[2023-03-17 07:01:51,201] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:01:51,201] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:01:51,201] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd2dbf0f-aa20-406e-90b5-fb3ff5a4e0a9/dqc_reference
[2023-03-17 07:01:52,291] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:01:52,291] [INFO] Task started: Prodigal
[2023-03-17 07:01:52,291] [INFO] Running command: cat /var/lib/cwl/stg8ed31ca1-6981-4e89-ad03-7d955fa29508/OceanDNA-b45239.fa | prodigal -d OceanDNA-b45239/cds.fna -a OceanDNA-b45239/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:02:20,662] [INFO] Task succeeded: Prodigal
[2023-03-17 07:02:20,663] [INFO] Task started: HMMsearch
[2023-03-17 07:02:20,663] [INFO] Running command: hmmsearch --tblout OceanDNA-b45239/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd2dbf0f-aa20-406e-90b5-fb3ff5a4e0a9/dqc_reference/reference_markers.hmm OceanDNA-b45239/protein.faa > /dev/null
[2023-03-17 07:02:20,898] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:02:20,899] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8ed31ca1-6981-4e89-ad03-7d955fa29508/OceanDNA-b45239.fa]
[2023-03-17 07:02:20,926] [INFO] Query marker FASTA was written to OceanDNA-b45239/markers.fasta
[2023-03-17 07:02:20,927] [INFO] Task started: Blastn
[2023-03-17 07:02:20,927] [INFO] Running command: blastn -query OceanDNA-b45239/markers.fasta -db /var/lib/cwl/stgcd2dbf0f-aa20-406e-90b5-fb3ff5a4e0a9/dqc_reference/reference_markers.fasta -out OceanDNA-b45239/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:02:21,476] [INFO] Task succeeded: Blastn
[2023-03-17 07:02:21,477] [INFO] Selected 13 target genomes.
[2023-03-17 07:02:21,477] [INFO] Target genome list was writen to OceanDNA-b45239/target_genomes.txt
[2023-03-17 07:02:21,484] [INFO] Task started: fastANI
[2023-03-17 07:02:21,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ed31ca1-6981-4e89-ad03-7d955fa29508/OceanDNA-b45239.fa --refList OceanDNA-b45239/target_genomes.txt --output OceanDNA-b45239/fastani_result.tsv --threads 1
[2023-03-17 07:02:30,289] [INFO] Task succeeded: fastANI
[2023-03-17 07:02:30,290] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd2dbf0f-aa20-406e-90b5-fb3ff5a4e0a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:02:30,290] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd2dbf0f-aa20-406e-90b5-fb3ff5a4e0a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:02:30,290] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:02:30,290] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 07:02:30,290] [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 07:02:30,290] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45239/tc_result.tsv
[2023-03-17 07:02:30,291] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:02:30,291] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:02:30,291] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd2dbf0f-aa20-406e-90b5-fb3ff5a4e0a9/dqc_reference/checkm_data
[2023-03-17 07:02:30,294] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:02:30,299] [INFO] Task started: CheckM
[2023-03-17 07:02:30,299] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45239/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45239/checkm_input OceanDNA-b45239/checkm_result
[2023-03-17 07:03:38,869] [INFO] Task succeeded: CheckM
[2023-03-17 07:03:38,870] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:03:38,873] [INFO] ===== Completeness check finished =====
[2023-03-17 07:03:38,873] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:03:38,873] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45239/markers.fasta)
[2023-03-17 07:03:38,873] [INFO] Task started: Blastn
[2023-03-17 07:03:38,873] [INFO] Running command: blastn -query OceanDNA-b45239/markers.fasta -db /var/lib/cwl/stgcd2dbf0f-aa20-406e-90b5-fb3ff5a4e0a9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45239/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:03:40,020] [INFO] Task succeeded: Blastn
[2023-03-17 07:03:40,020] [INFO] Selected 16 target genomes.
[2023-03-17 07:03:40,021] [INFO] Target genome list was writen to OceanDNA-b45239/target_genomes_gtdb.txt
[2023-03-17 07:03:40,485] [INFO] Task started: fastANI
[2023-03-17 07:03:40,485] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ed31ca1-6981-4e89-ad03-7d955fa29508/OceanDNA-b45239.fa --refList OceanDNA-b45239/target_genomes_gtdb.txt --output OceanDNA-b45239/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:03:52,232] [INFO] Task succeeded: fastANI
[2023-03-17 07:03:52,235] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 07:03:52,235] [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_002730875.1	s__UBA3465 sp002730875	99.9904	1562	1565	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptonemataceae;g__UBA3465	95.0	99.98	99.97	0.99	0.98	7	conclusive
GCA_002729885.1	s__UBA3465 sp002729885	78.7543	518	1565	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptonemataceae;g__UBA3465	95.0	99.96	99.92	0.99	0.98	4	-
GCA_002717505.1	s__UBA3465 sp002717505	78.2467	442	1565	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptonemataceae;g__UBA3465	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:03:52,235] [INFO] GTDB search result was written to OceanDNA-b45239/result_gtdb.tsv
[2023-03-17 07:03:52,236] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:03:52,236] [INFO] DFAST_QC result json was written to OceanDNA-b45239/dqc_result.json
[2023-03-17 07:03:52,236] [INFO] DFAST_QC completed!
[2023-03-17 07:03:52,236] [INFO] Total running time: 0h2m1s