[2023-03-16 09:58:17,584] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:58:17,584] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:58:17,584] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f8fd55e-4cd1-4f5e-a7b8-d45670fb807a/dqc_reference
[2023-03-16 09:58:18,655] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:58:18,655] [INFO] Task started: Prodigal
[2023-03-16 09:58:18,655] [INFO] Running command: cat /var/lib/cwl/stg4d59a1af-6b60-42f7-8eaf-d5ebd594ce5b/OceanDNA-b8730.fa | prodigal -d OceanDNA-b8730/cds.fna -a OceanDNA-b8730/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:58:27,281] [INFO] Task succeeded: Prodigal
[2023-03-16 09:58:27,281] [INFO] Task started: HMMsearch
[2023-03-16 09:58:27,281] [INFO] Running command: hmmsearch --tblout OceanDNA-b8730/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f8fd55e-4cd1-4f5e-a7b8-d45670fb807a/dqc_reference/reference_markers.hmm OceanDNA-b8730/protein.faa > /dev/null
[2023-03-16 09:58:27,456] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:58:27,456] [INFO] Found 6/6 markers.
[2023-03-16 09:58:27,467] [INFO] Query marker FASTA was written to OceanDNA-b8730/markers.fasta
[2023-03-16 09:58:27,468] [INFO] Task started: Blastn
[2023-03-16 09:58:27,468] [INFO] Running command: blastn -query OceanDNA-b8730/markers.fasta -db /var/lib/cwl/stg8f8fd55e-4cd1-4f5e-a7b8-d45670fb807a/dqc_reference/reference_markers.fasta -out OceanDNA-b8730/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:58:28,055] [INFO] Task succeeded: Blastn
[2023-03-16 09:58:28,056] [INFO] Selected 30 target genomes.
[2023-03-16 09:58:28,057] [INFO] Target genome list was writen to OceanDNA-b8730/target_genomes.txt
[2023-03-16 09:58:28,078] [INFO] Task started: fastANI
[2023-03-16 09:58:28,079] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d59a1af-6b60-42f7-8eaf-d5ebd594ce5b/OceanDNA-b8730.fa --refList OceanDNA-b8730/target_genomes.txt --output OceanDNA-b8730/fastani_result.tsv --threads 1
[2023-03-16 09:58:44,146] [INFO] Task succeeded: fastANI
[2023-03-16 09:58:44,147] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f8fd55e-4cd1-4f5e-a7b8-d45670fb807a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:58:44,147] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f8fd55e-4cd1-4f5e-a7b8-d45670fb807a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:58:44,147] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:58:44,147] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 09:58:44,147] [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 09:58:44,148] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8730/tc_result.tsv
[2023-03-16 09:58:44,148] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:58:44,148] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:58:44,148] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f8fd55e-4cd1-4f5e-a7b8-d45670fb807a/dqc_reference/checkm_data
[2023-03-16 09:58:44,151] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:58:44,168] [INFO] Task started: CheckM
[2023-03-16 09:58:44,168] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8730/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8730/checkm_input OceanDNA-b8730/checkm_result
[2023-03-16 09:59:10,521] [INFO] Task succeeded: CheckM
[2023-03-16 09:59:10,521] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:59:10,523] [INFO] ===== Completeness check finished =====
[2023-03-16 09:59:10,523] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:59:10,523] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8730/markers.fasta)
[2023-03-16 09:59:10,524] [INFO] Task started: Blastn
[2023-03-16 09:59:10,525] [INFO] Running command: blastn -query OceanDNA-b8730/markers.fasta -db /var/lib/cwl/stg8f8fd55e-4cd1-4f5e-a7b8-d45670fb807a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8730/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:59:11,512] [INFO] Task succeeded: Blastn
[2023-03-16 09:59:11,513] [INFO] Selected 14 target genomes.
[2023-03-16 09:59:11,513] [INFO] Target genome list was writen to OceanDNA-b8730/target_genomes_gtdb.txt
[2023-03-16 09:59:11,518] [INFO] Task started: fastANI
[2023-03-16 09:59:11,518] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d59a1af-6b60-42f7-8eaf-d5ebd594ce5b/OceanDNA-b8730.fa --refList OceanDNA-b8730/target_genomes_gtdb.txt --output OceanDNA-b8730/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:59:15,547] [INFO] Task succeeded: fastANI
[2023-03-16 09:59:15,554] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 09:59:15,555] [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_002457735.1	s__MED-G13 sp002457735	99.3824	332	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902525795.1	s__MED-G13 sp902525795	88.055	301	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902602415.1	s__MED-G13 sp902602415	87.8546	357	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	99.01	98.13	0.87	0.81	5	-
GCA_902604715.1	s__MED-G13 sp902604715	77.5005	127	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	97.66	97.66	0.81	0.81	2	-
GCA_902626365.1	s__MED-G13 sp902626365	77.3718	115	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	96.07	96.07	0.74	0.74	2	-
GCA_902517895.1	s__MED-G13 sp902517895	77.3554	109	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902626585.1	s__MED-G13 sp902626585	77.2816	118	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008081325.1	s__MED-G13 sp008081325	77.2399	79	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902518355.1	s__MED-G13 sp902518355	77.2322	144	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	96.57	96.00	0.86	0.83	4	-
GCA_902557655.1	s__MED-G13 sp902557655	77.1759	139	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	99.84	99.84	0.82	0.82	2	-
GCA_902560045.1	s__MED-G13 sp902560045	77.0476	104	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	99.04	98.52	0.67	0.66	3	-
GCA_902509675.1	s__MED-G13 sp902509675	76.5153	84	466	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:59:15,555] [INFO] GTDB search result was written to OceanDNA-b8730/result_gtdb.tsv
[2023-03-16 09:59:15,555] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:59:15,556] [INFO] DFAST_QC result json was written to OceanDNA-b8730/dqc_result.json
[2023-03-16 09:59:15,556] [INFO] DFAST_QC completed!
[2023-03-16 09:59:15,556] [INFO] Total running time: 0h0m58s