeeded: fastANI
[2023-03-17 08:57:35,005] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 08:57:35,005] [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_016780945.1	s__Aquiluna sp016780945	96.2384	121	171	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aquiluna	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003149555.1	s__Aquiluna sp003149555	81.7684	131	171	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aquiluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402685.1	s__Aquiluna sp018402685	79.0536	65	171	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aquiluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002479805.1	s__Aquiluna sp002479805	78.2063	50	171	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Aquiluna	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 08:57:35,007] [INFO] GTDB search result was written to OceanDNA-b2519/result_gtdb.tsv
[2023-03-17 08:57:35,009] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:57:35,011] [INFO] DFAST_QC result json was written to OceanDNA-b2519/dqc_result.json
[2023-03-17 08:57:35,012] [INFO] DFAST_QC completed!
[2023-03-17 08:57:35,012] [INFO] Total running time: 0h0m54s