[2023-03-14 13:19:07,366] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:19:07,366] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:19:07,366] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f89b63c-c6da-481a-bb14-13993232d4a7/dqc_reference
[2023-03-14 13:19:08,531] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:19:08,531] [INFO] Task started: Prodigal
[2023-03-14 13:19:08,531] [INFO] Running command: cat /var/lib/cwl/stg40e1f372-0df0-463a-9670-b9bcc5f20ea0/OceanDNA-b11689.fa | prodigal -d OceanDNA-b11689/cds.fna -a OceanDNA-b11689/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:19:22,928] [INFO] Task succeeded: Prodigal
[2023-03-14 13:19:22,928] [INFO] Task started: HMMsearch
[2023-03-14 13:19:22,928] [INFO] Running command: hmmsearch --tblout OceanDNA-b11689/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f89b63c-c6da-481a-bb14-13993232d4a7/dqc_reference/reference_markers.hmm OceanDNA-b11689/protein.faa > /dev/null
[2023-03-14 13:19:23,278] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:19:23,278] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg40e1f372-0df0-463a-9670-b9bcc5f20ea0/OceanDNA-b11689.fa]
[2023-03-14 13:19:23,292] [INFO] Query marker FASTA was written to OceanDNA-b11689/markers.fasta
[2023-03-14 13:19:23,296] [INFO] Task started: Blastn
[2023-03-14 13:19:23,296] [INFO] Running command: blastn -query OceanDNA-b11689/markers.fasta -db /var/lib/cwl/stg6f89b63c-c6da-481a-bb14-13993232d4a7/dqc_reference/reference_markers.fasta -out OceanDNA-b11689/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:19:24,679] [INFO] Task succeeded: Blastn
[2023-03-14 13:19:24,680] [INFO] Selected 15 target genomes.
[2023-03-14 13:19:24,680] [INFO] Target genome list was writen to OceanDNA-b11689/target_genomes.txt
[2023-03-14 13:19:24,686] [INFO] Task started: fastANI
[2023-03-14 13:19:24,686] [INFO] Running command: fastANI --query /var/lib/cwl/stg40e1f372-0df0-463a-9670-b9bcc5f20ea0/OceanDNA-b11689.fa --refList OceanDNA-b11689/target_genomes.txt --output OceanDNA-b11689/fastani_result.tsv --threads 1
[2023-03-14 13:19:38,391] [INFO] Task succeeded: fastANI
[2023-03-14 13:19:38,392] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f89b63c-c6da-481a-bb14-13993232d4a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:19:38,392] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f89b63c-c6da-481a-bb14-13993232d4a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:19:38,392] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:19:38,392] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 13:19:38,392] [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 13:19:38,393] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11689/tc_result.tsv
[2023-03-14 13:19:38,393] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:19:38,393] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:19:38,393] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f89b63c-c6da-481a-bb14-13993232d4a7/dqc_reference/checkm_data
[2023-03-14 13:19:38,397] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:19:38,401] [INFO] Task started: CheckM
[2023-03-14 13:19:38,401] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11689/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11689/checkm_input OceanDNA-b11689/checkm_result
[2023-03-14 13:20:11,739] [INFO] Task succeeded: CheckM
[2023-03-14 13:20:11,740] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.24%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:20:11,742] [INFO] ===== Completeness check finished =====
[2023-03-14 13:20:11,742] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:20:11,742] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11689/markers.fasta)
[2023-03-14 13:20:11,743] [INFO] Task started: Blastn
[2023-03-14 13:20:11,743] [INFO] Running command: blastn -query OceanDNA-b11689/markers.fasta -db /var/lib/cwl/stg6f89b63c-c6da-481a-bb14-13993232d4a7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11689/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:20:12,420] [INFO] Task succeeded: Blastn
[2023-03-14 13:20:12,421] [INFO] Selected 12 target genomes.
[2023-03-14 13:20:12,421] [INFO] Target genome list was writen to OceanDNA-b11689/target_genomes_gtdb.txt
[2023-03-14 13:20:12,460] [INFO] Task started: fastANI
[2023-03-14 13:20:12,460] [INFO] Running command: fastANI --query /var/lib/cwl/stg40e1f372-0df0-463a-9670-b9bcc5f20ea0/OceanDNA-b11689.fa --refList OceanDNA-b11689/target_genomes_gtdb.txt --output OceanDNA-b11689/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:20:22,156] [INFO] Task succeeded: fastANI
[2023-03-14 13:20:22,160] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 13:20:22,161] [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_002323795.1	s__UA16 sp002323795	87.0424	232	255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	99.84	99.84	0.86	0.86	2	-
GCA_905479395.1	s__UA16 sp905479395	79.3126	148	255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	98.40	98.40	0.84	0.84	2	-
GCA_016777435.1	s__UA16 sp016777435	78.5146	83	255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478895.1	s__UA16 sp905478895	78.3683	60	255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002477505.1	s__UA16 sp002477505	78.118	92	255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	99.58	99.42	0.88	0.80	7	-
--------------------------------------------------------------------------------
[2023-03-14 13:20:22,162] [INFO] GTDB search result was written to OceanDNA-b11689/result_gtdb.tsv
[2023-03-14 13:20:22,162] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:20:22,163] [INFO] DFAST_QC result json was written to OceanDNA-b11689/dqc_result.json
[2023-03-14 13:20:22,163] [INFO] DFAST_QC completed!
[2023-03-14 13:20:22,163] [INFO] Total running time: 0h1m15s