[2023-03-16 16:47:23,820] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:47:23,822] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:47:23,822] [INFO] DQC Reference Directory: /var/lib/cwl/stg832c2315-5e2b-4809-a00c-5e7f47266f1c/dqc_reference
[2023-03-16 16:47:25,736] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:47:25,737] [INFO] Task started: Prodigal
[2023-03-16 16:47:25,737] [INFO] Running command: cat /var/lib/cwl/stg8e14d992-03c8-45d3-87ad-ee49873c35ab/OceanDNA-b5198.fa | prodigal -d OceanDNA-b5198/cds.fna -a OceanDNA-b5198/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:47:37,194] [INFO] Task succeeded: Prodigal
[2023-03-16 16:47:37,195] [INFO] Task started: HMMsearch
[2023-03-16 16:47:37,195] [INFO] Running command: hmmsearch --tblout OceanDNA-b5198/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg832c2315-5e2b-4809-a00c-5e7f47266f1c/dqc_reference/reference_markers.hmm OceanDNA-b5198/protein.faa > /dev/null
[2023-03-16 16:47:37,393] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:47:37,394] [INFO] Found 6/6 markers.
[2023-03-16 16:47:37,408] [INFO] Query marker FASTA was written to OceanDNA-b5198/markers.fasta
[2023-03-16 16:47:37,409] [INFO] Task started: Blastn
[2023-03-16 16:47:37,409] [INFO] Running command: blastn -query OceanDNA-b5198/markers.fasta -db /var/lib/cwl/stg832c2315-5e2b-4809-a00c-5e7f47266f1c/dqc_reference/reference_markers.fasta -out OceanDNA-b5198/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:47:37,946] [INFO] Task succeeded: Blastn
[2023-03-16 16:47:37,946] [INFO] Selected 36 target genomes.
[2023-03-16 16:47:37,947] [INFO] Target genome list was writen to OceanDNA-b5198/target_genomes.txt
[2023-03-16 16:47:37,970] [INFO] Task started: fastANI
[2023-03-16 16:47:37,970] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e14d992-03c8-45d3-87ad-ee49873c35ab/OceanDNA-b5198.fa --refList OceanDNA-b5198/target_genomes.txt --output OceanDNA-b5198/fastani_result.tsv --threads 1
[2023-03-16 16:48:03,850] [INFO] Task succeeded: fastANI
[2023-03-16 16:48:03,850] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg832c2315-5e2b-4809-a00c-5e7f47266f1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:48:03,851] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg832c2315-5e2b-4809-a00c-5e7f47266f1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:48:03,851] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:48:03,851] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 16:48:03,851] [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
--------------------------------------------------------------------------------
[2023-03-16 16:48:03,852] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5198/tc_result.tsv
[2023-03-16 16:48:03,852] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:48:03,852] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:48:03,852] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg832c2315-5e2b-4809-a00c-5e7f47266f1c/dqc_reference/checkm_data
[2023-03-16 16:48:03,855] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:48:03,859] [INFO] Task started: CheckM
[2023-03-16 16:48:03,859] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5198/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5198/checkm_input OceanDNA-b5198/checkm_result
[2023-03-16 16:48:35,785] [INFO] Task succeeded: CheckM
[2023-03-16 16:48:35,786] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 16:48:35,788] [INFO] ===== Completeness check finished =====
[2023-03-16 16:48:35,788] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:48:35,788] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5198/markers.fasta)
[2023-03-16 16:48:35,801] [INFO] Task started: Blastn
[2023-03-16 16:48:35,802] [INFO] Running command: blastn -query OceanDNA-b5198/markers.fasta -db /var/lib/cwl/stg832c2315-5e2b-4809-a00c-5e7f47266f1c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5198/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:48:36,670] [INFO] Task succeeded: Blastn
[2023-03-16 16:48:36,671] [INFO] Selected 30 target genomes.
[2023-03-16 16:48:36,671] [INFO] Target genome list was writen to OceanDNA-b5198/target_genomes_gtdb.txt
[2023-03-16 16:48:36,754] [INFO] Task started: fastANI
[2023-03-16 16:48:36,754] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e14d992-03c8-45d3-87ad-ee49873c35ab/OceanDNA-b5198.fa --refList OceanDNA-b5198/target_genomes_gtdb.txt --output OceanDNA-b5198/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:48:58,793] [INFO] Task succeeded: fastANI
[2023-03-16 16:48:58,796] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 16:48:58,797] [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_002715345.1	s__UBA7312 sp002715345	87.7181	240	524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA7312;g__UBA7312	95.0	98.83	98.83	0.52	0.52	2	-
GCA_902580855.1	s__UBA7312 sp902580855	87.2555	314	524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA7312;g__UBA7312	95.0	98.52	98.52	0.60	0.60	2	-
GCA_016779935.1	s__GCA-2862585 sp016779935	76.9461	59	524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA7312;g__GCA-2862585	95.0	99.89	99.89	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-16 16:48:58,797] [INFO] GTDB search result was written to OceanDNA-b5198/result_gtdb.tsv
[2023-03-16 16:48:58,797] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:48:58,798] [INFO] DFAST_QC result json was written to OceanDNA-b5198/dqc_result.json
[2023-03-16 16:48:58,798] [INFO] DFAST_QC completed!
[2023-03-16 16:48:58,798] [INFO] Total running time: 0h1m35s