[2023-06-13 03:18:00,453] [INFO] DFAST_QC pipeline started.
[2023-06-13 03:18:00,484] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 03:18:00,484] [INFO] DQC Reference Directory: /var/lib/cwl/stg33255d26-6875-4f3c-8324-0a3074f365dd/dqc_reference
[2023-06-13 03:18:02,757] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 03:18:02,758] [INFO] Task started: Prodigal
[2023-06-13 03:18:02,759] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d7a63e6-2242-44fc-920a-7d013ca7bff5/GCA_022448615.1_ASM2244861v1_genomic.fna.gz | prodigal -d GCA_022448615.1_ASM2244861v1_genomic.fna/cds.fna -a GCA_022448615.1_ASM2244861v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 03:18:12,796] [INFO] Task succeeded: Prodigal
[2023-06-13 03:18:12,796] [INFO] Task started: HMMsearch
[2023-06-13 03:18:12,796] [INFO] Running command: hmmsearch --tblout GCA_022448615.1_ASM2244861v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33255d26-6875-4f3c-8324-0a3074f365dd/dqc_reference/reference_markers.hmm GCA_022448615.1_ASM2244861v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 03:18:13,112] [INFO] Task succeeded: HMMsearch
[2023-06-13 03:18:13,113] [INFO] Found 6/6 markers.
[2023-06-13 03:18:13,156] [INFO] Query marker FASTA was written to GCA_022448615.1_ASM2244861v1_genomic.fna/markers.fasta
[2023-06-13 03:18:13,156] [INFO] Task started: Blastn
[2023-06-13 03:18:13,156] [INFO] Running command: blastn -query GCA_022448615.1_ASM2244861v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33255d26-6875-4f3c-8324-0a3074f365dd/dqc_reference/reference_markers.fasta -out GCA_022448615.1_ASM2244861v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 03:18:13,709] [INFO] Task succeeded: Blastn
[2023-06-13 03:18:13,715] [INFO] Selected 18 target genomes.
[2023-06-13 03:18:13,715] [INFO] Target genome list was writen to GCA_022448615.1_ASM2244861v1_genomic.fna/target_genomes.txt
[2023-06-13 03:18:13,747] [INFO] Task started: fastANI
[2023-06-13 03:18:13,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d7a63e6-2242-44fc-920a-7d013ca7bff5/GCA_022448615.1_ASM2244861v1_genomic.fna.gz --refList GCA_022448615.1_ASM2244861v1_genomic.fna/target_genomes.txt --output GCA_022448615.1_ASM2244861v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 03:18:26,983] [INFO] Task succeeded: fastANI
[2023-06-13 03:18:26,983] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33255d26-6875-4f3c-8324-0a3074f365dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 03:18:26,983] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33255d26-6875-4f3c-8324-0a3074f365dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 03:18:26,992] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 03:18:26,992] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 03:18:26,992] [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	80.8355	1324	2175	95	below_threshold
Crocosphaera watsonii	strain=WH 8501	GCA_000167195.1	263511	263511	suspected-type	True	75.7968	72	2175	95	below_threshold
Crocosphaera chwakensis	strain=CCY0110	GCA_000169335.1	2546361	2546361	type	True	75.4029	89	2175	95	below_threshold
Cylindrospermopsis raciborskii	strain=Cr2010	GCA_003367075.2	77022	77022	reftype	True	75.3624	51	2175	95	below_threshold
Anabaena cylindrica	strain=PCC 7122	GCA_000317695.1	1165	1165	type	True	75.3349	84	2175	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	75.324	85	2175	95	below_threshold
Crocosphaera subtropica	strain=ATCC 51142	GCA_000017845.1	2546360	2546360	type	True	75.2581	70	2175	95	below_threshold
Microcystis aeruginosa	strain=NIES-843	GCA_000010625.1	1126	1126	suspected-type	True	75.164	63	2175	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 03:18:26,994] [INFO] DFAST Taxonomy check result was written to GCA_022448615.1_ASM2244861v1_genomic.fna/tc_result.tsv
[2023-06-13 03:18:26,995] [INFO] ===== Taxonomy check completed =====
[2023-06-13 03:18:26,995] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 03:18:26,995] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33255d26-6875-4f3c-8324-0a3074f365dd/dqc_reference/checkm_data
[2023-06-13 03:18:26,996] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 03:18:27,071] [INFO] Task started: CheckM
[2023-06-13 03:18:27,072] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022448615.1_ASM2244861v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022448615.1_ASM2244861v1_genomic.fna/checkm_input GCA_022448615.1_ASM2244861v1_genomic.fna/checkm_result
[2023-06-13 03:19:01,879] [INFO] Task succeeded: CheckM
[2023-06-13 03:19:01,881] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 03:19:01,904] [INFO] ===== Completeness check finished =====
[2023-06-13 03:19:01,905] [INFO] ===== Start GTDB Search =====
[2023-06-13 03:19:01,906] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022448615.1_ASM2244861v1_genomic.fna/markers.fasta)
[2023-06-13 03:19:01,907] [INFO] Task started: Blastn
[2023-06-13 03:19:01,907] [INFO] Running command: blastn -query GCA_022448615.1_ASM2244861v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33255d26-6875-4f3c-8324-0a3074f365dd/dqc_reference/reference_markers_gtdb.fasta -out GCA_022448615.1_ASM2244861v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 03:19:02,643] [INFO] Task succeeded: Blastn
[2023-06-13 03:19:02,648] [INFO] Selected 8 target genomes.
[2023-06-13 03:19:02,649] [INFO] Target genome list was writen to GCA_022448615.1_ASM2244861v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 03:19:02,667] [INFO] Task started: fastANI
[2023-06-13 03:19:02,667] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d7a63e6-2242-44fc-920a-7d013ca7bff5/GCA_022448615.1_ASM2244861v1_genomic.fna.gz --refList GCA_022448615.1_ASM2244861v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022448615.1_ASM2244861v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 03:19:21,429] [INFO] Task succeeded: fastANI
[2023-06-13 03:19:21,443] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 03:19:21,443] [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_000014265.1	s__Trichodesmium erythraeum	99.3007	2128	2175	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Trichodesmium	95.0	99.96	99.96	0.99	0.99	2	conclusive
GCA_010672085.1	s__Trichodesmium sp010672085	83.9623	1585	2175	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Trichodesmium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003838195.1	s__Okeania hirsuta	80.8787	1315	2175	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Okeania	95.0	98.05	95.33	0.88	0.84	10	-
GCA_010692555.1	s__Okeania sp010692555	80.6587	1377	2175	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Okeania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010672455.1	s__Okeania sp010672455	80.6428	1469	2175	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	80.6293	1389	2175	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	80.6266	1368	2175	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	80.5805	1412	2175	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Okeania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 03:19:21,446] [INFO] GTDB search result was written to GCA_022448615.1_ASM2244861v1_genomic.fna/result_gtdb.tsv
[2023-06-13 03:19:21,446] [INFO] ===== GTDB Search completed =====
[2023-06-13 03:19:21,450] [INFO] DFAST_QC result json was written to GCA_022448615.1_ASM2244861v1_genomic.fna/dqc_result.json
[2023-06-13 03:19:21,450] [INFO] DFAST_QC completed!
[2023-06-13 03:19:21,450] [INFO] Total running time: 0h1m21s