[2023-06-05 13:01:17,651] [INFO] DFAST_QC pipeline started.
[2023-06-05 13:01:17,653] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 13:01:17,653] [INFO] DQC Reference Directory: /var/lib/cwl/stga445dee6-3060-4d46-944a-50fa6c6ccb70/dqc_reference
[2023-06-05 13:01:18,807] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 13:01:18,808] [INFO] Task started: Prodigal
[2023-06-05 13:01:18,808] [INFO] Running command: gunzip -c /var/lib/cwl/stgdbb541be-0b80-4f20-ac38-b27e96b8055c/GCA_902529355.1_AG-896-N09_genomic.fna.gz | prodigal -d GCA_902529355.1_AG-896-N09_genomic.fna/cds.fna -a GCA_902529355.1_AG-896-N09_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 13:01:21,225] [INFO] Task succeeded: Prodigal
[2023-06-05 13:01:21,226] [INFO] Task started: HMMsearch
[2023-06-05 13:01:21,226] [INFO] Running command: hmmsearch --tblout GCA_902529355.1_AG-896-N09_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga445dee6-3060-4d46-944a-50fa6c6ccb70/dqc_reference/reference_markers.hmm GCA_902529355.1_AG-896-N09_genomic.fna/protein.faa > /dev/null
[2023-06-05 13:01:21,409] [INFO] Task succeeded: HMMsearch
[2023-06-05 13:01:21,411] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgdbb541be-0b80-4f20-ac38-b27e96b8055c/GCA_902529355.1_AG-896-N09_genomic.fna.gz]
[2023-06-05 13:01:21,428] [INFO] Query marker FASTA was written to GCA_902529355.1_AG-896-N09_genomic.fna/markers.fasta
[2023-06-05 13:01:21,429] [INFO] Task started: Blastn
[2023-06-05 13:01:21,429] [INFO] Running command: blastn -query GCA_902529355.1_AG-896-N09_genomic.fna/markers.fasta -db /var/lib/cwl/stga445dee6-3060-4d46-944a-50fa6c6ccb70/dqc_reference/reference_markers.fasta -out GCA_902529355.1_AG-896-N09_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:01:21,898] [INFO] Task succeeded: Blastn
[2023-06-05 13:01:21,903] [INFO] Selected 5 target genomes.
[2023-06-05 13:01:21,903] [INFO] Target genome list was writen to GCA_902529355.1_AG-896-N09_genomic.fna/target_genomes.txt
[2023-06-05 13:01:21,906] [INFO] Task started: fastANI
[2023-06-05 13:01:21,906] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbb541be-0b80-4f20-ac38-b27e96b8055c/GCA_902529355.1_AG-896-N09_genomic.fna.gz --refList GCA_902529355.1_AG-896-N09_genomic.fna/target_genomes.txt --output GCA_902529355.1_AG-896-N09_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 13:01:24,549] [INFO] Task succeeded: fastANI
[2023-06-05 13:01:24,550] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga445dee6-3060-4d46-944a-50fa6c6ccb70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 13:01:24,551] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga445dee6-3060-4d46-944a-50fa6c6ccb70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 13:01:24,553] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 13:01:24,553] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 13:01:24,553] [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
--------------------------------------------------------------------------------
[2023-06-05 13:01:24,556] [INFO] DFAST Taxonomy check result was written to GCA_902529355.1_AG-896-N09_genomic.fna/tc_result.tsv
[2023-06-05 13:01:24,556] [INFO] ===== Taxonomy check completed =====
[2023-06-05 13:01:24,557] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 13:01:24,557] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga445dee6-3060-4d46-944a-50fa6c6ccb70/dqc_reference/checkm_data
[2023-06-05 13:01:24,561] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 13:01:24,577] [INFO] Task started: CheckM
[2023-06-05 13:01:24,578] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902529355.1_AG-896-N09_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902529355.1_AG-896-N09_genomic.fna/checkm_input GCA_902529355.1_AG-896-N09_genomic.fna/checkm_result
[2023-06-05 13:01:39,563] [INFO] Task succeeded: CheckM
[2023-06-05 13:01:39,565] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.61%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 13:01:39,586] [INFO] ===== Completeness check finished =====
[2023-06-05 13:01:39,586] [INFO] ===== Start GTDB Search =====
[2023-06-05 13:01:39,586] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902529355.1_AG-896-N09_genomic.fna/markers.fasta)
[2023-06-05 13:01:39,587] [INFO] Task started: Blastn
[2023-06-05 13:01:39,587] [INFO] Running command: blastn -query GCA_902529355.1_AG-896-N09_genomic.fna/markers.fasta -db /var/lib/cwl/stga445dee6-3060-4d46-944a-50fa6c6ccb70/dqc_reference/reference_markers_gtdb.fasta -out GCA_902529355.1_AG-896-N09_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:01:40,000] [INFO] Task succeeded: Blastn
[2023-06-05 13:01:40,004] [INFO] Selected 5 target genomes.
[2023-06-05 13:01:40,004] [INFO] Target genome list was writen to GCA_902529355.1_AG-896-N09_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 13:01:40,033] [INFO] Task started: fastANI
[2023-06-05 13:01:40,033] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbb541be-0b80-4f20-ac38-b27e96b8055c/GCA_902529355.1_AG-896-N09_genomic.fna.gz --refList GCA_902529355.1_AG-896-N09_genomic.fna/target_genomes_gtdb.txt --output GCA_902529355.1_AG-896-N09_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 13:01:41,472] [INFO] Task succeeded: fastANI
[2023-06-05 13:01:41,481] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 13:01:41,482] [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_002026165.1	s__Prochlorococcus_A sp002026165	92.4353	184	270	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902571335.1	s__Prochlorococcus_A sp902571335	92.4306	200	270	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003216535.1	s__Prochlorococcus_A sp003216535	92.1334	227	270	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003214235.1	s__Prochlorococcus_A sp003214235	88.9975	165	270	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000759855.1	s__Prochlorococcus_A marinus_N	88.5025	218	270	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Prochlorococcus_A	95.0	99.96	99.95	0.99	0.98	3	-
--------------------------------------------------------------------------------
[2023-06-05 13:01:41,484] [INFO] GTDB search result was written to GCA_902529355.1_AG-896-N09_genomic.fna/result_gtdb.tsv
[2023-06-05 13:01:41,485] [INFO] ===== GTDB Search completed =====
[2023-06-05 13:01:41,488] [INFO] DFAST_QC result json was written to GCA_902529355.1_AG-896-N09_genomic.fna/dqc_result.json
[2023-06-05 13:01:41,489] [INFO] DFAST_QC completed!
[2023-06-05 13:01:41,489] [INFO] Total running time: 0h0m24s