[2023-03-15 16:25:56,992] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:25:57,003] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:25:57,003] [INFO] DQC Reference Directory: /var/lib/cwl/stg85999887-b006-424d-b474-b9ac58c7f1d4/dqc_reference
[2023-03-15 16:25:58,596] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:25:58,596] [INFO] Task started: Prodigal
[2023-03-15 16:25:58,596] [INFO] Running command: cat /var/lib/cwl/stg4d194618-6731-4a90-8117-417928b9bc38/OceanDNA-b6876.fa | prodigal -d OceanDNA-b6876/cds.fna -a OceanDNA-b6876/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:26:06,332] [INFO] Task succeeded: Prodigal
[2023-03-15 16:26:06,333] [INFO] Task started: HMMsearch
[2023-03-15 16:26:06,333] [INFO] Running command: hmmsearch --tblout OceanDNA-b6876/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85999887-b006-424d-b474-b9ac58c7f1d4/dqc_reference/reference_markers.hmm OceanDNA-b6876/protein.faa > /dev/null
[2023-03-15 16:26:06,513] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:26:06,514] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4d194618-6731-4a90-8117-417928b9bc38/OceanDNA-b6876.fa]
[2023-03-15 16:26:06,571] [INFO] Query marker FASTA was written to OceanDNA-b6876/markers.fasta
[2023-03-15 16:26:06,573] [INFO] Task started: Blastn
[2023-03-15 16:26:06,573] [INFO] Running command: blastn -query OceanDNA-b6876/markers.fasta -db /var/lib/cwl/stg85999887-b006-424d-b474-b9ac58c7f1d4/dqc_reference/reference_markers.fasta -out OceanDNA-b6876/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:26:07,175] [INFO] Task succeeded: Blastn
[2023-03-15 16:26:07,193] [INFO] Selected 26 target genomes.
[2023-03-15 16:26:07,193] [INFO] Target genome list was writen to OceanDNA-b6876/target_genomes.txt
[2023-03-15 16:26:07,208] [INFO] Task started: fastANI
[2023-03-15 16:26:07,208] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d194618-6731-4a90-8117-417928b9bc38/OceanDNA-b6876.fa --refList OceanDNA-b6876/target_genomes.txt --output OceanDNA-b6876/fastani_result.tsv --threads 1
[2023-03-15 16:26:21,643] [INFO] Task succeeded: fastANI
[2023-03-15 16:26:21,644] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85999887-b006-424d-b474-b9ac58c7f1d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:26:21,644] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85999887-b006-424d-b474-b9ac58c7f1d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:26:21,644] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:26:21,644] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 16:26:21,644] [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
--------------------------------------------------------------------------------
[2023-03-15 16:26:21,649] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6876/tc_result.tsv
[2023-03-15 16:26:21,657] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:26:21,658] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:26:21,658] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85999887-b006-424d-b474-b9ac58c7f1d4/dqc_reference/checkm_data
[2023-03-15 16:26:21,661] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:26:21,678] [INFO] Task started: CheckM
[2023-03-15 16:26:21,678] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6876/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6876/checkm_input OceanDNA-b6876/checkm_result
[2023-03-15 16:26:46,353] [INFO] Task succeeded: CheckM
[2023-03-15 16:26:46,353] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:26:46,408] [INFO] ===== Completeness check finished =====
[2023-03-15 16:26:46,408] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:26:46,408] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6876/markers.fasta)
[2023-03-15 16:26:46,408] [INFO] Task started: Blastn
[2023-03-15 16:26:46,408] [INFO] Running command: blastn -query OceanDNA-b6876/markers.fasta -db /var/lib/cwl/stg85999887-b006-424d-b474-b9ac58c7f1d4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6876/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:26:47,374] [INFO] Task succeeded: Blastn
[2023-03-15 16:26:47,386] [INFO] Selected 19 target genomes.
[2023-03-15 16:26:47,386] [INFO] Target genome list was writen to OceanDNA-b6876/target_genomes_gtdb.txt
[2023-03-15 16:26:47,406] [INFO] Task started: fastANI
[2023-03-15 16:26:47,406] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d194618-6731-4a90-8117-417928b9bc38/OceanDNA-b6876.fa --refList OceanDNA-b6876/target_genomes_gtdb.txt --output OceanDNA-b6876/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:26:54,407] [INFO] Task succeeded: fastANI
[2023-03-15 16:26:54,411] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 16:26:54,411] [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_905182735.1	s__GCA-002723295 sp905182735	81.2585	342	428	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002723295	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002690805.1	s__GCA-002723295 sp002690805	77.7788	161	428	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002723295	95.0	97.07	97.07	0.76	0.76	2	-
GCA_002713495.1	s__GCA-002723295 sp002713495	76.6368	93	428	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002723295	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721275.1	s__GCA-002723295 sp002721275	76.2781	96	428	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002723295	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002719315.1	s__GCA-2719315 sp002719315	76.2052	71	428	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2719315	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 16:26:54,414] [INFO] GTDB search result was written to OceanDNA-b6876/result_gtdb.tsv
[2023-03-15 16:26:54,417] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:26:54,422] [INFO] DFAST_QC result json was written to OceanDNA-b6876/dqc_result.json
[2023-03-15 16:26:54,422] [INFO] DFAST_QC completed!
[2023-03-15 16:26:54,423] [INFO] Total running time: 0h0m57s