[2023-03-14 11:40:05,548] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:40:05,550] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:40:05,550] [INFO] DQC Reference Directory: /var/lib/cwl/stg17b09d80-22f1-4763-84d8-76aa0fad6ddc/dqc_reference
[2023-03-14 11:40:06,637] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:40:06,638] [INFO] Task started: Prodigal
[2023-03-14 11:40:06,638] [INFO] Running command: cat /var/lib/cwl/stgdb7dca46-f220-4a9b-967e-29ac6b9fa03a/OceanDNA-b20633.fa | prodigal -d OceanDNA-b20633/cds.fna -a OceanDNA-b20633/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:40:15,917] [INFO] Task succeeded: Prodigal
[2023-03-14 11:40:15,917] [INFO] Task started: HMMsearch
[2023-03-14 11:40:15,918] [INFO] Running command: hmmsearch --tblout OceanDNA-b20633/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg17b09d80-22f1-4763-84d8-76aa0fad6ddc/dqc_reference/reference_markers.hmm OceanDNA-b20633/protein.faa > /dev/null
[2023-03-14 11:40:16,069] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:40:16,069] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdb7dca46-f220-4a9b-967e-29ac6b9fa03a/OceanDNA-b20633.fa]
[2023-03-14 11:40:16,084] [INFO] Query marker FASTA was written to OceanDNA-b20633/markers.fasta
[2023-03-14 11:40:16,084] [INFO] Task started: Blastn
[2023-03-14 11:40:16,084] [INFO] Running command: blastn -query OceanDNA-b20633/markers.fasta -db /var/lib/cwl/stg17b09d80-22f1-4763-84d8-76aa0fad6ddc/dqc_reference/reference_markers.fasta -out OceanDNA-b20633/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:40:16,596] [INFO] Task succeeded: Blastn
[2023-03-14 11:40:16,601] [INFO] Selected 17 target genomes.
[2023-03-14 11:40:16,601] [INFO] Target genome list was writen to OceanDNA-b20633/target_genomes.txt
[2023-03-14 11:40:16,609] [INFO] Task started: fastANI
[2023-03-14 11:40:16,610] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb7dca46-f220-4a9b-967e-29ac6b9fa03a/OceanDNA-b20633.fa --refList OceanDNA-b20633/target_genomes.txt --output OceanDNA-b20633/fastani_result.tsv --threads 1
[2023-03-14 11:40:23,716] [INFO] Task succeeded: fastANI
[2023-03-14 11:40:23,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg17b09d80-22f1-4763-84d8-76aa0fad6ddc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:40:23,716] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg17b09d80-22f1-4763-84d8-76aa0fad6ddc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:40:23,717] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:40:23,717] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:40:23,717] [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
--------------------------------------------------------------------------------
[2023-03-14 11:40:23,718] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20633/tc_result.tsv
[2023-03-14 11:40:23,718] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:40:23,718] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:40:23,719] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg17b09d80-22f1-4763-84d8-76aa0fad6ddc/dqc_reference/checkm_data
[2023-03-14 11:40:23,721] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:40:23,726] [INFO] Task started: CheckM
[2023-03-14 11:40:23,726] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20633/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20633/checkm_input OceanDNA-b20633/checkm_result
[2023-03-14 11:40:50,961] [INFO] Task succeeded: CheckM
[2023-03-14 11:40:50,961] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:40:50,975] [INFO] ===== Completeness check finished =====
[2023-03-14 11:40:50,975] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:40:50,975] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20633/markers.fasta)
[2023-03-14 11:40:50,976] [INFO] Task started: Blastn
[2023-03-14 11:40:50,976] [INFO] Running command: blastn -query OceanDNA-b20633/markers.fasta -db /var/lib/cwl/stg17b09d80-22f1-4763-84d8-76aa0fad6ddc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20633/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:40:51,693] [INFO] Task succeeded: Blastn
[2023-03-14 11:40:51,698] [INFO] Selected 15 target genomes.
[2023-03-14 11:40:51,698] [INFO] Target genome list was writen to OceanDNA-b20633/target_genomes_gtdb.txt
[2023-03-14 11:40:51,708] [INFO] Task started: fastANI
[2023-03-14 11:40:51,708] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb7dca46-f220-4a9b-967e-29ac6b9fa03a/OceanDNA-b20633.fa --refList OceanDNA-b20633/target_genomes_gtdb.txt --output OceanDNA-b20633/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:40:57,055] [INFO] Task succeeded: fastANI
[2023-03-14 11:40:57,057] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:40:57,057] [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_002689995.1	s__GCA-2689995 sp002689995	99.9137	596	622	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-2689995;g__GCA-2689995	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014381925.1	s__GCA-2689995 sp014381925	76.9865	193	622	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__SCGC-AAA003-L08;f__GCA-2689995;g__GCA-2689995	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:40:57,059] [INFO] GTDB search result was written to OceanDNA-b20633/result_gtdb.tsv
[2023-03-14 11:40:57,063] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:40:57,065] [INFO] DFAST_QC result json was written to OceanDNA-b20633/dqc_result.json
[2023-03-14 11:40:57,065] [INFO] DFAST_QC completed!
[2023-03-14 11:40:57,065] [INFO] Total running time: 0h0m52s