[2023-03-17 08:47:57,443] [INFO] DFAST_QC pipeline started.
[2023-03-17 08:47:57,443] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 08:47:57,443] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe4689d0-3f31-46c9-a5b8-8136f2c91a9c/dqc_reference
[2023-03-17 08:48:01,514] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 08:48:01,515] [INFO] Task started: Prodigal
[2023-03-17 08:48:01,515] [INFO] Running command: cat /var/lib/cwl/stg529abcb2-21b1-4576-8f7d-78d89e780f2d/OceanDNA-b12873.fa | prodigal -d OceanDNA-b12873/cds.fna -a OceanDNA-b12873/protein.faa -g 11 -q > /dev/null
[2023-03-17 08:48:25,291] [INFO] Task succeeded: Prodigal
[2023-03-17 08:48:25,292] [INFO] Task started: HMMsearch
[2023-03-17 08:48:25,292] [INFO] Running command: hmmsearch --tblout OceanDNA-b12873/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe4689d0-3f31-46c9-a5b8-8136f2c91a9c/dqc_reference/reference_markers.hmm OceanDNA-b12873/protein.faa > /dev/null
[2023-03-17 08:48:25,553] [INFO] Task succeeded: HMMsearch
[2023-03-17 08:48:25,554] [INFO] Found 6/6 markers.
[2023-03-17 08:48:25,575] [INFO] Query marker FASTA was written to OceanDNA-b12873/markers.fasta
[2023-03-17 08:48:25,576] [INFO] Task started: Blastn
[2023-03-17 08:48:25,576] [INFO] Running command: blastn -query OceanDNA-b12873/markers.fasta -db /var/lib/cwl/stgbe4689d0-3f31-46c9-a5b8-8136f2c91a9c/dqc_reference/reference_markers.fasta -out OceanDNA-b12873/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:48:28,237] [INFO] Task succeeded: Blastn
[2023-03-17 08:48:28,237] [INFO] Selected 23 target genomes.
[2023-03-17 08:48:28,238] [INFO] Target genome list was writen to OceanDNA-b12873/target_genomes.txt
[2023-03-17 08:48:28,437] [INFO] Task started: fastANI
[2023-03-17 08:48:28,437] [INFO] Running command: fastANI --query /var/lib/cwl/stg529abcb2-21b1-4576-8f7d-78d89e780f2d/OceanDNA-b12873.fa --refList OceanDNA-b12873/target_genomes.txt --output OceanDNA-b12873/fastani_result.tsv --threads 1
[2023-03-17 08:48:45,042] [INFO] Task succeeded: fastANI
[2023-03-17 08:48:45,043] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe4689d0-3f31-46c9-a5b8-8136f2c91a9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 08:48:45,043] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe4689d0-3f31-46c9-a5b8-8136f2c91a9c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 08:48:45,113] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 08:48:45,113] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 08:48:45,113] [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
Daejeonella rubra	strain=DSM 24536	GCA_900103545.1	990371	990371	type	True	78.4243	301	1168	95	below_threshold
Daejeonella oryzae	strain=DSM 19973	GCA_000422945.1	1122943	1122943	type	True	77.8981	83	1168	95	below_threshold
Flavihumibacter soli	strain=R14	GCA_010692725.1	2705549	2705549	type	True	77.7933	57	1168	95	below_threshold
Daejeonella lutea	strain=DSM 22385	GCA_900168015.1	572036	572036	type	True	77.7095	136	1168	95	below_threshold
Pedobacter mongoliensis	strain=KCTC 52859	GCA_024436395.1	2100740	2100740	type	True	77.0728	52	1168	95	below_threshold
Pedobacter chinensis	strain=JDX94	GCA_003339865.1	2282421	2282421	type	True	76.4778	55	1168	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 08:48:45,113] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12873/tc_result.tsv
[2023-03-17 08:48:45,113] [INFO] ===== Taxonomy check completed =====
[2023-03-17 08:48:45,113] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 08:48:45,113] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe4689d0-3f31-46c9-a5b8-8136f2c91a9c/dqc_reference/checkm_data
[2023-03-17 08:48:45,114] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 08:48:45,433] [INFO] Task started: CheckM
[2023-03-17 08:48:45,433] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12873/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12873/checkm_input OceanDNA-b12873/checkm_result
[2023-03-17 08:49:51,158] [INFO] Task succeeded: CheckM
[2023-03-17 08:49:51,158] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 08:49:51,162] [INFO] ===== Completeness check finished =====
[2023-03-17 08:49:51,162] [INFO] ===== Start GTDB Search =====
[2023-03-17 08:49:51,162] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12873/markers.fasta)
[2023-03-17 08:49:51,164] [INFO] Task started: Blastn
[2023-03-17 08:49:51,164] [INFO] Running command: blastn -query OceanDNA-b12873/markers.fasta -db /var/lib/cwl/stgbe4689d0-3f31-46c9-a5b8-8136f2c91a9c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12873/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 08:49:52,357] [INFO] Task succeeded: Blastn
[2023-03-17 08:49:52,358] [INFO] Selected 23 target genomes.
[2023-03-17 08:49:52,358] [INFO] Target genome list was writen to OceanDNA-b12873/target_genomes_gtdb.txt
[2023-03-17 08:49:53,611] [INFO] Task started: fastANI
[2023-03-17 08:49:53,611] [INFO] Running command: fastANI --query /var/lib/cwl/stg529abcb2-21b1-4576-8f7d-78d89e780f2d/OceanDNA-b12873.fa --refList OceanDNA-b12873/target_genomes_gtdb.txt --output OceanDNA-b12873/fastani_result_gtdb.tsv --threads 1
[2023-03-17 08:50:09,307] [INFO] Task succeeded: fastANI
[2023-03-17 08:50:09,314] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 08:50:09,314] [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_002257025.1	s__Daejeonella sp002257025	79.5241	414	1168	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900103545.1	s__Daejeonella rubra	78.4364	300	1168	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017495225.1	s__Daejeonella sp017495225	77.9233	188	1168	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422945.1	s__Daejeonella oryzae	77.8981	83	1168	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168015.1	s__Daejeonella lutea	77.7095	136	1168	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903821625.1	s__Daejeonella sp903821625	77.2972	189	1168	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016868395.1	s__Daejeonella sp016868395	77.1661	201	1168	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003339865.1	s__Pedobacter chinensis	76.4778	55	1168	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725795.1	s__Pedobacter jejuensis	76.3943	51	1168	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830615.1	s__Mucilaginibacter frigoritolerans	76.3534	54	1168	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 08:50:09,314] [INFO] GTDB search result was written to OceanDNA-b12873/result_gtdb.tsv
[2023-03-17 08:50:09,315] [INFO] ===== GTDB Search completed =====
[2023-03-17 08:50:09,316] [INFO] DFAST_QC result json was written to OceanDNA-b12873/dqc_result.json
[2023-03-17 08:50:09,316] [INFO] DFAST_QC completed!
[2023-03-17 08:50:09,316] [INFO] Total running time: 0h2m12s