[2023-03-16 04:38:30,105] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:38:30,105] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:38:30,106] [INFO] DQC Reference Directory: /var/lib/cwl/stgc05482db-4ea1-4444-820d-8ef2250e4154/dqc_reference
[2023-03-16 04:38:31,217] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:38:31,217] [INFO] Task started: Prodigal
[2023-03-16 04:38:31,217] [INFO] Running command: cat /var/lib/cwl/stgce81c6b7-a76d-42ba-a7e0-6d4ae409b294/OceanDNA-b16480.fa | prodigal -d OceanDNA-b16480/cds.fna -a OceanDNA-b16480/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:38:51,143] [INFO] Task succeeded: Prodigal
[2023-03-16 04:38:51,143] [INFO] Task started: HMMsearch
[2023-03-16 04:38:51,143] [INFO] Running command: hmmsearch --tblout OceanDNA-b16480/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc05482db-4ea1-4444-820d-8ef2250e4154/dqc_reference/reference_markers.hmm OceanDNA-b16480/protein.faa > /dev/null
[2023-03-16 04:38:51,309] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:38:51,310] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgce81c6b7-a76d-42ba-a7e0-6d4ae409b294/OceanDNA-b16480.fa]
[2023-03-16 04:38:51,326] [INFO] Query marker FASTA was written to OceanDNA-b16480/markers.fasta
[2023-03-16 04:38:51,328] [INFO] Task started: Blastn
[2023-03-16 04:38:51,328] [INFO] Running command: blastn -query OceanDNA-b16480/markers.fasta -db /var/lib/cwl/stgc05482db-4ea1-4444-820d-8ef2250e4154/dqc_reference/reference_markers.fasta -out OceanDNA-b16480/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:38:51,881] [INFO] Task succeeded: Blastn
[2023-03-16 04:38:51,882] [INFO] Selected 22 target genomes.
[2023-03-16 04:38:51,882] [INFO] Target genome list was writen to OceanDNA-b16480/target_genomes.txt
[2023-03-16 04:38:51,895] [INFO] Task started: fastANI
[2023-03-16 04:38:51,895] [INFO] Running command: fastANI --query /var/lib/cwl/stgce81c6b7-a76d-42ba-a7e0-6d4ae409b294/OceanDNA-b16480.fa --refList OceanDNA-b16480/target_genomes.txt --output OceanDNA-b16480/fastani_result.tsv --threads 1
[2023-03-16 04:39:05,603] [INFO] Task succeeded: fastANI
[2023-03-16 04:39:05,603] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc05482db-4ea1-4444-820d-8ef2250e4154/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:39:05,603] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc05482db-4ea1-4444-820d-8ef2250e4154/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:39:05,607] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:39:05,607] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:39:05,607] [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	77.4249	120	749	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:39:05,607] [INFO] DFAST Taxonomy check result was written to OceanDNA-b16480/tc_result.tsv
[2023-03-16 04:39:05,607] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:39:05,607] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:39:05,607] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc05482db-4ea1-4444-820d-8ef2250e4154/dqc_reference/checkm_data
[2023-03-16 04:39:05,608] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:39:05,612] [INFO] Task started: CheckM
[2023-03-16 04:39:05,612] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b16480/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b16480/checkm_input OceanDNA-b16480/checkm_result
[2023-03-16 04:39:59,301] [INFO] Task succeeded: CheckM
[2023-03-16 04:39:59,301] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 04:39:59,303] [INFO] ===== Completeness check finished =====
[2023-03-16 04:39:59,303] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:39:59,304] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b16480/markers.fasta)
[2023-03-16 04:39:59,305] [INFO] Task started: Blastn
[2023-03-16 04:39:59,305] [INFO] Running command: blastn -query OceanDNA-b16480/markers.fasta -db /var/lib/cwl/stgc05482db-4ea1-4444-820d-8ef2250e4154/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b16480/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:40:00,202] [INFO] Task succeeded: Blastn
[2023-03-16 04:40:00,202] [INFO] Selected 7 target genomes.
[2023-03-16 04:40:00,202] [INFO] Target genome list was writen to OceanDNA-b16480/target_genomes_gtdb.txt
[2023-03-16 04:40:00,231] [INFO] Task started: fastANI
[2023-03-16 04:40:00,231] [INFO] Running command: fastANI --query /var/lib/cwl/stgce81c6b7-a76d-42ba-a7e0-6d4ae409b294/OceanDNA-b16480.fa --refList OceanDNA-b16480/target_genomes_gtdb.txt --output OceanDNA-b16480/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:40:04,059] [INFO] Task succeeded: fastANI
[2023-03-16 04:40:04,064] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 04:40:04,064] [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	97.0727	626	749	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	conclusive
GCF_014279775.1	s__Synechococcus_C sp002500205	90.4751	583	749	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	-
GCA_003210315.1	s__Synechococcus_C sp003210315	87.4835	344	749	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	-
GCF_000230675.1	s__Synechococcus_C sp000230675	87.388	589	749	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	87.3768	600	749	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	87.1094	595	749	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_003210755.1	s__Synechococcus_C sp003210755	80.4759	390	749	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	-
--------------------------------------------------------------------------------
[2023-03-16 04:40:04,064] [INFO] GTDB search result was written to OceanDNA-b16480/result_gtdb.tsv
[2023-03-16 04:40:04,064] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:40:04,065] [INFO] DFAST_QC result json was written to OceanDNA-b16480/dqc_result.json
[2023-03-16 04:40:04,065] [INFO] DFAST_QC completed!
[2023-03-16 04:40:04,065] [INFO] Total running time: 0h1m34s