[2023-03-18 21:08:06,175] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:08:06,176] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:08:06,176] [INFO] DQC Reference Directory: /var/lib/cwl/stge38f389c-21ed-4e9f-af74-e5e6d09a2a9a/dqc_reference
[2023-03-18 21:08:07,299] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:08:07,299] [INFO] Task started: Prodigal
[2023-03-18 21:08:07,299] [INFO] Running command: cat /var/lib/cwl/stgbeca3b0a-d156-4eef-a028-099aacbf32f3/OceanDNA-b42121.fa | prodigal -d OceanDNA-b42121/cds.fna -a OceanDNA-b42121/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:08:11,624] [INFO] Task succeeded: Prodigal
[2023-03-18 21:08:11,624] [INFO] Task started: HMMsearch
[2023-03-18 21:08:11,624] [INFO] Running command: hmmsearch --tblout OceanDNA-b42121/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge38f389c-21ed-4e9f-af74-e5e6d09a2a9a/dqc_reference/reference_markers.hmm OceanDNA-b42121/protein.faa > /dev/null
[2023-03-18 21:08:11,774] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:08:11,774] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgbeca3b0a-d156-4eef-a028-099aacbf32f3/OceanDNA-b42121.fa]
[2023-03-18 21:08:11,782] [INFO] Query marker FASTA was written to OceanDNA-b42121/markers.fasta
[2023-03-18 21:08:11,784] [INFO] Task started: Blastn
[2023-03-18 21:08:11,784] [INFO] Running command: blastn -query OceanDNA-b42121/markers.fasta -db /var/lib/cwl/stge38f389c-21ed-4e9f-af74-e5e6d09a2a9a/dqc_reference/reference_markers.fasta -out OceanDNA-b42121/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:08:12,343] [INFO] Task succeeded: Blastn
[2023-03-18 21:08:12,343] [INFO] Selected 19 target genomes.
[2023-03-18 21:08:12,344] [INFO] Target genome list was writen to OceanDNA-b42121/target_genomes.txt
[2023-03-18 21:08:12,353] [INFO] Task started: fastANI
[2023-03-18 21:08:12,353] [INFO] Running command: fastANI --query /var/lib/cwl/stgbeca3b0a-d156-4eef-a028-099aacbf32f3/OceanDNA-b42121.fa --refList OceanDNA-b42121/target_genomes.txt --output OceanDNA-b42121/fastani_result.tsv --threads 1
[2023-03-18 21:08:21,548] [INFO] Task succeeded: fastANI
[2023-03-18 21:08:21,549] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge38f389c-21ed-4e9f-af74-e5e6d09a2a9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:08:21,549] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge38f389c-21ed-4e9f-af74-e5e6d09a2a9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:08:21,549] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:08:21,549] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:08:21,549] [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
--------------------------------------------------------------------------------
[2023-03-18 21:08:21,549] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42121/tc_result.tsv
[2023-03-18 21:08:21,550] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:08:21,550] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:08:21,550] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge38f389c-21ed-4e9f-af74-e5e6d09a2a9a/dqc_reference/checkm_data
[2023-03-18 21:08:21,552] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:08:21,752] [INFO] Task started: CheckM
[2023-03-18 21:08:21,752] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42121/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42121/checkm_input OceanDNA-b42121/checkm_result
[2023-03-18 21:08:38,554] [INFO] Task succeeded: CheckM
[2023-03-18 21:08:38,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.59%
Contamintation: 1.80%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 21:08:38,556] [INFO] ===== Completeness check finished =====
[2023-03-18 21:08:38,556] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:08:38,556] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42121/markers.fasta)
[2023-03-18 21:08:38,558] [INFO] Task started: Blastn
[2023-03-18 21:08:38,558] [INFO] Running command: blastn -query OceanDNA-b42121/markers.fasta -db /var/lib/cwl/stge38f389c-21ed-4e9f-af74-e5e6d09a2a9a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42121/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:08:39,506] [INFO] Task succeeded: Blastn
[2023-03-18 21:08:39,506] [INFO] Selected 14 target genomes.
[2023-03-18 21:08:39,507] [INFO] Target genome list was writen to OceanDNA-b42121/target_genomes_gtdb.txt
[2023-03-18 21:08:39,522] [INFO] Task started: fastANI
[2023-03-18 21:08:39,523] [INFO] Running command: fastANI --query /var/lib/cwl/stgbeca3b0a-d156-4eef-a028-099aacbf32f3/OceanDNA-b42121.fa --refList OceanDNA-b42121/target_genomes_gtdb.txt --output OceanDNA-b42121/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:08:42,551] [INFO] Task succeeded: fastANI
[2023-03-18 21:08:42,558] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:08:42,558] [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_902602595.1	s__D2472 sp902602595	94.2115	225	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902593675.1	s__D2472 sp902593675	85.6576	223	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902596165.1	s__D2472 sp902596165	85.5451	206	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902511575.1	s__D2472 sp902511575	85.1492	202	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902509555.1	s__D2472 sp902509555	85.0287	149	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003283765.1	s__D2472 sp003283765	84.831	174	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902513515.1	s__D2472 sp902513515	83.6388	154	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902512655.1	s__D2472 sp902512655	83.4937	134	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595065.1	s__D2472 sp902595065	83.1124	203	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.09	97.88	0.94	0.91	4	-
GCA_902511425.1	s__D2472 sp902511425	82.0396	146	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779505.1	s__D2472 sp016779505	81.9242	131	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.99	98.50	0.76	0.70	3	-
GCA_000307935.1	s__D2472 sp000307935	80.4931	142	259	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:08:42,558] [INFO] GTDB search result was written to OceanDNA-b42121/result_gtdb.tsv
[2023-03-18 21:08:42,559] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:08:42,560] [INFO] DFAST_QC result json was written to OceanDNA-b42121/dqc_result.json
[2023-03-18 21:08:42,560] [INFO] DFAST_QC completed!
[2023-03-18 21:08:42,560] [INFO] Total running time: 0h0m36s