[2023-03-17 00:45:47,082] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:45:47,082] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:45:47,082] [INFO] DQC Reference Directory: /var/lib/cwl/stg2964cc44-1823-47b0-b956-505436534241/dqc_reference
[2023-03-17 00:45:48,284] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:45:48,285] [INFO] Task started: Prodigal
[2023-03-17 00:45:48,285] [INFO] Running command: cat /var/lib/cwl/stgbee9aef0-4ab3-4e97-b014-8171374405e3/OceanDNA-b16151.fa | prodigal -d OceanDNA-b16151/cds.fna -a OceanDNA-b16151/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:46:07,520] [INFO] Task succeeded: Prodigal
[2023-03-17 00:46:07,520] [INFO] Task started: HMMsearch
[2023-03-17 00:46:07,520] [INFO] Running command: hmmsearch --tblout OceanDNA-b16151/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2964cc44-1823-47b0-b956-505436534241/dqc_reference/reference_markers.hmm OceanDNA-b16151/protein.faa > /dev/null
[2023-03-17 00:46:07,744] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:46:07,744] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgbee9aef0-4ab3-4e97-b014-8171374405e3/OceanDNA-b16151.fa]
[2023-03-17 00:46:07,770] [INFO] Query marker FASTA was written to OceanDNA-b16151/markers.fasta
[2023-03-17 00:46:07,771] [INFO] Task started: Blastn
[2023-03-17 00:46:07,771] [INFO] Running command: blastn -query OceanDNA-b16151/markers.fasta -db /var/lib/cwl/stg2964cc44-1823-47b0-b956-505436534241/dqc_reference/reference_markers.fasta -out OceanDNA-b16151/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:46:08,284] [INFO] Task succeeded: Blastn
[2023-03-17 00:46:08,285] [INFO] Selected 19 target genomes.
[2023-03-17 00:46:08,285] [INFO] Target genome list was writen to OceanDNA-b16151/target_genomes.txt
[2023-03-17 00:46:08,328] [INFO] Task started: fastANI
[2023-03-17 00:46:08,328] [INFO] Running command: fastANI --query /var/lib/cwl/stgbee9aef0-4ab3-4e97-b014-8171374405e3/OceanDNA-b16151.fa --refList OceanDNA-b16151/target_genomes.txt --output OceanDNA-b16151/fastani_result.tsv --threads 1
[2023-03-17 00:46:19,747] [INFO] Task succeeded: fastANI
[2023-03-17 00:46:19,748] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2964cc44-1823-47b0-b956-505436534241/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:46:19,748] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2964cc44-1823-47b0-b956-505436534241/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:46:19,751] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:46:19,751] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 00:46:19,751] [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
Waterburya agarophytonicola	strain=KI4	GCA_020640915.1	2886916	2886916	type	True	78.8368	592	1250	95	below_threshold
Stanieria cyanosphaera	strain=PCC 7437	GCA_000317575.1	102116	102116	type	True	75.7872	152	1250	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 00:46:19,751] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16151/tc_result.tsv
[2023-03-17 00:46:19,752] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:46:19,752] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:46:19,752] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2964cc44-1823-47b0-b956-505436534241/dqc_reference/checkm_data
[2023-03-17 00:46:19,752] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:46:19,779] [INFO] Task started: CheckM
[2023-03-17 00:46:19,780] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16151/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16151/checkm_input OceanDNA-b16151/checkm_result
[2023-03-17 00:47:08,631] [INFO] Task succeeded: CheckM
[2023-03-17 00:47:08,632] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.78%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:47:08,635] [INFO] ===== Completeness check finished =====
[2023-03-17 00:47:08,635] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:47:08,635] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16151/markers.fasta)
[2023-03-17 00:47:08,637] [INFO] Task started: Blastn
[2023-03-17 00:47:08,637] [INFO] Running command: blastn -query OceanDNA-b16151/markers.fasta -db /var/lib/cwl/stg2964cc44-1823-47b0-b956-505436534241/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16151/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:47:09,380] [INFO] Task succeeded: Blastn
[2023-03-17 00:47:09,381] [INFO] Selected 20 target genomes.
[2023-03-17 00:47:09,381] [INFO] Target genome list was writen to OceanDNA-b16151/target_genomes_gtdb.txt
[2023-03-17 00:47:09,644] [INFO] Task started: fastANI
[2023-03-17 00:47:09,645] [INFO] Running command: fastANI --query /var/lib/cwl/stgbee9aef0-4ab3-4e97-b014-8171374405e3/OceanDNA-b16151.fa --refList OceanDNA-b16151/target_genomes_gtdb.txt --output OceanDNA-b16151/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:47:29,898] [INFO] Task succeeded: fastANI
[2023-03-17 00:47:29,904] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:47:29,904] [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_015207195.1	s__Pleurocapsa sp015207195	77.5477	377	1250	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000332195.1	s__Pleurocapsa sp000332195	77.4145	411	1250	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002368355.1	s__Pleurocapsa sp002368355	77.137	302	1250	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012034765.1	s__Pleurocapsa sp012034765	77.0768	296	1250	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	99.36	99.13	0.90	0.87	3	-
GCF_003003995.1	s__Pleurocapsa sp003003995	76.8601	296	1250	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900659865.1	s__Hyella patelloides	75.9751	179	1250	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Hyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355455.1	s__Stanieria sp002355455	75.8338	160	1250	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Stanieria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317575.1	s__Stanieria cyanosphaera	75.7953	151	1250	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Stanieria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 00:47:29,904] [INFO] GTDB search result was written to OceanDNA-b16151/result_gtdb.tsv
[2023-03-17 00:47:29,904] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:47:29,905] [INFO] DFAST_QC result json was written to OceanDNA-b16151/dqc_result.json
[2023-03-17 00:47:29,905] [INFO] DFAST_QC completed!
[2023-03-17 00:47:29,905] [INFO] Total running time: 0h1m43s