[2023-03-19 00:15:41,729] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:15:41,729] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:15:41,729] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c0f405d-fa3a-449d-a6b0-d87ead984802/dqc_reference
[2023-03-19 00:15:43,441] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:15:43,441] [INFO] Task started: Prodigal
[2023-03-19 00:15:43,442] [INFO] Running command: cat /var/lib/cwl/stg2f493a7b-a6ef-4e61-862f-58f2da0cc59b/OceanDNA-b16580.fa | prodigal -d OceanDNA-b16580/cds.fna -a OceanDNA-b16580/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:16:01,226] [INFO] Task succeeded: Prodigal
[2023-03-19 00:16:01,226] [INFO] Task started: HMMsearch
[2023-03-19 00:16:01,226] [INFO] Running command: hmmsearch --tblout OceanDNA-b16580/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c0f405d-fa3a-449d-a6b0-d87ead984802/dqc_reference/reference_markers.hmm OceanDNA-b16580/protein.faa > /dev/null
[2023-03-19 00:16:01,400] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:16:01,400] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2f493a7b-a6ef-4e61-862f-58f2da0cc59b/OceanDNA-b16580.fa]
[2023-03-19 00:16:01,419] [INFO] Query marker FASTA was written to OceanDNA-b16580/markers.fasta
[2023-03-19 00:16:01,420] [INFO] Task started: Blastn
[2023-03-19 00:16:01,420] [INFO] Running command: blastn -query OceanDNA-b16580/markers.fasta -db /var/lib/cwl/stg2c0f405d-fa3a-449d-a6b0-d87ead984802/dqc_reference/reference_markers.fasta -out OceanDNA-b16580/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:16:02,088] [INFO] Task succeeded: Blastn
[2023-03-19 00:16:02,089] [INFO] Selected 21 target genomes.
[2023-03-19 00:16:02,089] [INFO] Target genome list was writen to OceanDNA-b16580/target_genomes.txt
[2023-03-19 00:16:02,103] [INFO] Task started: fastANI
[2023-03-19 00:16:02,103] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f493a7b-a6ef-4e61-862f-58f2da0cc59b/OceanDNA-b16580.fa --refList OceanDNA-b16580/target_genomes.txt --output OceanDNA-b16580/fastani_result.tsv --threads 1
[2023-03-19 00:16:18,253] [INFO] Task succeeded: fastANI
[2023-03-19 00:16:18,254] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c0f405d-fa3a-449d-a6b0-d87ead984802/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:16:18,254] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c0f405d-fa3a-449d-a6b0-d87ead984802/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:16:18,257] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:16:18,257] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 00:16:18,257] [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
Parasynechococcus marenigrum	strain=WH 8102	GCA_000195975.1	2881428	2881428	type	True	78.9694	196	555	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 00:16:18,258] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16580/tc_result.tsv
[2023-03-19 00:16:18,258] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:16:18,258] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:16:18,258] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c0f405d-fa3a-449d-a6b0-d87ead984802/dqc_reference/checkm_data
[2023-03-19 00:16:18,259] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:16:18,304] [INFO] Task started: CheckM
[2023-03-19 00:16:18,304] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16580/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16580/checkm_input OceanDNA-b16580/checkm_result
[2023-03-19 00:17:07,882] [INFO] Task succeeded: CheckM
[2023-03-19 00:17:07,883] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 5.59%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 00:17:07,885] [INFO] ===== Completeness check finished =====
[2023-03-19 00:17:07,885] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:17:07,886] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16580/markers.fasta)
[2023-03-19 00:17:07,886] [INFO] Task started: Blastn
[2023-03-19 00:17:07,886] [INFO] Running command: blastn -query OceanDNA-b16580/markers.fasta -db /var/lib/cwl/stg2c0f405d-fa3a-449d-a6b0-d87ead984802/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16580/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:17:08,858] [INFO] Task succeeded: Blastn
[2023-03-19 00:17:08,859] [INFO] Selected 7 target genomes.
[2023-03-19 00:17:08,859] [INFO] Target genome list was writen to OceanDNA-b16580/target_genomes_gtdb.txt
[2023-03-19 00:17:08,867] [INFO] Task started: fastANI
[2023-03-19 00:17:08,867] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f493a7b-a6ef-4e61-862f-58f2da0cc59b/OceanDNA-b16580.fa --refList OceanDNA-b16580/target_genomes_gtdb.txt --output OceanDNA-b16580/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:17:12,274] [INFO] Task succeeded: fastANI
[2023-03-19 00:17:12,279] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:17:12,282] [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_000063505.1	s__Synechococcus_C sp000063505	97.615	508	555	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	97.52	97.52	0.89	0.89	2	conclusive
GCF_014279795.1	s__Synechococcus_C sp014279795	89.4777	515	555	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	96.67	96.56	0.92	0.91	3	-
GCF_014279875.1	s__Synechococcus_C sp002172935	88.2375	502	555	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	98.09	98.09	0.93	0.93	2	-
GCF_000153285.1	s__Synechococcus_C sp000153285	85.7129	494	555	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011523835.1	s__Synechococcus_C sp011523835	85.2993	373	555	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014279815.1	s__Synechococcus_C sp014279815	79.1159	282	555	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014279895.1	s__Synechococcus_E sp002724845	78.8379	206	555	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	96.37	95.03	0.93	0.89	13	-
--------------------------------------------------------------------------------
[2023-03-19 00:17:12,282] [INFO] GTDB search result was written to OceanDNA-b16580/result_gtdb.tsv
[2023-03-19 00:17:12,282] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:17:12,284] [INFO] DFAST_QC result json was written to OceanDNA-b16580/dqc_result.json
[2023-03-19 00:17:12,284] [INFO] DFAST_QC completed!
[2023-03-19 00:17:12,284] [INFO] Total running time: 0h1m31s