[2023-03-17 10:48:45,616] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:48:45,616] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:48:45,616] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d9d46b6-fcd1-46bc-bea7-90ab35b40f52/dqc_reference
[2023-03-17 10:48:46,737] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:48:46,738] [INFO] Task started: Prodigal
[2023-03-17 10:48:46,738] [INFO] Running command: cat /var/lib/cwl/stgfbf0c5b6-c1de-4ba9-810e-524515ad9f98/OceanDNA-b13943.fa | prodigal -d OceanDNA-b13943/cds.fna -a OceanDNA-b13943/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:48:51,521] [INFO] Task succeeded: Prodigal
[2023-03-17 10:48:51,522] [INFO] Task started: HMMsearch
[2023-03-17 10:48:51,522] [INFO] Running command: hmmsearch --tblout OceanDNA-b13943/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d9d46b6-fcd1-46bc-bea7-90ab35b40f52/dqc_reference/reference_markers.hmm OceanDNA-b13943/protein.faa > /dev/null
[2023-03-17 10:48:51,750] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:48:51,750] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfbf0c5b6-c1de-4ba9-810e-524515ad9f98/OceanDNA-b13943.fa]
[2023-03-17 10:48:51,760] [INFO] Query marker FASTA was written to OceanDNA-b13943/markers.fasta
[2023-03-17 10:48:51,760] [INFO] Task started: Blastn
[2023-03-17 10:48:51,760] [INFO] Running command: blastn -query OceanDNA-b13943/markers.fasta -db /var/lib/cwl/stg7d9d46b6-fcd1-46bc-bea7-90ab35b40f52/dqc_reference/reference_markers.fasta -out OceanDNA-b13943/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:48:52,258] [INFO] Task succeeded: Blastn
[2023-03-17 10:48:52,259] [INFO] Selected 10 target genomes.
[2023-03-17 10:48:52,259] [INFO] Target genome list was writen to OceanDNA-b13943/target_genomes.txt
[2023-03-17 10:48:52,266] [INFO] Task started: fastANI
[2023-03-17 10:48:52,266] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbf0c5b6-c1de-4ba9-810e-524515ad9f98/OceanDNA-b13943.fa --refList OceanDNA-b13943/target_genomes.txt --output OceanDNA-b13943/fastani_result.tsv --threads 1
[2023-03-17 10:48:56,758] [INFO] Task succeeded: fastANI
[2023-03-17 10:48:56,759] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d9d46b6-fcd1-46bc-bea7-90ab35b40f52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:48:56,759] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d9d46b6-fcd1-46bc-bea7-90ab35b40f52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:48:56,759] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:48:56,759] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 10:48:56,759] [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 10:48:56,760] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13943/tc_result.tsv
[2023-03-17 10:48:56,760] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:48:56,760] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:48:56,760] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d9d46b6-fcd1-46bc-bea7-90ab35b40f52/dqc_reference/checkm_data
[2023-03-17 10:48:56,763] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:48:56,768] [INFO] Task started: CheckM
[2023-03-17 10:48:56,768] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13943/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13943/checkm_input OceanDNA-b13943/checkm_result
[2023-03-17 10:49:15,181] [INFO] Task succeeded: CheckM
[2023-03-17 10:49:15,181] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:49:15,182] [INFO] ===== Completeness check finished =====
[2023-03-17 10:49:15,183] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:49:15,183] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13943/markers.fasta)
[2023-03-17 10:49:15,183] [INFO] Task started: Blastn
[2023-03-17 10:49:15,183] [INFO] Running command: blastn -query OceanDNA-b13943/markers.fasta -db /var/lib/cwl/stg7d9d46b6-fcd1-46bc-bea7-90ab35b40f52/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13943/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:49:15,835] [INFO] Task succeeded: Blastn
[2023-03-17 10:49:15,836] [INFO] Selected 11 target genomes.
[2023-03-17 10:49:15,836] [INFO] Target genome list was writen to OceanDNA-b13943/target_genomes_gtdb.txt
[2023-03-17 10:49:16,104] [INFO] Task started: fastANI
[2023-03-17 10:49:16,104] [INFO] Running command: fastANI --query /var/lib/cwl/stgfbf0c5b6-c1de-4ba9-810e-524515ad9f98/OceanDNA-b13943.fa --refList OceanDNA-b13943/target_genomes_gtdb.txt --output OceanDNA-b13943/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:49:19,737] [INFO] Task succeeded: fastANI
[2023-03-17 10:49:19,740] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 10:49:19,740] [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_002699485.1	s__UBA2962 sp002699485	83.751	257	300	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA2962;g__UBA2962	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003228095.2	s__UBA2962 sp003228095	83.3089	234	300	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA2962;g__UBA2962	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002311285.1	s__UBA2962 sp002311285	79.5546	121	300	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA2962;g__UBA2962	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009392275.1	s__UBA2962 sp002728115	79.5527	217	300	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA2962;g__UBA2962	95.0	99.96	99.93	0.87	0.87	3	-
--------------------------------------------------------------------------------
[2023-03-17 10:49:19,741] [INFO] GTDB search result was written to OceanDNA-b13943/result_gtdb.tsv
[2023-03-17 10:49:19,741] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:49:19,742] [INFO] DFAST_QC result json was written to OceanDNA-b13943/dqc_result.json
[2023-03-17 10:49:19,742] [INFO] DFAST_QC completed!
[2023-03-17 10:49:19,742] [INFO] Total running time: 0h0m34s