[2023-03-17 10:48:45,541] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:48:45,541] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:48:45,541] [INFO] DQC Reference Directory: /var/lib/cwl/stg28efb250-ec50-4a1c-aa28-e90d07161c75/dqc_reference
[2023-03-17 10:48:46,719] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:48:46,719] [INFO] Task started: Prodigal
[2023-03-17 10:48:46,720] [INFO] Running command: cat /var/lib/cwl/stg6acb71b3-e54e-446d-b248-4bf673c1a3a2/OceanDNA-b16702.fa | prodigal -d OceanDNA-b16702/cds.fna -a OceanDNA-b16702/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:49:01,382] [INFO] Task succeeded: Prodigal
[2023-03-17 10:49:01,382] [INFO] Task started: HMMsearch
[2023-03-17 10:49:01,382] [INFO] Running command: hmmsearch --tblout OceanDNA-b16702/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28efb250-ec50-4a1c-aa28-e90d07161c75/dqc_reference/reference_markers.hmm OceanDNA-b16702/protein.faa > /dev/null
[2023-03-17 10:49:01,589] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:49:01,590] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6acb71b3-e54e-446d-b248-4bf673c1a3a2/OceanDNA-b16702.fa]
[2023-03-17 10:49:01,604] [INFO] Query marker FASTA was written to OceanDNA-b16702/markers.fasta
[2023-03-17 10:49:01,605] [INFO] Task started: Blastn
[2023-03-17 10:49:01,606] [INFO] Running command: blastn -query OceanDNA-b16702/markers.fasta -db /var/lib/cwl/stg28efb250-ec50-4a1c-aa28-e90d07161c75/dqc_reference/reference_markers.fasta -out OceanDNA-b16702/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:49:02,175] [INFO] Task succeeded: Blastn
[2023-03-17 10:49:02,177] [INFO] Selected 18 target genomes.
[2023-03-17 10:49:02,177] [INFO] Target genome list was writen to OceanDNA-b16702/target_genomes.txt
[2023-03-17 10:49:02,268] [INFO] Task started: fastANI
[2023-03-17 10:49:02,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg6acb71b3-e54e-446d-b248-4bf673c1a3a2/OceanDNA-b16702.fa --refList OceanDNA-b16702/target_genomes.txt --output OceanDNA-b16702/fastani_result.tsv --threads 1
[2023-03-17 10:49:16,456] [INFO] Task succeeded: fastANI
[2023-03-17 10:49:16,457] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28efb250-ec50-4a1c-aa28-e90d07161c75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:49:16,457] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28efb250-ec50-4a1c-aa28-e90d07161c75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:49:16,460] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:49:16,460] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 10:49:16,460] [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	76.439	65	560	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 10:49:16,461] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16702/tc_result.tsv
[2023-03-17 10:49:16,461] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:49:16,461] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:49:16,461] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28efb250-ec50-4a1c-aa28-e90d07161c75/dqc_reference/checkm_data
[2023-03-17 10:49:16,462] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:49:16,469] [INFO] Task started: CheckM
[2023-03-17 10:49:16,469] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16702/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16702/checkm_input OceanDNA-b16702/checkm_result
[2023-03-17 10:49:58,324] [INFO] Task succeeded: CheckM
[2023-03-17 10:49:58,325] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.12%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:49:58,327] [INFO] ===== Completeness check finished =====
[2023-03-17 10:49:58,327] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:49:58,327] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16702/markers.fasta)
[2023-03-17 10:49:58,328] [INFO] Task started: Blastn
[2023-03-17 10:49:58,328] [INFO] Running command: blastn -query OceanDNA-b16702/markers.fasta -db /var/lib/cwl/stg28efb250-ec50-4a1c-aa28-e90d07161c75/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16702/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:49:59,072] [INFO] Task succeeded: Blastn
[2023-03-17 10:49:59,072] [INFO] Selected 19 target genomes.
[2023-03-17 10:49:59,073] [INFO] Target genome list was writen to OceanDNA-b16702/target_genomes_gtdb.txt
[2023-03-17 10:49:59,307] [INFO] Task started: fastANI
[2023-03-17 10:49:59,307] [INFO] Running command: fastANI --query /var/lib/cwl/stg6acb71b3-e54e-446d-b248-4bf673c1a3a2/OceanDNA-b16702.fa --refList OceanDNA-b16702/target_genomes_gtdb.txt --output OceanDNA-b16702/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:50:08,252] [INFO] Task succeeded: fastANI
[2023-03-17 10:50:08,259] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 10:50:08,260] [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_003210755.1	s__Synechococcus_C sp003210755	98.3696	464	560	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	98.42	98.23	0.77	0.74	4	conclusive
GCF_014279775.1	s__Synechococcus_C sp002500205	80.8924	369	560	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_014279835.1	s__Synechococcus_C sp014279835	80.6919	385	560	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_000230675.1	s__Synechococcus_C sp000230675	80.4028	387	560	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	-
GCF_000014585.1	s__Synechococcus_C sp000014585	80.396	389	560	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	80.3925	377	560	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_003210315.1	s__Synechococcus_C sp003210315	80.3588	222	560	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	96.13	96.13	0.52	0.52	2	-
GCA_011525445.1	s__Synechococcus_C sp011525445	78.1024	182	560	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_004209775.1	s__Synechococcus_C sp004209775	76.7777	87	560	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014280035.1	s__Synechococcus_C sp002693285	76.4985	99	560	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_C	95.0	98.95	98.86	0.95	0.94	3	-
GCF_900474185.1	s__Synechococcus_E sp900474185	76.3567	75	560	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	95.68	95.24	0.90	0.90	3	-
--------------------------------------------------------------------------------
[2023-03-17 10:50:08,260] [INFO] GTDB search result was written to OceanDNA-b16702/result_gtdb.tsv
[2023-03-17 10:50:08,260] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:50:08,261] [INFO] DFAST_QC result json was written to OceanDNA-b16702/dqc_result.json
[2023-03-17 10:50:08,262] [INFO] DFAST_QC completed!
[2023-03-17 10:50:08,262] [INFO] Total running time: 0h1m23s