[2023-03-15 16:25:57,000] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:25:57,008] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:25:57,008] [INFO] DQC Reference Directory: /var/lib/cwl/stg2078d71a-9fa6-4fa6-80ff-653a39673df2/dqc_reference
[2023-03-15 16:25:58,597] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:25:58,598] [INFO] Task started: Prodigal
[2023-03-15 16:25:58,598] [INFO] Running command: cat /var/lib/cwl/stg3f3784fa-cb09-4b43-aa9c-badd0c0dd097/OceanDNA-b19824.fa | prodigal -d OceanDNA-b19824/cds.fna -a OceanDNA-b19824/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:26:07,017] [INFO] Task succeeded: Prodigal
[2023-03-15 16:26:07,018] [INFO] Task started: HMMsearch
[2023-03-15 16:26:07,018] [INFO] Running command: hmmsearch --tblout OceanDNA-b19824/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2078d71a-9fa6-4fa6-80ff-653a39673df2/dqc_reference/reference_markers.hmm OceanDNA-b19824/protein.faa > /dev/null
[2023-03-15 16:26:07,187] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:26:07,187] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3f3784fa-cb09-4b43-aa9c-badd0c0dd097/OceanDNA-b19824.fa]
[2023-03-15 16:26:07,231] [INFO] Query marker FASTA was written to OceanDNA-b19824/markers.fasta
[2023-03-15 16:26:07,232] [INFO] Task started: Blastn
[2023-03-15 16:26:07,232] [INFO] Running command: blastn -query OceanDNA-b19824/markers.fasta -db /var/lib/cwl/stg2078d71a-9fa6-4fa6-80ff-653a39673df2/dqc_reference/reference_markers.fasta -out OceanDNA-b19824/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:26:07,730] [INFO] Task succeeded: Blastn
[2023-03-15 16:26:07,755] [INFO] Selected 10 target genomes.
[2023-03-15 16:26:07,755] [INFO] Target genome list was writen to OceanDNA-b19824/target_genomes.txt
[2023-03-15 16:26:07,761] [INFO] Task started: fastANI
[2023-03-15 16:26:07,761] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f3784fa-cb09-4b43-aa9c-badd0c0dd097/OceanDNA-b19824.fa --refList OceanDNA-b19824/target_genomes.txt --output OceanDNA-b19824/fastani_result.tsv --threads 1
[2023-03-15 16:26:11,391] [INFO] Task succeeded: fastANI
[2023-03-15 16:26:11,392] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2078d71a-9fa6-4fa6-80ff-653a39673df2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:26:11,392] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2078d71a-9fa6-4fa6-80ff-653a39673df2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:26:11,392] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:26:11,392] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 16:26:11,392] [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 16:26:11,398] [INFO] DFAST Taxonomy check result was written to OceanDNA-b19824/tc_result.tsv
[2023-03-15 16:26:11,417] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:26:11,417] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:26:11,417] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2078d71a-9fa6-4fa6-80ff-653a39673df2/dqc_reference/checkm_data
[2023-03-15 16:26:11,420] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:26:11,426] [INFO] Task started: CheckM
[2023-03-15 16:26:11,426] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b19824/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b19824/checkm_input OceanDNA-b19824/checkm_result
[2023-03-15 16:26:36,380] [INFO] Task succeeded: CheckM
[2023-03-15 16:26:36,380] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:26:36,460] [INFO] ===== Completeness check finished =====
[2023-03-15 16:26:36,460] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:26:36,461] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b19824/markers.fasta)
[2023-03-15 16:26:36,462] [INFO] Task started: Blastn
[2023-03-15 16:26:36,462] [INFO] Running command: blastn -query OceanDNA-b19824/markers.fasta -db /var/lib/cwl/stg2078d71a-9fa6-4fa6-80ff-653a39673df2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b19824/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:26:37,120] [INFO] Task succeeded: Blastn
[2023-03-15 16:26:37,146] [INFO] Selected 19 target genomes.
[2023-03-15 16:26:37,147] [INFO] Target genome list was writen to OceanDNA-b19824/target_genomes_gtdb.txt
[2023-03-15 16:26:37,166] [INFO] Task started: fastANI
[2023-03-15 16:26:37,166] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f3784fa-cb09-4b43-aa9c-badd0c0dd097/OceanDNA-b19824.fa --refList OceanDNA-b19824/target_genomes_gtdb.txt --output OceanDNA-b19824/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:26:44,375] [INFO] Task succeeded: fastANI
[2023-03-15 16:26:44,378] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 16:26:44,378] [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_018674095.1	s__GCA-2722105 sp018674095	76.2184	63	517	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	99.41	99.30	0.88	0.82	13	-
GCA_018649625.1	s__GCA-2722105 sp018649625	75.9752	73	517	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	99.96	99.90	0.93	0.85	15	-
GCA_002718285.1	s__UBA2134 sp002718285	75.5158	51	517	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__UBA2134	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 16:26:44,381] [INFO] GTDB search result was written to OceanDNA-b19824/result_gtdb.tsv
[2023-03-15 16:26:44,384] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:26:44,387] [INFO] DFAST_QC result json was written to OceanDNA-b19824/dqc_result.json
[2023-03-15 16:26:44,387] [INFO] DFAST_QC completed!
[2023-03-15 16:26:44,387] [INFO] Total running time: 0h0m47s