[2023-03-19 00:01:03,333] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:01:03,333] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:01:03,333] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c2fbaac-ab3e-42ef-b378-4f43389be97a/dqc_reference
[2023-03-19 00:01:04,496] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:01:04,496] [INFO] Task started: Prodigal
[2023-03-19 00:01:04,497] [INFO] Running command: cat /var/lib/cwl/stg009e0c1e-1999-429f-8584-f22c3dbb8126/OceanDNA-b12852.fa | prodigal -d OceanDNA-b12852/cds.fna -a OceanDNA-b12852/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:01:14,135] [INFO] Task succeeded: Prodigal
[2023-03-19 00:01:14,135] [INFO] Task started: HMMsearch
[2023-03-19 00:01:14,135] [INFO] Running command: hmmsearch --tblout OceanDNA-b12852/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c2fbaac-ab3e-42ef-b378-4f43389be97a/dqc_reference/reference_markers.hmm OceanDNA-b12852/protein.faa > /dev/null
[2023-03-19 00:01:14,410] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:01:14,410] [INFO] Found 6/6 markers.
[2023-03-19 00:01:14,426] [INFO] Query marker FASTA was written to OceanDNA-b12852/markers.fasta
[2023-03-19 00:01:14,426] [INFO] Task started: Blastn
[2023-03-19 00:01:14,426] [INFO] Running command: blastn -query OceanDNA-b12852/markers.fasta -db /var/lib/cwl/stg1c2fbaac-ab3e-42ef-b378-4f43389be97a/dqc_reference/reference_markers.fasta -out OceanDNA-b12852/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:01:14,975] [INFO] Task succeeded: Blastn
[2023-03-19 00:01:14,976] [INFO] Selected 22 target genomes.
[2023-03-19 00:01:14,976] [INFO] Target genome list was writen to OceanDNA-b12852/target_genomes.txt
[2023-03-19 00:01:14,987] [INFO] Task started: fastANI
[2023-03-19 00:01:14,987] [INFO] Running command: fastANI --query /var/lib/cwl/stg009e0c1e-1999-429f-8584-f22c3dbb8126/OceanDNA-b12852.fa --refList OceanDNA-b12852/target_genomes.txt --output OceanDNA-b12852/fastani_result.tsv --threads 1
[2023-03-19 00:01:27,262] [INFO] Task succeeded: fastANI
[2023-03-19 00:01:27,263] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c2fbaac-ab3e-42ef-b378-4f43389be97a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:01:27,263] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c2fbaac-ab3e-42ef-b378-4f43389be97a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:01:27,263] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:01:27,263] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:01:27,263] [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
--------------------------------------------------------------------------------
[2023-03-19 00:01:27,263] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12852/tc_result.tsv
[2023-03-19 00:01:27,263] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:01:27,264] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:01:27,264] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c2fbaac-ab3e-42ef-b378-4f43389be97a/dqc_reference/checkm_data
[2023-03-19 00:01:27,266] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:01:27,270] [INFO] Task started: CheckM
[2023-03-19 00:01:27,270] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12852/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12852/checkm_input OceanDNA-b12852/checkm_result
[2023-03-19 00:01:56,093] [INFO] Task succeeded: CheckM
[2023-03-19 00:01:56,093] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.93%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 00:01:56,095] [INFO] ===== Completeness check finished =====
[2023-03-19 00:01:56,095] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:01:56,095] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12852/markers.fasta)
[2023-03-19 00:01:56,095] [INFO] Task started: Blastn
[2023-03-19 00:01:56,096] [INFO] Running command: blastn -query OceanDNA-b12852/markers.fasta -db /var/lib/cwl/stg1c2fbaac-ab3e-42ef-b378-4f43389be97a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12852/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:01:56,780] [INFO] Task succeeded: Blastn
[2023-03-19 00:01:56,781] [INFO] Selected 19 target genomes.
[2023-03-19 00:01:56,781] [INFO] Target genome list was writen to OceanDNA-b12852/target_genomes_gtdb.txt
[2023-03-19 00:01:56,851] [INFO] Task started: fastANI
[2023-03-19 00:01:56,851] [INFO] Running command: fastANI --query /var/lib/cwl/stg009e0c1e-1999-429f-8584-f22c3dbb8126/OceanDNA-b12852.fa --refList OceanDNA-b12852/target_genomes_gtdb.txt --output OceanDNA-b12852/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:02:07,026] [INFO] Task succeeded: fastANI
[2023-03-19 00:02:07,029] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:02:07,029] [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_017857855.1	s__UBA9320 sp003516975	96.8959	374	415	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	99.31	99.21	0.89	0.84	3	conclusive
GCA_002384205.1	s__UBA9320 sp002384205	91.7912	342	415	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	99.10	99.10	0.80	0.80	2	-
GCA_018402155.1	s__UBA9320 sp018402155	77.337	53	415	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002746305.1	s__UBA9320 sp002746305	76.7651	65	415	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__NS11-12g;f__UBA9320;g__UBA9320	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:02:07,030] [INFO] GTDB search result was written to OceanDNA-b12852/result_gtdb.tsv
[2023-03-19 00:02:07,030] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:02:07,030] [INFO] DFAST_QC result json was written to OceanDNA-b12852/dqc_result.json
[2023-03-19 00:02:07,030] [INFO] DFAST_QC completed!
[2023-03-19 00:02:07,030] [INFO] Total running time: 0h1m4s