[2023-03-16 05:32:42,934] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:32:42,934] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:32:42,934] [INFO] DQC Reference Directory: /var/lib/cwl/stg9bbe0c3e-7e3a-4698-8c21-9708d41685c0/dqc_reference
[2023-03-16 05:32:44,050] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:32:44,050] [INFO] Task started: Prodigal
[2023-03-16 05:32:44,050] [INFO] Running command: cat /var/lib/cwl/stg7f890930-65f2-488d-ab78-881e2d4d93c0/OceanDNA-a1816.fa | prodigal -d OceanDNA-a1816/cds.fna -a OceanDNA-a1816/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:32:55,057] [INFO] Task succeeded: Prodigal
[2023-03-16 05:32:55,057] [INFO] Task started: HMMsearch
[2023-03-16 05:32:55,057] [INFO] Running command: hmmsearch --tblout OceanDNA-a1816/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9bbe0c3e-7e3a-4698-8c21-9708d41685c0/dqc_reference/reference_markers.hmm OceanDNA-a1816/protein.faa > /dev/null
[2023-03-16 05:32:55,218] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:32:55,219] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg7f890930-65f2-488d-ab78-881e2d4d93c0/OceanDNA-a1816.fa]
[2023-03-16 05:32:55,232] [INFO] Query marker FASTA was written to OceanDNA-a1816/markers.fasta
[2023-03-16 05:32:55,232] [INFO] Task started: Blastn
[2023-03-16 05:32:55,232] [INFO] Running command: blastn -query OceanDNA-a1816/markers.fasta -db /var/lib/cwl/stg9bbe0c3e-7e3a-4698-8c21-9708d41685c0/dqc_reference/reference_markers.fasta -out OceanDNA-a1816/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:32:55,658] [INFO] Task succeeded: Blastn
[2023-03-16 05:32:55,659] [INFO] Selected 5 target genomes.
[2023-03-16 05:32:55,659] [INFO] Target genome list was writen to OceanDNA-a1816/target_genomes.txt
[2023-03-16 05:32:55,662] [INFO] Task started: fastANI
[2023-03-16 05:32:55,662] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f890930-65f2-488d-ab78-881e2d4d93c0/OceanDNA-a1816.fa --refList OceanDNA-a1816/target_genomes.txt --output OceanDNA-a1816/fastani_result.tsv --threads 1
[2023-03-16 05:32:57,871] [INFO] Task succeeded: fastANI
[2023-03-16 05:32:57,871] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9bbe0c3e-7e3a-4698-8c21-9708d41685c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:32:57,872] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9bbe0c3e-7e3a-4698-8c21-9708d41685c0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:32:57,872] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:32:57,872] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 05:32:57,872] [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
--------------------------------------------------------------------------------
[2023-03-16 05:32:57,872] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1816/tc_result.tsv
[2023-03-16 05:32:57,872] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:32:57,872] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:32:57,872] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9bbe0c3e-7e3a-4698-8c21-9708d41685c0/dqc_reference/checkm_data
[2023-03-16 05:32:57,928] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:32:57,931] [INFO] Task started: CheckM
[2023-03-16 05:32:57,931] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1816/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1816/checkm_input OceanDNA-a1816/checkm_result
[2023-03-16 05:33:31,073] [INFO] Task succeeded: CheckM
[2023-03-16 05:33:31,074] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 05:33:31,076] [INFO] ===== Completeness check finished =====
[2023-03-16 05:33:31,076] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:33:31,076] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1816/markers.fasta)
[2023-03-16 05:33:31,077] [INFO] Task started: Blastn
[2023-03-16 05:33:31,077] [INFO] Running command: blastn -query OceanDNA-a1816/markers.fasta -db /var/lib/cwl/stg9bbe0c3e-7e3a-4698-8c21-9708d41685c0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1816/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:33:31,901] [INFO] Task succeeded: Blastn
[2023-03-16 05:33:31,902] [INFO] Selected 8 target genomes.
[2023-03-16 05:33:31,902] [INFO] Target genome list was writen to OceanDNA-a1816/target_genomes_gtdb.txt
[2023-03-16 05:33:31,983] [INFO] Task started: fastANI
[2023-03-16 05:33:31,983] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f890930-65f2-488d-ab78-881e2d4d93c0/OceanDNA-a1816.fa --refList OceanDNA-a1816/target_genomes_gtdb.txt --output OceanDNA-a1816/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:33:34,599] [INFO] Task succeeded: fastANI
[2023-03-16 05:33:34,601] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 05:33:34,601] [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_018649825.1	s__PSPT01 sp018649825	99.5214	517	633	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__PSPT01	95.0	99.45	99.35	0.83	0.82	4	conclusive
GCA_004195635.1	s__PSPT01 sp004195635	93.6257	483	633	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__PSPT01	95.0	99.90	99.86	0.87	0.82	3	-
--------------------------------------------------------------------------------
[2023-03-16 05:33:34,602] [INFO] GTDB search result was written to OceanDNA-a1816/result_gtdb.tsv
[2023-03-16 05:33:34,602] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:33:34,602] [INFO] DFAST_QC result json was written to OceanDNA-a1816/dqc_result.json
[2023-03-16 05:33:34,602] [INFO] DFAST_QC completed!
[2023-03-16 05:33:34,602] [INFO] Total running time: 0h0m52s