[2023-03-18 21:15:29,380] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:15:29,381] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:15:29,381] [INFO] DQC Reference Directory: /var/lib/cwl/stge368dbed-55f9-41e6-9831-9e37eacb303f/dqc_reference
[2023-03-18 21:15:31,043] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:15:31,043] [INFO] Task started: Prodigal
[2023-03-18 21:15:31,044] [INFO] Running command: cat /var/lib/cwl/stg2425a764-3afe-41ef-852f-8f8338685561/OceanDNA-b14754.fa | prodigal -d OceanDNA-b14754/cds.fna -a OceanDNA-b14754/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:15:35,131] [INFO] Task succeeded: Prodigal
[2023-03-18 21:15:35,132] [INFO] Task started: HMMsearch
[2023-03-18 21:15:35,132] [INFO] Running command: hmmsearch --tblout OceanDNA-b14754/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge368dbed-55f9-41e6-9831-9e37eacb303f/dqc_reference/reference_markers.hmm OceanDNA-b14754/protein.faa > /dev/null
[2023-03-18 21:15:35,279] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:15:35,279] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg2425a764-3afe-41ef-852f-8f8338685561/OceanDNA-b14754.fa]
[2023-03-18 21:15:35,297] [INFO] Query marker FASTA was written to OceanDNA-b14754/markers.fasta
[2023-03-18 21:15:35,299] [INFO] Task started: Blastn
[2023-03-18 21:15:35,299] [INFO] Running command: blastn -query OceanDNA-b14754/markers.fasta -db /var/lib/cwl/stge368dbed-55f9-41e6-9831-9e37eacb303f/dqc_reference/reference_markers.fasta -out OceanDNA-b14754/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:15:37,131] [INFO] Task succeeded: Blastn
[2023-03-18 21:15:37,135] [INFO] Selected 10 target genomes.
[2023-03-18 21:15:37,135] [INFO] Target genome list was writen to OceanDNA-b14754/target_genomes.txt
[2023-03-18 21:15:37,142] [INFO] Task started: fastANI
[2023-03-18 21:15:37,142] [INFO] Running command: fastANI --query /var/lib/cwl/stg2425a764-3afe-41ef-852f-8f8338685561/OceanDNA-b14754.fa --refList OceanDNA-b14754/target_genomes.txt --output OceanDNA-b14754/fastani_result.tsv --threads 1
[2023-03-18 21:15:42,500] [INFO] Task succeeded: fastANI
[2023-03-18 21:15:42,501] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge368dbed-55f9-41e6-9831-9e37eacb303f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:15:42,501] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge368dbed-55f9-41e6-9831-9e37eacb303f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:15:42,501] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:15:42,501] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:15:42,502] [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
--------------------------------------------------------------------------------
[2023-03-18 21:15:42,502] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14754/tc_result.tsv
[2023-03-18 21:15:42,502] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:15:42,502] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:15:42,502] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge368dbed-55f9-41e6-9831-9e37eacb303f/dqc_reference/checkm_data
[2023-03-18 21:15:42,505] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:15:42,508] [INFO] Task started: CheckM
[2023-03-18 21:15:42,508] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14754/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14754/checkm_input OceanDNA-b14754/checkm_result
[2023-03-18 21:15:59,223] [INFO] Task succeeded: CheckM
[2023-03-18 21:15:59,224] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:15:59,234] [INFO] ===== Completeness check finished =====
[2023-03-18 21:15:59,235] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:15:59,235] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14754/markers.fasta)
[2023-03-18 21:15:59,235] [INFO] Task started: Blastn
[2023-03-18 21:15:59,235] [INFO] Running command: blastn -query OceanDNA-b14754/markers.fasta -db /var/lib/cwl/stge368dbed-55f9-41e6-9831-9e37eacb303f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14754/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:15:59,689] [INFO] Task succeeded: Blastn
[2023-03-18 21:15:59,690] [INFO] Selected 14 target genomes.
[2023-03-18 21:15:59,690] [INFO] Target genome list was writen to OceanDNA-b14754/target_genomes_gtdb.txt
[2023-03-18 21:15:59,729] [INFO] Task started: fastANI
[2023-03-18 21:15:59,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg2425a764-3afe-41ef-852f-8f8338685561/OceanDNA-b14754.fa --refList OceanDNA-b14754/target_genomes_gtdb.txt --output OceanDNA-b14754/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:16:03,141] [INFO] Task succeeded: fastANI
[2023-03-18 21:16:03,146] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:16:03,146] [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_013911545.1	s__GCA-002700125 sp013911545	79.7627	117	260	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__GCA-002700125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902620405.1	s__GCA-002700125 sp902620405	79.4003	146	260	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__GCA-002700125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002727435.1	s__GCA-002700125 sp002727435	78.6783	87	260	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__GCA-002700125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721675.1	s__GCA-002700125 sp002721675	77.1218	56	260	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__GCA-002700125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239735.1	s__GCA-002700125 sp014239735	76.8659	73	260	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__GCA-002700125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002723375.1	s__GCA-002700125 sp002723375	76.6992	56	260	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__TMED-70;g__GCA-002700125	95.0	96.02	96.02	0.65	0.65	2	-
--------------------------------------------------------------------------------
[2023-03-18 21:16:03,146] [INFO] GTDB search result was written to OceanDNA-b14754/result_gtdb.tsv
[2023-03-18 21:16:03,146] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:16:03,147] [INFO] DFAST_QC result json was written to OceanDNA-b14754/dqc_result.json
[2023-03-18 21:16:03,148] [INFO] DFAST_QC completed!
[2023-03-18 21:16:03,148] [INFO] Total running time: 0h0m34s