[2023-03-18 03:27:00,428] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:27:00,428] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:27:00,428] [INFO] DQC Reference Directory: /var/lib/cwl/stga84189e3-3494-4bc2-ba0b-a6f907d1011c/dqc_reference
[2023-03-18 03:27:01,575] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:27:01,576] [INFO] Task started: Prodigal
[2023-03-18 03:27:01,576] [INFO] Running command: cat /var/lib/cwl/stgaeefd2f8-7f17-42df-a20e-7dd5890362db/OceanDNA-b14761.fa | prodigal -d OceanDNA-b14761/cds.fna -a OceanDNA-b14761/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:27:05,497] [INFO] Task succeeded: Prodigal
[2023-03-18 03:27:05,497] [INFO] Task started: HMMsearch
[2023-03-18 03:27:05,497] [INFO] Running command: hmmsearch --tblout OceanDNA-b14761/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga84189e3-3494-4bc2-ba0b-a6f907d1011c/dqc_reference/reference_markers.hmm OceanDNA-b14761/protein.faa > /dev/null
[2023-03-18 03:27:05,665] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:27:05,665] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgaeefd2f8-7f17-42df-a20e-7dd5890362db/OceanDNA-b14761.fa]
[2023-03-18 03:27:05,674] [INFO] Query marker FASTA was written to OceanDNA-b14761/markers.fasta
[2023-03-18 03:27:05,676] [INFO] Task started: Blastn
[2023-03-18 03:27:05,676] [INFO] Running command: blastn -query OceanDNA-b14761/markers.fasta -db /var/lib/cwl/stga84189e3-3494-4bc2-ba0b-a6f907d1011c/dqc_reference/reference_markers.fasta -out OceanDNA-b14761/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:27:06,369] [INFO] Task succeeded: Blastn
[2023-03-18 03:27:06,369] [INFO] Selected 11 target genomes.
[2023-03-18 03:27:06,370] [INFO] Target genome list was writen to OceanDNA-b14761/target_genomes.txt
[2023-03-18 03:27:06,376] [INFO] Task started: fastANI
[2023-03-18 03:27:06,376] [INFO] Running command: fastANI --query /var/lib/cwl/stgaeefd2f8-7f17-42df-a20e-7dd5890362db/OceanDNA-b14761.fa --refList OceanDNA-b14761/target_genomes.txt --output OceanDNA-b14761/fastani_result.tsv --threads 1
[2023-03-18 03:27:12,120] [INFO] Task succeeded: fastANI
[2023-03-18 03:27:12,120] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga84189e3-3494-4bc2-ba0b-a6f907d1011c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:27:12,121] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga84189e3-3494-4bc2-ba0b-a6f907d1011c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:27:12,121] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:27:12,121] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 03:27:12,121] [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 03:27:12,121] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14761/tc_result.tsv
[2023-03-18 03:27:12,121] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:27:12,121] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:27:12,121] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga84189e3-3494-4bc2-ba0b-a6f907d1011c/dqc_reference/checkm_data
[2023-03-18 03:27:12,132] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:27:12,134] [INFO] Task started: CheckM
[2023-03-18 03:27:12,134] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14761/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14761/checkm_input OceanDNA-b14761/checkm_result
[2023-03-18 03:27:32,734] [INFO] Task succeeded: CheckM
[2023-03-18 03:27:32,734] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 6.25%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 03:27:32,736] [INFO] ===== Completeness check finished =====
[2023-03-18 03:27:32,736] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:27:32,736] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14761/markers.fasta)
[2023-03-18 03:27:32,738] [INFO] Task started: Blastn
[2023-03-18 03:27:32,738] [INFO] Running command: blastn -query OceanDNA-b14761/markers.fasta -db /var/lib/cwl/stga84189e3-3494-4bc2-ba0b-a6f907d1011c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14761/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:27:33,992] [INFO] Task succeeded: Blastn
[2023-03-18 03:27:33,992] [INFO] Selected 13 target genomes.
[2023-03-18 03:27:33,992] [INFO] Target genome list was writen to OceanDNA-b14761/target_genomes_gtdb.txt
[2023-03-18 03:27:34,022] [INFO] Task started: fastANI
[2023-03-18 03:27:34,022] [INFO] Running command: fastANI --query /var/lib/cwl/stgaeefd2f8-7f17-42df-a20e-7dd5890362db/OceanDNA-b14761.fa --refList OceanDNA-b14761/target_genomes_gtdb.txt --output OceanDNA-b14761/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:27:36,826] [INFO] Task succeeded: fastANI
[2023-03-18 03:27:36,829] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 03:27:36,829] [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	84.9218	118	237	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	79.1387	125	237	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	78.8248	82	237	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	77.1066	59	237	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	-
--------------------------------------------------------------------------------
[2023-03-18 03:27:36,830] [INFO] GTDB search result was written to OceanDNA-b14761/result_gtdb.tsv
[2023-03-18 03:27:36,830] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:27:36,830] [INFO] DFAST_QC result json was written to OceanDNA-b14761/dqc_result.json
[2023-03-18 03:27:36,830] [INFO] DFAST_QC completed!
[2023-03-18 03:27:36,830] [INFO] Total running time: 0h0m36s