[2023-06-27 03:44:46,163] [INFO] DFAST_QC pipeline started.
[2023-06-27 03:44:46,165] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 03:44:46,165] [INFO] DQC Reference Directory: /var/lib/cwl/stg291b8559-7bdd-4452-b113-26e2259dcd59/dqc_reference
[2023-06-27 03:44:48,849] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 03:44:48,850] [INFO] Task started: Prodigal
[2023-06-27 03:44:48,850] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc7595e8-06aa-427b-9f04-9532eb3d0521/GCA_026706885.1_ASM2670688v1_genomic.fna.gz | prodigal -d GCA_026706885.1_ASM2670688v1_genomic.fna/cds.fna -a GCA_026706885.1_ASM2670688v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 03:44:58,908] [INFO] Task succeeded: Prodigal
[2023-06-27 03:44:58,908] [INFO] Task started: HMMsearch
[2023-06-27 03:44:58,908] [INFO] Running command: hmmsearch --tblout GCA_026706885.1_ASM2670688v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg291b8559-7bdd-4452-b113-26e2259dcd59/dqc_reference/reference_markers.hmm GCA_026706885.1_ASM2670688v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 03:44:59,059] [INFO] Task succeeded: HMMsearch
[2023-06-27 03:44:59,060] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdc7595e8-06aa-427b-9f04-9532eb3d0521/GCA_026706885.1_ASM2670688v1_genomic.fna.gz]
[2023-06-27 03:44:59,079] [INFO] Query marker FASTA was written to GCA_026706885.1_ASM2670688v1_genomic.fna/markers.fasta
[2023-06-27 03:44:59,080] [INFO] Task started: Blastn
[2023-06-27 03:44:59,080] [INFO] Running command: blastn -query GCA_026706885.1_ASM2670688v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg291b8559-7bdd-4452-b113-26e2259dcd59/dqc_reference/reference_markers.fasta -out GCA_026706885.1_ASM2670688v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 03:44:59,668] [INFO] Task succeeded: Blastn
[2023-06-27 03:44:59,671] [INFO] Selected 21 target genomes.
[2023-06-27 03:44:59,671] [INFO] Target genome list was writen to GCA_026706885.1_ASM2670688v1_genomic.fna/target_genomes.txt
[2023-06-27 03:44:59,677] [INFO] Task started: fastANI
[2023-06-27 03:44:59,677] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc7595e8-06aa-427b-9f04-9532eb3d0521/GCA_026706885.1_ASM2670688v1_genomic.fna.gz --refList GCA_026706885.1_ASM2670688v1_genomic.fna/target_genomes.txt --output GCA_026706885.1_ASM2670688v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 03:45:11,274] [INFO] Task succeeded: fastANI
[2023-06-27 03:45:11,275] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg291b8559-7bdd-4452-b113-26e2259dcd59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 03:45:11,275] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg291b8559-7bdd-4452-b113-26e2259dcd59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 03:45:11,279] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 03:45:11,279] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 03:45:11,279] [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	81.1687	288	420	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 03:45:11,281] [INFO] DFAST Taxonomy check result was written to GCA_026706885.1_ASM2670688v1_genomic.fna/tc_result.tsv
[2023-06-27 03:45:11,281] [INFO] ===== Taxonomy check completed =====
[2023-06-27 03:45:11,282] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 03:45:11,282] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg291b8559-7bdd-4452-b113-26e2259dcd59/dqc_reference/checkm_data
[2023-06-27 03:45:11,283] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 03:45:11,304] [INFO] Task started: CheckM
[2023-06-27 03:45:11,304] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026706885.1_ASM2670688v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026706885.1_ASM2670688v1_genomic.fna/checkm_input GCA_026706885.1_ASM2670688v1_genomic.fna/checkm_result
[2023-06-27 03:45:36,715] [INFO] Task succeeded: CheckM
[2023-06-27 03:45:36,716] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-27 03:45:36,732] [INFO] ===== Completeness check finished =====
[2023-06-27 03:45:36,732] [INFO] ===== Start GTDB Search =====
[2023-06-27 03:45:36,733] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026706885.1_ASM2670688v1_genomic.fna/markers.fasta)
[2023-06-27 03:45:36,733] [INFO] Task started: Blastn
[2023-06-27 03:45:36,733] [INFO] Running command: blastn -query GCA_026706885.1_ASM2670688v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg291b8559-7bdd-4452-b113-26e2259dcd59/dqc_reference/reference_markers_gtdb.fasta -out GCA_026706885.1_ASM2670688v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 03:45:37,612] [INFO] Task succeeded: Blastn
[2023-06-27 03:45:37,615] [INFO] Selected 7 target genomes.
[2023-06-27 03:45:37,616] [INFO] Target genome list was writen to GCA_026706885.1_ASM2670688v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 03:45:37,620] [INFO] Task started: fastANI
[2023-06-27 03:45:37,620] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc7595e8-06aa-427b-9f04-9532eb3d0521/GCA_026706885.1_ASM2670688v1_genomic.fna.gz --refList GCA_026706885.1_ASM2670688v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026706885.1_ASM2670688v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 03:45:40,598] [INFO] Task succeeded: fastANI
[2023-06-27 03:45:40,605] [INFO] Found 7 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-27 03:45:40,605] [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_014279895.1	s__Synechococcus_E sp002724845	97.683	406	420	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	inconclusive
GCF_000161795.2	s__Synechococcus_E sp000161795	95.2615	407	420	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_000012625.1	s__Synechococcus_E sp000012625	93.3592	406	420	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	95.15	95.15	0.92	0.92	2	-
GCA_013911515.1	s__Synechococcus_E sp013911515	92.2617	363	420	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737595.1	s__Synechococcus_E sp000737595	90.1533	399	420	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779825.1	s__Synechococcus_E sp016779825	89.8842	321	420	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003209165.1	s__Synechococcus_E sp003209165	88.8653	336	420	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 03:45:40,607] [INFO] GTDB search result was written to GCA_026706885.1_ASM2670688v1_genomic.fna/result_gtdb.tsv
[2023-06-27 03:45:40,608] [INFO] ===== GTDB Search completed =====
[2023-06-27 03:45:40,610] [INFO] DFAST_QC result json was written to GCA_026706885.1_ASM2670688v1_genomic.fna/dqc_result.json
[2023-06-27 03:45:40,611] [INFO] DFAST_QC completed!
[2023-06-27 03:45:40,611] [INFO] Total running time: 0h0m54s