[2023-03-15 03:14:16,339] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:14:16,339] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:14:16,339] [INFO] DQC Reference Directory: /var/lib/cwl/stgb967d677-f0d9-4133-9299-b21757780fb3/dqc_reference
[2023-03-15 03:14:17,588] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:14:17,588] [INFO] Task started: Prodigal
[2023-03-15 03:14:17,589] [INFO] Running command: cat /var/lib/cwl/stgcedb691f-f1eb-429e-85d4-0de754ea5f27/OceanDNA-b15513.fa | prodigal -d OceanDNA-b15513/cds.fna -a OceanDNA-b15513/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:14:37,462] [INFO] Task succeeded: Prodigal
[2023-03-15 03:14:37,462] [INFO] Task started: HMMsearch
[2023-03-15 03:14:37,462] [INFO] Running command: hmmsearch --tblout OceanDNA-b15513/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb967d677-f0d9-4133-9299-b21757780fb3/dqc_reference/reference_markers.hmm OceanDNA-b15513/protein.faa > /dev/null
[2023-03-15 03:14:37,715] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:14:37,716] [INFO] Found 6/6 markers.
[2023-03-15 03:14:37,736] [INFO] Query marker FASTA was written to OceanDNA-b15513/markers.fasta
[2023-03-15 03:14:37,736] [INFO] Task started: Blastn
[2023-03-15 03:14:37,736] [INFO] Running command: blastn -query OceanDNA-b15513/markers.fasta -db /var/lib/cwl/stgb967d677-f0d9-4133-9299-b21757780fb3/dqc_reference/reference_markers.fasta -out OceanDNA-b15513/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:14:38,258] [INFO] Task succeeded: Blastn
[2023-03-15 03:14:38,259] [INFO] Selected 15 target genomes.
[2023-03-15 03:14:38,259] [INFO] Target genome list was writen to OceanDNA-b15513/target_genomes.txt
[2023-03-15 03:14:38,269] [INFO] Task started: fastANI
[2023-03-15 03:14:38,269] [INFO] Running command: fastANI --query /var/lib/cwl/stgcedb691f-f1eb-429e-85d4-0de754ea5f27/OceanDNA-b15513.fa --refList OceanDNA-b15513/target_genomes.txt --output OceanDNA-b15513/fastani_result.tsv --threads 1
[2023-03-15 03:14:48,955] [INFO] Task succeeded: fastANI
[2023-03-15 03:14:48,955] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb967d677-f0d9-4133-9299-b21757780fb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:14:48,956] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb967d677-f0d9-4133-9299-b21757780fb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:14:48,956] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:14:48,956] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 03:14:48,956] [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
--------------------------------------------------------------------------------
[2023-03-15 03:14:48,957] [INFO] DFAST Taxonomy check result was written to OceanDNA-b15513/tc_result.tsv
[2023-03-15 03:14:48,957] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:14:48,957] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:14:48,957] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb967d677-f0d9-4133-9299-b21757780fb3/dqc_reference/checkm_data
[2023-03-15 03:14:48,960] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:14:48,964] [INFO] Task started: CheckM
[2023-03-15 03:14:48,965] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b15513/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b15513/checkm_input OceanDNA-b15513/checkm_result
[2023-03-15 03:15:38,987] [INFO] Task succeeded: CheckM
[2023-03-15 03:15:38,988] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:15:38,990] [INFO] ===== Completeness check finished =====
[2023-03-15 03:15:38,991] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:15:38,991] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b15513/markers.fasta)
[2023-03-15 03:15:38,991] [INFO] Task started: Blastn
[2023-03-15 03:15:38,991] [INFO] Running command: blastn -query OceanDNA-b15513/markers.fasta -db /var/lib/cwl/stgb967d677-f0d9-4133-9299-b21757780fb3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b15513/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:15:39,742] [INFO] Task succeeded: Blastn
[2023-03-15 03:15:39,743] [INFO] Selected 25 target genomes.
[2023-03-15 03:15:39,743] [INFO] Target genome list was writen to OceanDNA-b15513/target_genomes_gtdb.txt
[2023-03-15 03:15:39,763] [INFO] Task started: fastANI
[2023-03-15 03:15:39,763] [INFO] Running command: fastANI --query /var/lib/cwl/stgcedb691f-f1eb-429e-85d4-0de754ea5f27/OceanDNA-b15513.fa --refList OceanDNA-b15513/target_genomes_gtdb.txt --output OceanDNA-b15513/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:15:51,973] [INFO] Task succeeded: fastANI
[2023-03-15 03:15:51,979] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:15:51,979] [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_002710215.1	s__UBA11650 sp002710215	76.8111	106	1069	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA11650	95.0	99.22	99.06	0.76	0.73	3	-
GCA_002816575.1	s__UBA9611 sp002816575	76.5455	68	1069	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002238505.1	s__Bin22 sp002238505	76.2452	72	1069	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__Bin22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721995.1	s__UBA9611 sp002721995	76.2267	84	1069	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	99.09	98.66	0.88	0.85	7	-
GCA_013204585.1	s__UBA9611 sp013204585	76.1649	59	1069	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002238825.1	s__Bin87 sp002238825	76.1622	67	1069	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__Bin87	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872385.1	s__SHYG01 sp016872385	76.0489	82	1069	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__SHYG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002816585.1	s__UBA9611 sp002816585	75.946	67	1069	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__UBA9611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009840135.1	s__Bin22 sp009840135	75.8818	82	1069	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA3495;f__UBA3495;g__Bin22	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 03:15:51,979] [INFO] GTDB search result was written to OceanDNA-b15513/result_gtdb.tsv
[2023-03-15 03:15:51,980] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:15:51,980] [INFO] DFAST_QC result json was written to OceanDNA-b15513/dqc_result.json
[2023-03-15 03:15:51,980] [INFO] DFAST_QC completed!
[2023-03-15 03:15:51,981] [INFO] Total running time: 0h1m36s