[2023-03-17 07:28:31,296] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:28:31,296] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:28:31,296] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d0b83c2-1459-4b05-bed5-88c8e67d1c8f/dqc_reference
[2023-03-17 07:28:33,078] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:28:33,079] [INFO] Task started: Prodigal
[2023-03-17 07:28:33,079] [INFO] Running command: cat /var/lib/cwl/stg28970657-9ea5-4c63-bd17-ca65dc53fd07/OceanDNA-b16508.fa | prodigal -d OceanDNA-b16508/cds.fna -a OceanDNA-b16508/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:28:39,685] [INFO] Task succeeded: Prodigal
[2023-03-17 07:28:39,686] [INFO] Task started: HMMsearch
[2023-03-17 07:28:39,686] [INFO] Running command: hmmsearch --tblout OceanDNA-b16508/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d0b83c2-1459-4b05-bed5-88c8e67d1c8f/dqc_reference/reference_markers.hmm OceanDNA-b16508/protein.faa > /dev/null
[2023-03-17 07:28:39,852] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:28:39,853] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg28970657-9ea5-4c63-bd17-ca65dc53fd07/OceanDNA-b16508.fa]
[2023-03-17 07:28:39,863] [INFO] Query marker FASTA was written to OceanDNA-b16508/markers.fasta
[2023-03-17 07:28:39,863] [INFO] Task started: Blastn
[2023-03-17 07:28:39,863] [INFO] Running command: blastn -query OceanDNA-b16508/markers.fasta -db /var/lib/cwl/stg4d0b83c2-1459-4b05-bed5-88c8e67d1c8f/dqc_reference/reference_markers.fasta -out OceanDNA-b16508/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:28:40,297] [INFO] Task succeeded: Blastn
[2023-03-17 07:28:40,298] [INFO] Selected 13 target genomes.
[2023-03-17 07:28:40,298] [INFO] Target genome list was writen to OceanDNA-b16508/target_genomes.txt
[2023-03-17 07:28:40,306] [INFO] Task started: fastANI
[2023-03-17 07:28:40,306] [INFO] Running command: fastANI --query /var/lib/cwl/stg28970657-9ea5-4c63-bd17-ca65dc53fd07/OceanDNA-b16508.fa --refList OceanDNA-b16508/target_genomes.txt --output OceanDNA-b16508/fastani_result.tsv --threads 1
[2023-03-17 07:28:48,306] [INFO] Task succeeded: fastANI
[2023-03-17 07:28:48,306] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d0b83c2-1459-4b05-bed5-88c8e67d1c8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:28:48,307] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d0b83c2-1459-4b05-bed5-88c8e67d1c8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:28:48,307] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:28:48,307] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 07:28:48,307] [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
--------------------------------------------------------------------------------
[2023-03-17 07:28:48,307] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16508/tc_result.tsv
[2023-03-17 07:28:48,307] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:28:48,307] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:28:48,307] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d0b83c2-1459-4b05-bed5-88c8e67d1c8f/dqc_reference/checkm_data
[2023-03-17 07:28:48,310] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:28:48,312] [INFO] Task started: CheckM
[2023-03-17 07:28:48,312] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16508/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16508/checkm_input OceanDNA-b16508/checkm_result
[2023-03-17 07:29:11,878] [INFO] Task succeeded: CheckM
[2023-03-17 07:29:11,878] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.11%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:29:11,880] [INFO] ===== Completeness check finished =====
[2023-03-17 07:29:11,880] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:29:11,880] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16508/markers.fasta)
[2023-03-17 07:29:11,880] [INFO] Task started: Blastn
[2023-03-17 07:29:11,880] [INFO] Running command: blastn -query OceanDNA-b16508/markers.fasta -db /var/lib/cwl/stg4d0b83c2-1459-4b05-bed5-88c8e67d1c8f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16508/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:29:12,337] [INFO] Task succeeded: Blastn
[2023-03-17 07:29:12,338] [INFO] Selected 7 target genomes.
[2023-03-17 07:29:12,338] [INFO] Target genome list was writen to OceanDNA-b16508/target_genomes_gtdb.txt
[2023-03-17 07:29:12,435] [INFO] Task started: fastANI
[2023-03-17 07:29:12,435] [INFO] Running command: fastANI --query /var/lib/cwl/stg28970657-9ea5-4c63-bd17-ca65dc53fd07/OceanDNA-b16508.fa --refList OceanDNA-b16508/target_genomes_gtdb.txt --output OceanDNA-b16508/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:29:14,965] [INFO] Task succeeded: fastANI
[2023-03-17 07:29:14,969] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:29:14,969] [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_014279835.1	s__Synechococcus_C sp014279835	92.4718	59	59	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	96.93	96.36	0.92	0.87	4	-
GCF_014279775.1	s__Synechococcus_C sp002500205	91.4867	58	59	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	99.03	97.76	0.95	0.86	9	-
GCF_000014585.1	s__Synechococcus_C sp000014585	88.2385	58	59	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_001040845.1	s__Synechococcus_C sp001040845	87.701	59	59	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_000230675.1	s__Synechococcus_C sp000230675	87.5117	58	59	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	96.29	95.09	0.90	0.84	8	-
--------------------------------------------------------------------------------
[2023-03-17 07:29:14,969] [INFO] GTDB search result was written to OceanDNA-b16508/result_gtdb.tsv
[2023-03-17 07:29:14,969] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:29:14,970] [INFO] DFAST_QC result json was written to OceanDNA-b16508/dqc_result.json
[2023-03-17 07:29:14,970] [INFO] DFAST_QC completed!
[2023-03-17 07:29:14,970] [INFO] Total running time: 0h0m44s