[2023-06-05 12:50:10,010] [INFO] DFAST_QC pipeline started.
[2023-06-05 12:50:10,012] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 12:50:10,013] [INFO] DQC Reference Directory: /var/lib/cwl/stg4584430d-9508-4d64-a54f-b052f60e9fcb/dqc_reference
[2023-06-05 12:50:11,242] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 12:50:11,243] [INFO] Task started: Prodigal
[2023-06-05 12:50:11,243] [INFO] Running command: gunzip -c /var/lib/cwl/stge9a3bfea-82fd-4ee5-a43b-6fe4a35604ad/GCA_010692585.1_ASM1069258v1_genomic.fna.gz | prodigal -d GCA_010692585.1_ASM1069258v1_genomic.fna/cds.fna -a GCA_010692585.1_ASM1069258v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 12:50:25,308] [INFO] Task succeeded: Prodigal
[2023-06-05 12:50:25,309] [INFO] Task started: HMMsearch
[2023-06-05 12:50:25,309] [INFO] Running command: hmmsearch --tblout GCA_010692585.1_ASM1069258v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4584430d-9508-4d64-a54f-b052f60e9fcb/dqc_reference/reference_markers.hmm GCA_010692585.1_ASM1069258v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 12:50:25,691] [INFO] Task succeeded: HMMsearch
[2023-06-05 12:50:25,693] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge9a3bfea-82fd-4ee5-a43b-6fe4a35604ad/GCA_010692585.1_ASM1069258v1_genomic.fna.gz]
[2023-06-05 12:50:25,762] [INFO] Query marker FASTA was written to GCA_010692585.1_ASM1069258v1_genomic.fna/markers.fasta
[2023-06-05 12:50:25,763] [INFO] Task started: Blastn
[2023-06-05 12:50:25,763] [INFO] Running command: blastn -query GCA_010692585.1_ASM1069258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4584430d-9508-4d64-a54f-b052f60e9fcb/dqc_reference/reference_markers.fasta -out GCA_010692585.1_ASM1069258v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:50:26,350] [INFO] Task succeeded: Blastn
[2023-06-05 12:50:26,354] [INFO] Selected 10 target genomes.
[2023-06-05 12:50:26,355] [INFO] Target genome list was writen to GCA_010692585.1_ASM1069258v1_genomic.fna/target_genomes.txt
[2023-06-05 12:50:26,357] [INFO] Task started: fastANI
[2023-06-05 12:50:26,358] [INFO] Running command: fastANI --query /var/lib/cwl/stge9a3bfea-82fd-4ee5-a43b-6fe4a35604ad/GCA_010692585.1_ASM1069258v1_genomic.fna.gz --refList GCA_010692585.1_ASM1069258v1_genomic.fna/target_genomes.txt --output GCA_010692585.1_ASM1069258v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 12:50:39,501] [INFO] Task succeeded: fastANI
[2023-06-05 12:50:39,502] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4584430d-9508-4d64-a54f-b052f60e9fcb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 12:50:39,503] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4584430d-9508-4d64-a54f-b052f60e9fcb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 12:50:39,511] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2023-06-05 12:50:39,512] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-05 12:50:39,512] [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
Okeania hirsuta	strain=PAB10Feb10-1	GCA_003838195.1	1458930	1458930	type	True	96.2262	913	1103	95	conclusive
Limnospira indica	strain=PCC 8005	GCA_000973065.1	147322	147322	type	True	75.7311	59	1103	95	below_threshold
Limnospira indica	strain=PCC 8005	GCA_000176895.2	147322	147322	type	True	75.4413	59	1103	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_003990575.1	1124	1124	type	True	75.2336	50	1103	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 12:50:39,514] [INFO] DFAST Taxonomy check result was written to GCA_010692585.1_ASM1069258v1_genomic.fna/tc_result.tsv
[2023-06-05 12:50:39,515] [INFO] ===== Taxonomy check completed =====
[2023-06-05 12:50:39,516] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 12:50:39,516] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4584430d-9508-4d64-a54f-b052f60e9fcb/dqc_reference/checkm_data
[2023-06-05 12:50:39,518] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 12:50:39,612] [INFO] Task started: CheckM
[2023-06-05 12:50:39,613] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_010692585.1_ASM1069258v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_010692585.1_ASM1069258v1_genomic.fna/checkm_input GCA_010692585.1_ASM1069258v1_genomic.fna/checkm_result
[2023-06-05 12:51:26,304] [INFO] Task succeeded: CheckM
[2023-06-05 12:51:26,306] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.42%
Contamintation: 31.90%
Strain heterogeneity: 29.63%
--------------------------------------------------------------------------------
[2023-06-05 12:51:26,346] [INFO] ===== Completeness check finished =====
[2023-06-05 12:51:26,346] [INFO] ===== Start GTDB Search =====
[2023-06-05 12:51:26,348] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_010692585.1_ASM1069258v1_genomic.fna/markers.fasta)
[2023-06-05 12:51:26,348] [INFO] Task started: Blastn
[2023-06-05 12:51:26,348] [INFO] Running command: blastn -query GCA_010692585.1_ASM1069258v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4584430d-9508-4d64-a54f-b052f60e9fcb/dqc_reference/reference_markers_gtdb.fasta -out GCA_010692585.1_ASM1069258v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:51:27,217] [INFO] Task succeeded: Blastn
[2023-06-05 12:51:27,223] [INFO] Selected 17 target genomes.
[2023-06-05 12:51:27,223] [INFO] Target genome list was writen to GCA_010692585.1_ASM1069258v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 12:51:27,252] [INFO] Task started: fastANI
[2023-06-05 12:51:27,252] [INFO] Running command: fastANI --query /var/lib/cwl/stge9a3bfea-82fd-4ee5-a43b-6fe4a35604ad/GCA_010692585.1_ASM1069258v1_genomic.fna.gz --refList GCA_010692585.1_ASM1069258v1_genomic.fna/target_genomes_gtdb.txt --output GCA_010692585.1_ASM1069258v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 12:52:09,639] [INFO] Task succeeded: fastANI
[2023-06-05 12:52:09,648] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 12:52:09,649] [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_003838195.1	s__Okeania hirsuta	96.269	911	1103	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Okeania	95.0	98.05	95.33	0.88	0.84	10	conclusive
GCA_010672455.1	s__Okeania sp010672455	91.5845	926	1103	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Okeania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010672585.1	s__Okeania sp010672585	90.5978	890	1103	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Okeania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010672525.1	s__Okeania sp010672525	90.4764	891	1103	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Okeania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014132355.1	s__Okeania sp014132355	89.7348	875	1103	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Okeania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010692555.1	s__Okeania sp010692555	89.2471	889	1103	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Okeania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010672085.1	s__Trichodesmium sp010672085	82.2986	822	1103	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Trichodesmium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900009135.1	s__Planktothrix sp900009135	75.9393	55	1103	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Planktothrix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 12:52:09,653] [INFO] GTDB search result was written to GCA_010692585.1_ASM1069258v1_genomic.fna/result_gtdb.tsv
[2023-06-05 12:52:09,653] [INFO] ===== GTDB Search completed =====
[2023-06-05 12:52:09,657] [INFO] DFAST_QC result json was written to GCA_010692585.1_ASM1069258v1_genomic.fna/dqc_result.json
[2023-06-05 12:52:09,657] [INFO] DFAST_QC completed!
[2023-06-05 12:52:09,657] [INFO] Total running time: 0h1m60s