[2023-03-16 04:31:43,756] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:31:43,756] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:31:43,756] [INFO] DQC Reference Directory: /var/lib/cwl/stg31c7024f-4d0e-4188-a71b-ec3d33da5c7e/dqc_reference
[2023-03-16 04:31:45,527] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:31:45,527] [INFO] Task started: Prodigal
[2023-03-16 04:31:45,527] [INFO] Running command: cat /var/lib/cwl/stge678ec8f-5039-47c7-a1c9-d3208463763b/OceanDNA-b16173.fa | prodigal -d OceanDNA-b16173/cds.fna -a OceanDNA-b16173/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:32:04,146] [INFO] Task succeeded: Prodigal
[2023-03-16 04:32:04,146] [INFO] Task started: HMMsearch
[2023-03-16 04:32:04,147] [INFO] Running command: hmmsearch --tblout OceanDNA-b16173/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31c7024f-4d0e-4188-a71b-ec3d33da5c7e/dqc_reference/reference_markers.hmm OceanDNA-b16173/protein.faa > /dev/null
[2023-03-16 04:32:04,389] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:32:04,390] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge678ec8f-5039-47c7-a1c9-d3208463763b/OceanDNA-b16173.fa]
[2023-03-16 04:32:04,415] [INFO] Query marker FASTA was written to OceanDNA-b16173/markers.fasta
[2023-03-16 04:32:04,416] [INFO] Task started: Blastn
[2023-03-16 04:32:04,416] [INFO] Running command: blastn -query OceanDNA-b16173/markers.fasta -db /var/lib/cwl/stg31c7024f-4d0e-4188-a71b-ec3d33da5c7e/dqc_reference/reference_markers.fasta -out OceanDNA-b16173/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:32:04,931] [INFO] Task succeeded: Blastn
[2023-03-16 04:32:04,932] [INFO] Selected 11 target genomes.
[2023-03-16 04:32:04,932] [INFO] Target genome list was writen to OceanDNA-b16173/target_genomes.txt
[2023-03-16 04:32:04,940] [INFO] Task started: fastANI
[2023-03-16 04:32:04,940] [INFO] Running command: fastANI --query /var/lib/cwl/stge678ec8f-5039-47c7-a1c9-d3208463763b/OceanDNA-b16173.fa --refList OceanDNA-b16173/target_genomes.txt --output OceanDNA-b16173/fastani_result.tsv --threads 1
[2023-03-16 04:32:11,443] [INFO] Task succeeded: fastANI
[2023-03-16 04:32:11,444] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31c7024f-4d0e-4188-a71b-ec3d33da5c7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:32:11,444] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31c7024f-4d0e-4188-a71b-ec3d33da5c7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:32:11,447] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:32:11,447] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:32:11,447] [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
Stanieria cyanosphaera	strain=PCC 7437	GCA_000317575.1	102116	102116	type	True	75.7227	104	1190	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:32:11,448] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16173/tc_result.tsv
[2023-03-16 04:32:11,448] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:32:11,448] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:32:11,448] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31c7024f-4d0e-4188-a71b-ec3d33da5c7e/dqc_reference/checkm_data
[2023-03-16 04:32:11,449] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:32:11,816] [INFO] Task started: CheckM
[2023-03-16 04:32:11,816] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16173/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16173/checkm_input OceanDNA-b16173/checkm_result
[2023-03-16 04:32:59,891] [INFO] Task succeeded: CheckM
[2023-03-16 04:32:59,892] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 10.42%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 04:32:59,914] [INFO] ===== Completeness check finished =====
[2023-03-16 04:32:59,914] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:32:59,914] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16173/markers.fasta)
[2023-03-16 04:32:59,915] [INFO] Task started: Blastn
[2023-03-16 04:32:59,915] [INFO] Running command: blastn -query OceanDNA-b16173/markers.fasta -db /var/lib/cwl/stg31c7024f-4d0e-4188-a71b-ec3d33da5c7e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16173/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:33:00,614] [INFO] Task succeeded: Blastn
[2023-03-16 04:33:00,615] [INFO] Selected 21 target genomes.
[2023-03-16 04:33:00,615] [INFO] Target genome list was writen to OceanDNA-b16173/target_genomes_gtdb.txt
[2023-03-16 04:33:00,637] [INFO] Task started: fastANI
[2023-03-16 04:33:00,638] [INFO] Running command: fastANI --query /var/lib/cwl/stge678ec8f-5039-47c7-a1c9-d3208463763b/OceanDNA-b16173.fa --refList OceanDNA-b16173/target_genomes_gtdb.txt --output OceanDNA-b16173/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:33:14,847] [INFO] Task succeeded: fastANI
[2023-03-16 04:33:14,852] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:33:14,852] [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
GCF_000317575.1	s__Stanieria cyanosphaera	75.7347	103	1190	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Stanieria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000332055.1	s__Xenococcus sp000332055	75.6812	115	1190	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Xenococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003995.1	s__Pleurocapsa sp003003995	75.6489	76	1190	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	75.6486	75	1190	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002355455.1	s__Stanieria sp002355455	75.5844	103	1190	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Stanieria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015207585.1	s__LEGE-06147 sp015207585	75.1987	69	1190	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__LEGE-06147	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:33:14,853] [INFO] GTDB search result was written to OceanDNA-b16173/result_gtdb.tsv
[2023-03-16 04:33:14,853] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:33:14,854] [INFO] DFAST_QC result json was written to OceanDNA-b16173/dqc_result.json
[2023-03-16 04:33:14,854] [INFO] DFAST_QC completed!
[2023-03-16 04:33:14,854] [INFO] Total running time: 0h1m31s