[2023-06-19 08:50:07,045] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:50:07,049] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:50:07,049] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c21b456-719f-43c5-a0da-23b137ae2368/dqc_reference
[2023-06-19 08:50:08,240] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:50:08,241] [INFO] Task started: Prodigal
[2023-06-19 08:50:08,241] [INFO] Running command: gunzip -c /var/lib/cwl/stg7730f18e-a6ba-47af-b9c7-9140d56f638d/GCA_018623125.1_ASM1862312v1_genomic.fna.gz | prodigal -d GCA_018623125.1_ASM1862312v1_genomic.fna/cds.fna -a GCA_018623125.1_ASM1862312v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:50:15,533] [INFO] Task succeeded: Prodigal
[2023-06-19 08:50:15,533] [INFO] Task started: HMMsearch
[2023-06-19 08:50:15,533] [INFO] Running command: hmmsearch --tblout GCA_018623125.1_ASM1862312v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c21b456-719f-43c5-a0da-23b137ae2368/dqc_reference/reference_markers.hmm GCA_018623125.1_ASM1862312v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:50:15,667] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:50:15,668] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg7730f18e-a6ba-47af-b9c7-9140d56f638d/GCA_018623125.1_ASM1862312v1_genomic.fna.gz]
[2023-06-19 08:50:15,685] [INFO] Query marker FASTA was written to GCA_018623125.1_ASM1862312v1_genomic.fna/markers.fasta
[2023-06-19 08:50:15,686] [INFO] Task started: Blastn
[2023-06-19 08:50:15,686] [INFO] Running command: blastn -query GCA_018623125.1_ASM1862312v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c21b456-719f-43c5-a0da-23b137ae2368/dqc_reference/reference_markers.fasta -out GCA_018623125.1_ASM1862312v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:50:16,164] [INFO] Task succeeded: Blastn
[2023-06-19 08:50:16,167] [INFO] Selected 10 target genomes.
[2023-06-19 08:50:16,168] [INFO] Target genome list was writen to GCA_018623125.1_ASM1862312v1_genomic.fna/target_genomes.txt
[2023-06-19 08:50:16,169] [INFO] Task started: fastANI
[2023-06-19 08:50:16,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg7730f18e-a6ba-47af-b9c7-9140d56f638d/GCA_018623125.1_ASM1862312v1_genomic.fna.gz --refList GCA_018623125.1_ASM1862312v1_genomic.fna/target_genomes.txt --output GCA_018623125.1_ASM1862312v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:50:24,558] [INFO] Task succeeded: fastANI
[2023-06-19 08:50:24,559] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c21b456-719f-43c5-a0da-23b137ae2368/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:50:24,559] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c21b456-719f-43c5-a0da-23b137ae2368/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:50:24,562] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:50:24,562] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 08:50:24,563] [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	86.8848	297	305	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 08:50:24,564] [INFO] DFAST Taxonomy check result was written to GCA_018623125.1_ASM1862312v1_genomic.fna/tc_result.tsv
[2023-06-19 08:50:24,565] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:50:24,565] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:50:24,565] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c21b456-719f-43c5-a0da-23b137ae2368/dqc_reference/checkm_data
[2023-06-19 08:50:24,566] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:50:24,582] [INFO] Task started: CheckM
[2023-06-19 08:50:24,583] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018623125.1_ASM1862312v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018623125.1_ASM1862312v1_genomic.fna/checkm_input GCA_018623125.1_ASM1862312v1_genomic.fna/checkm_result
[2023-06-19 08:50:51,006] [INFO] Task succeeded: CheckM
[2023-06-19 08:50:51,009] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.23%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:50:51,029] [INFO] ===== Completeness check finished =====
[2023-06-19 08:50:51,029] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:50:51,029] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018623125.1_ASM1862312v1_genomic.fna/markers.fasta)
[2023-06-19 08:50:51,030] [INFO] Task started: Blastn
[2023-06-19 08:50:51,030] [INFO] Running command: blastn -query GCA_018623125.1_ASM1862312v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c21b456-719f-43c5-a0da-23b137ae2368/dqc_reference/reference_markers_gtdb.fasta -out GCA_018623125.1_ASM1862312v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:50:51,460] [INFO] Task succeeded: Blastn
[2023-06-19 08:50:51,470] [INFO] Selected 6 target genomes.
[2023-06-19 08:50:51,470] [INFO] Target genome list was writen to GCA_018623125.1_ASM1862312v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:50:51,475] [INFO] Task started: fastANI
[2023-06-19 08:50:51,475] [INFO] Running command: fastANI --query /var/lib/cwl/stg7730f18e-a6ba-47af-b9c7-9140d56f638d/GCA_018623125.1_ASM1862312v1_genomic.fna.gz --refList GCA_018623125.1_ASM1862312v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018623125.1_ASM1862312v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:50:53,842] [INFO] Task succeeded: fastANI
[2023-06-19 08:50:53,850] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:50:53,850] [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_014280175.1	s__Synechococcus_E sp004212765	96.9567	296	305	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	98.21	96.96	0.98	0.97	4	conclusive
GCF_014280195.1	s__Synechococcus_E sp014280195	86.9793	294	305	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_000195975.1	s__Synechococcus_E sp000195975	86.8848	297	305	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	98.37	97.74	0.92	0.91	7	-
GCA_003211535.1	s__Synechococcus_E sp003211535	85.4694	239	305	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_002170825.1	s__Synechococcus_E sp002170825	80.4409	166	305	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Synechococcus_E	95.0	98.06	98.06	0.77	0.77	2	-
GCF_000737535.1	s__Synechococcus_E sp000737535	78.6624	164	305	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	-
--------------------------------------------------------------------------------
[2023-06-19 08:50:53,852] [INFO] GTDB search result was written to GCA_018623125.1_ASM1862312v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:50:53,852] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:50:53,857] [INFO] DFAST_QC result json was written to GCA_018623125.1_ASM1862312v1_genomic.fna/dqc_result.json
[2023-06-19 08:50:53,857] [INFO] DFAST_QC completed!
[2023-06-19 08:50:53,858] [INFO] Total running time: 0h0m47s