[2023-03-16 16:04:03,877] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:04:03,877] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:04:03,877] [INFO] DQC Reference Directory: /var/lib/cwl/stgab0f3792-21de-44cb-9168-f4777b174668/dqc_reference
[2023-03-16 16:04:05,205] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:04:05,205] [INFO] Task started: Prodigal
[2023-03-16 16:04:05,205] [INFO] Running command: cat /var/lib/cwl/stgf25d49a3-d8f1-48f0-a3eb-c9dd818a2cf0/OceanDNA-b11343.fa | prodigal -d OceanDNA-b11343/cds.fna -a OceanDNA-b11343/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:04:18,923] [INFO] Task succeeded: Prodigal
[2023-03-16 16:04:18,923] [INFO] Task started: HMMsearch
[2023-03-16 16:04:18,923] [INFO] Running command: hmmsearch --tblout OceanDNA-b11343/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab0f3792-21de-44cb-9168-f4777b174668/dqc_reference/reference_markers.hmm OceanDNA-b11343/protein.faa > /dev/null
[2023-03-16 16:04:19,242] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:04:19,242] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf25d49a3-d8f1-48f0-a3eb-c9dd818a2cf0/OceanDNA-b11343.fa]
[2023-03-16 16:04:19,258] [INFO] Query marker FASTA was written to OceanDNA-b11343/markers.fasta
[2023-03-16 16:04:19,258] [INFO] Task started: Blastn
[2023-03-16 16:04:19,258] [INFO] Running command: blastn -query OceanDNA-b11343/markers.fasta -db /var/lib/cwl/stgab0f3792-21de-44cb-9168-f4777b174668/dqc_reference/reference_markers.fasta -out OceanDNA-b11343/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:04:19,776] [INFO] Task succeeded: Blastn
[2023-03-16 16:04:19,777] [INFO] Selected 27 target genomes.
[2023-03-16 16:04:19,777] [INFO] Target genome list was writen to OceanDNA-b11343/target_genomes.txt
[2023-03-16 16:04:19,794] [INFO] Task started: fastANI
[2023-03-16 16:04:19,794] [INFO] Running command: fastANI --query /var/lib/cwl/stgf25d49a3-d8f1-48f0-a3eb-c9dd818a2cf0/OceanDNA-b11343.fa --refList OceanDNA-b11343/target_genomes.txt --output OceanDNA-b11343/fastani_result.tsv --threads 1
[2023-03-16 16:04:42,661] [INFO] Task succeeded: fastANI
[2023-03-16 16:04:42,661] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab0f3792-21de-44cb-9168-f4777b174668/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:04:42,662] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab0f3792-21de-44cb-9168-f4777b174668/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:04:42,662] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:04:42,662] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 16:04:42,662] [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 16:04:42,662] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11343/tc_result.tsv
[2023-03-16 16:04:42,662] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:04:42,662] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:04:42,662] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab0f3792-21de-44cb-9168-f4777b174668/dqc_reference/checkm_data
[2023-03-16 16:04:42,666] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:04:42,669] [INFO] Task started: CheckM
[2023-03-16 16:04:42,669] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11343/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11343/checkm_input OceanDNA-b11343/checkm_result
[2023-03-16 16:05:31,881] [INFO] Task succeeded: CheckM
[2023-03-16 16:05:31,882] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 16:05:31,884] [INFO] ===== Completeness check finished =====
[2023-03-16 16:05:31,884] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:05:31,884] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11343/markers.fasta)
[2023-03-16 16:05:31,886] [INFO] Task started: Blastn
[2023-03-16 16:05:31,886] [INFO] Running command: blastn -query OceanDNA-b11343/markers.fasta -db /var/lib/cwl/stgab0f3792-21de-44cb-9168-f4777b174668/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11343/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:05:32,635] [INFO] Task succeeded: Blastn
[2023-03-16 16:05:32,636] [INFO] Selected 17 target genomes.
[2023-03-16 16:05:32,636] [INFO] Target genome list was writen to OceanDNA-b11343/target_genomes_gtdb.txt
[2023-03-16 16:05:33,313] [INFO] Task started: fastANI
[2023-03-16 16:05:33,313] [INFO] Running command: fastANI --query /var/lib/cwl/stgf25d49a3-d8f1-48f0-a3eb-c9dd818a2cf0/OceanDNA-b11343.fa --refList OceanDNA-b11343/target_genomes_gtdb.txt --output OceanDNA-b11343/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:05:40,495] [INFO] Task succeeded: fastANI
[2023-03-16 16:05:40,500] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 16:05:40,501] [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_003538555.1	s__UBA8316 sp003538555	98.035	312	596	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	98.54	98.54	0.88	0.88	2	conclusive
GCA_002716845.1	s__UBA8316 sp002716845	93.1918	386	596	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364535.1	s__UBA8316 sp002364535	78.0243	189	596	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.85	99.85	0.95	0.95	2	-
GCA_902619315.1	s__UBA8316 sp902619315	77.5148	105	596	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018647605.1	s__UBA8316 sp018647605	77.3383	171	596	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002390455.1	s__UBA8316 sp002390455	77.2274	173	596	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.09	98.50	0.88	0.83	3	-
GCA_018623955.1	s__UBA8316 sp018623955	77.0067	91	596	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009936675.1	s__UBA8316 sp009936675	76.9786	149	596	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.40	99.39	0.87	0.79	3	-
--------------------------------------------------------------------------------
[2023-03-16 16:05:40,501] [INFO] GTDB search result was written to OceanDNA-b11343/result_gtdb.tsv
[2023-03-16 16:05:40,501] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:05:40,502] [INFO] DFAST_QC result json was written to OceanDNA-b11343/dqc_result.json
[2023-03-16 16:05:40,502] [INFO] DFAST_QC completed!
[2023-03-16 16:05:40,502] [INFO] Total running time: 0h1m37s