[2023-03-15 15:51:29,967] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:51:29,967] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:51:29,967] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f945178-d510-4e29-9279-b0d898c9d8bb/dqc_reference
[2023-03-15 15:51:31,681] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:51:31,681] [INFO] Task started: Prodigal
[2023-03-15 15:51:31,681] [INFO] Running command: cat /var/lib/cwl/stg05287295-c8a4-46c5-99b6-a522cf6be6df/OceanDNA-a3031.fa | prodigal -d OceanDNA-a3031/cds.fna -a OceanDNA-a3031/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:51:39,071] [INFO] Task succeeded: Prodigal
[2023-03-15 15:51:39,072] [INFO] Task started: HMMsearch
[2023-03-15 15:51:39,072] [INFO] Running command: hmmsearch --tblout OceanDNA-a3031/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f945178-d510-4e29-9279-b0d898c9d8bb/dqc_reference/reference_markers.hmm OceanDNA-a3031/protein.faa > /dev/null
[2023-03-15 15:51:39,288] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:51:39,288] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg05287295-c8a4-46c5-99b6-a522cf6be6df/OceanDNA-a3031.fa]
[2023-03-15 15:51:39,298] [INFO] Query marker FASTA was written to OceanDNA-a3031/markers.fasta
[2023-03-15 15:51:39,300] [INFO] Task started: Blastn
[2023-03-15 15:51:39,300] [INFO] Running command: blastn -query OceanDNA-a3031/markers.fasta -db /var/lib/cwl/stg8f945178-d510-4e29-9279-b0d898c9d8bb/dqc_reference/reference_markers.fasta -out OceanDNA-a3031/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:51:41,561] [INFO] Task succeeded: Blastn
[2023-03-15 15:51:41,562] [INFO] Selected 2 target genomes.
[2023-03-15 15:51:41,562] [INFO] Target genome list was writen to OceanDNA-a3031/target_genomes.txt
[2023-03-15 15:51:41,564] [INFO] Task started: fastANI
[2023-03-15 15:51:41,564] [INFO] Running command: fastANI --query /var/lib/cwl/stg05287295-c8a4-46c5-99b6-a522cf6be6df/OceanDNA-a3031.fa --refList OceanDNA-a3031/target_genomes.txt --output OceanDNA-a3031/fastani_result.tsv --threads 1
[2023-03-15 15:51:42,293] [INFO] Task succeeded: fastANI
[2023-03-15 15:51:42,294] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f945178-d510-4e29-9279-b0d898c9d8bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:51:42,294] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f945178-d510-4e29-9279-b0d898c9d8bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:51:42,294] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:51:42,294] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 15:51:42,294] [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
--------------------------------------------------------------------------------
[2023-03-15 15:51:42,294] [INFO] DFAST Taxonomy check result was written to OceanDNA-a3031/tc_result.tsv
[2023-03-15 15:51:42,294] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:51:42,295] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:51:42,295] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f945178-d510-4e29-9279-b0d898c9d8bb/dqc_reference/checkm_data
[2023-03-15 15:51:42,354] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:51:42,753] [INFO] Task started: CheckM
[2023-03-15 15:51:42,753] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a3031/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a3031/checkm_input OceanDNA-a3031/checkm_result
[2023-03-15 15:52:13,394] [INFO] Task succeeded: CheckM
[2023-03-15 15:52:13,395] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.05%
Contamintation: 5.09%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-15 15:52:13,397] [INFO] ===== Completeness check finished =====
[2023-03-15 15:52:13,397] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:52:13,397] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a3031/markers.fasta)
[2023-03-15 15:52:13,399] [INFO] Task started: Blastn
[2023-03-15 15:52:13,399] [INFO] Running command: blastn -query OceanDNA-a3031/markers.fasta -db /var/lib/cwl/stg8f945178-d510-4e29-9279-b0d898c9d8bb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a3031/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:52:14,169] [INFO] Task succeeded: Blastn
[2023-03-15 15:52:14,170] [INFO] Selected 11 target genomes.
[2023-03-15 15:52:14,170] [INFO] Target genome list was writen to OceanDNA-a3031/target_genomes_gtdb.txt
[2023-03-15 15:52:14,190] [INFO] Task started: fastANI
[2023-03-15 15:52:14,190] [INFO] Running command: fastANI --query /var/lib/cwl/stg05287295-c8a4-46c5-99b6-a522cf6be6df/OceanDNA-a3031.fa --refList OceanDNA-a3031/target_genomes_gtdb.txt --output OceanDNA-a3031/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:52:17,477] [INFO] Task succeeded: fastANI
[2023-03-15 15:52:17,480] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 15:52:17,480] [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_002726495.1	s__Poseidonia sp002726495	80.5226	245	400	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	97.10	97.06	0.83	0.82	3	-
GCA_002505405.1	s__Poseidonia alphae	78.904	197	400	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.19	99.15	0.93	0.90	5	-
--------------------------------------------------------------------------------
[2023-03-15 15:52:17,480] [INFO] GTDB search result was written to OceanDNA-a3031/result_gtdb.tsv
[2023-03-15 15:52:17,480] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:52:17,481] [INFO] DFAST_QC result json was written to OceanDNA-a3031/dqc_result.json
[2023-03-15 15:52:17,481] [INFO] DFAST_QC completed!
[2023-03-15 15:52:17,481] [INFO] Total running time: 0h0m48s