[2023-03-16 07:49:29,130] [INFO] DFAST_QC pipeline started.
[2023-03-16 07:49:29,130] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 07:49:29,130] [INFO] DQC Reference Directory: /var/lib/cwl/stg8dd2ae35-32e7-435a-85ef-49d78bf8e7f4/dqc_reference
[2023-03-16 07:49:30,906] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 07:49:30,906] [INFO] Task started: Prodigal
[2023-03-16 07:49:30,907] [INFO] Running command: cat /var/lib/cwl/stgc08e400f-603c-48cf-af24-3aca2bee3a71/OceanDNA-b5018.fa | prodigal -d OceanDNA-b5018/cds.fna -a OceanDNA-b5018/protein.faa -g 11 -q > /dev/null
[2023-03-16 07:49:36,629] [INFO] Task succeeded: Prodigal
[2023-03-16 07:49:36,629] [INFO] Task started: HMMsearch
[2023-03-16 07:49:36,629] [INFO] Running command: hmmsearch --tblout OceanDNA-b5018/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8dd2ae35-32e7-435a-85ef-49d78bf8e7f4/dqc_reference/reference_markers.hmm OceanDNA-b5018/protein.faa > /dev/null
[2023-03-16 07:49:36,796] [INFO] Task succeeded: HMMsearch
[2023-03-16 07:49:36,797] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc08e400f-603c-48cf-af24-3aca2bee3a71/OceanDNA-b5018.fa]
[2023-03-16 07:49:36,807] [INFO] Query marker FASTA was written to OceanDNA-b5018/markers.fasta
[2023-03-16 07:49:36,807] [INFO] Task started: Blastn
[2023-03-16 07:49:36,807] [INFO] Running command: blastn -query OceanDNA-b5018/markers.fasta -db /var/lib/cwl/stg8dd2ae35-32e7-435a-85ef-49d78bf8e7f4/dqc_reference/reference_markers.fasta -out OceanDNA-b5018/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:49:37,642] [INFO] Task succeeded: Blastn
[2023-03-16 07:49:37,642] [INFO] Selected 33 target genomes.
[2023-03-16 07:49:37,643] [INFO] Target genome list was writen to OceanDNA-b5018/target_genomes.txt
[2023-03-16 07:49:37,662] [INFO] Task started: fastANI
[2023-03-16 07:49:37,662] [INFO] Running command: fastANI --query /var/lib/cwl/stgc08e400f-603c-48cf-af24-3aca2bee3a71/OceanDNA-b5018.fa --refList OceanDNA-b5018/target_genomes.txt --output OceanDNA-b5018/fastani_result.tsv --threads 1
[2023-03-16 07:49:54,646] [INFO] Task succeeded: fastANI
[2023-03-16 07:49:54,647] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8dd2ae35-32e7-435a-85ef-49d78bf8e7f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 07:49:54,647] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8dd2ae35-32e7-435a-85ef-49d78bf8e7f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 07:49:54,647] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 07:49:54,647] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 07:49:54,647] [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 07:49:54,647] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5018/tc_result.tsv
[2023-03-16 07:49:54,647] [INFO] ===== Taxonomy check completed =====
[2023-03-16 07:49:54,648] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 07:49:54,648] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8dd2ae35-32e7-435a-85ef-49d78bf8e7f4/dqc_reference/checkm_data
[2023-03-16 07:49:54,651] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 07:49:54,653] [INFO] Task started: CheckM
[2023-03-16 07:49:54,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5018/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5018/checkm_input OceanDNA-b5018/checkm_result
[2023-03-16 07:50:14,667] [INFO] Task succeeded: CheckM
[2023-03-16 07:50:14,668] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.93%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 07:50:14,669] [INFO] ===== Completeness check finished =====
[2023-03-16 07:50:14,670] [INFO] ===== Start GTDB Search =====
[2023-03-16 07:50:14,670] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5018/markers.fasta)
[2023-03-16 07:50:14,671] [INFO] Task started: Blastn
[2023-03-16 07:50:14,671] [INFO] Running command: blastn -query OceanDNA-b5018/markers.fasta -db /var/lib/cwl/stg8dd2ae35-32e7-435a-85ef-49d78bf8e7f4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5018/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:50:15,445] [INFO] Task succeeded: Blastn
[2023-03-16 07:50:15,446] [INFO] Selected 27 target genomes.
[2023-03-16 07:50:15,446] [INFO] Target genome list was writen to OceanDNA-b5018/target_genomes_gtdb.txt
[2023-03-16 07:50:15,675] [INFO] Task started: fastANI
[2023-03-16 07:50:15,675] [INFO] Running command: fastANI --query /var/lib/cwl/stgc08e400f-603c-48cf-af24-3aca2bee3a71/OceanDNA-b5018.fa --refList OceanDNA-b5018/target_genomes_gtdb.txt --output OceanDNA-b5018/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:50:23,024] [INFO] Task succeeded: fastANI
[2023-03-16 07:50:23,031] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:50:23,031] [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_002730985.1	s__BACL11 sp002730985	77.896	91	255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__BACL11	95.0	97.22	97.22	0.84	0.84	2	-
GCA_002693745.1	s__BACL11 sp002693745	77.7173	77	255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__BACL11	95.0	98.58	98.58	0.90	0.90	2	-
GCA_002705205.1	s__GCA-2705205 sp002705205	76.781	61	255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2705205	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478185.1	s__UWMA-0277 sp905478185	76.7323	69	255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	96.67	96.67	0.88	0.88	2	-
GCA_012960805.1	s__UWMA-0277 sp012960805	76.5013	52	255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479165.1	s__UWMA-0277 sp905479165	76.4452	65	255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018645865.1	s__UWMA-0277 sp018645865	76.3346	50	255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	99.24	99.14	0.74	0.70	3	-
GCA_905478765.1	s__UWMA-0277 sp905478765	76.2514	75	255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018652335.1	s__GCA-2683775 sp018652335	76.2083	59	255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2683775	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018664745.1	s__UWMA-0277 sp018664745	75.8865	55	255	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:50:23,031] [INFO] GTDB search result was written to OceanDNA-b5018/result_gtdb.tsv
[2023-03-16 07:50:23,031] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:50:23,032] [INFO] DFAST_QC result json was written to OceanDNA-b5018/dqc_result.json
[2023-03-16 07:50:23,032] [INFO] DFAST_QC completed!
[2023-03-16 07:50:23,032] [INFO] Total running time: 0h0m54s