[2024-01-25 18:41:05,905] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:41:05,906] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:41:05,906] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c9c7ce0-e2e6-4ac2-b012-fb74306f4ce6/dqc_reference
[2024-01-25 18:41:06,986] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:41:06,987] [INFO] Task started: Prodigal
[2024-01-25 18:41:06,987] [INFO] Running command: gunzip -c /var/lib/cwl/stg24b065ce-6659-484c-8617-926a076f0172/GCF_026802175.1_ASM2680217v1_genomic.fna.gz | prodigal -d GCF_026802175.1_ASM2680217v1_genomic.fna/cds.fna -a GCF_026802175.1_ASM2680217v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:41:20,409] [INFO] Task succeeded: Prodigal
[2024-01-25 18:41:20,409] [INFO] Task started: HMMsearch
[2024-01-25 18:41:20,409] [INFO] Running command: hmmsearch --tblout GCF_026802175.1_ASM2680217v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c9c7ce0-e2e6-4ac2-b012-fb74306f4ce6/dqc_reference/reference_markers.hmm GCF_026802175.1_ASM2680217v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:41:20,779] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:41:20,780] [INFO] Found 6/6 markers.
[2024-01-25 18:41:20,826] [INFO] Query marker FASTA was written to GCF_026802175.1_ASM2680217v1_genomic.fna/markers.fasta
[2024-01-25 18:41:20,827] [INFO] Task started: Blastn
[2024-01-25 18:41:20,827] [INFO] Running command: blastn -query GCF_026802175.1_ASM2680217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c9c7ce0-e2e6-4ac2-b012-fb74306f4ce6/dqc_reference/reference_markers.fasta -out GCF_026802175.1_ASM2680217v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:21,355] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:21,357] [INFO] Selected 22 target genomes.
[2024-01-25 18:41:21,358] [INFO] Target genome list was writen to GCF_026802175.1_ASM2680217v1_genomic.fna/target_genomes.txt
[2024-01-25 18:41:21,364] [INFO] Task started: fastANI
[2024-01-25 18:41:21,364] [INFO] Running command: fastANI --query /var/lib/cwl/stg24b065ce-6659-484c-8617-926a076f0172/GCF_026802175.1_ASM2680217v1_genomic.fna.gz --refList GCF_026802175.1_ASM2680217v1_genomic.fna/target_genomes.txt --output GCF_026802175.1_ASM2680217v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:41:40,611] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:40,611] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c9c7ce0-e2e6-4ac2-b012-fb74306f4ce6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:41:40,611] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c9c7ce0-e2e6-4ac2-b012-fb74306f4ce6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:41:40,617] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:41:40,617] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:41:40,617] [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
Leptodesmis sichuanensis	strain=PKUAC-SCTA121	GCA_021379005.1	2906798	2906798	type	True	77.8945	91	1936	95	below_threshold
Thermoleptolyngbya sichuanensis	strain=PKUAC-SCTA183	GCA_013177315.1	2885951	2885951	type	True	77.1427	119	1936	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_000317285.1	1124	1124	type	True	76.0983	56	1936	95	below_threshold
Oscillatoria acuminata	strain=PCC 6304	GCA_000317105.1	118323	118323	type	True	75.9875	63	1936	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_003990575.1	1124	1124	type	True	75.8712	57	1936	95	below_threshold
Iningainema tapete	strain=BLCC-T55	GCA_014698965.1	2806730	2806730	type	True	75.5271	52	1936	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:41:40,619] [INFO] DFAST Taxonomy check result was written to GCF_026802175.1_ASM2680217v1_genomic.fna/tc_result.tsv
[2024-01-25 18:41:40,619] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:41:40,619] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:41:40,619] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c9c7ce0-e2e6-4ac2-b012-fb74306f4ce6/dqc_reference/checkm_data
[2024-01-25 18:41:40,620] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:41:40,677] [INFO] Task started: CheckM
[2024-01-25 18:41:40,677] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026802175.1_ASM2680217v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026802175.1_ASM2680217v1_genomic.fna/checkm_input GCF_026802175.1_ASM2680217v1_genomic.fna/checkm_result
[2024-01-25 18:42:22,990] [INFO] Task succeeded: CheckM
[2024-01-25 18:42:22,991] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:42:23,007] [INFO] ===== Completeness check finished =====
[2024-01-25 18:42:23,008] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:42:23,008] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026802175.1_ASM2680217v1_genomic.fna/markers.fasta)
[2024-01-25 18:42:23,009] [INFO] Task started: Blastn
[2024-01-25 18:42:23,009] [INFO] Running command: blastn -query GCF_026802175.1_ASM2680217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c9c7ce0-e2e6-4ac2-b012-fb74306f4ce6/dqc_reference/reference_markers_gtdb.fasta -out GCF_026802175.1_ASM2680217v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:42:23,785] [INFO] Task succeeded: Blastn
[2024-01-25 18:42:23,788] [INFO] Selected 26 target genomes.
[2024-01-25 18:42:23,789] [INFO] Target genome list was writen to GCF_026802175.1_ASM2680217v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:42:23,806] [INFO] Task started: fastANI
[2024-01-25 18:42:23,806] [INFO] Running command: fastANI --query /var/lib/cwl/stg24b065ce-6659-484c-8617-926a076f0172/GCF_026802175.1_ASM2680217v1_genomic.fna.gz --refList GCF_026802175.1_ASM2680217v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026802175.1_ASM2680217v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:42:50,319] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:50,331] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:42:50,332] [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
GCA_003003615.1	s__CCP2 sp003003615	77.338	266	1936	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__CCP2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016807185.1	s__ULC077BIN1 sp016807185	76.6683	81	1936	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__ULC077BIN1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000733415.1	s__Elainella sp000733415	76.443	184	1936	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__Elainella	95.0	96.63	96.48	0.89	0.88	3	-
GCF_002215035.1	s__Leptolyngbya_A ohadii	76.4042	148	1936	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__Leptolyngbya_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012033255.1	s__JAAUSF01 sp012033255	76.3284	186	1936	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__JAAUSF01	95.0	99.58	99.58	0.90	0.90	2	-
GCA_012033495.1	s__Elainella sp012033495	76.1805	149	1936	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__Elainella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015207395.1	s__Nodosilinea sp015207395	76.1618	57	1936	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241845.1	s__Nodosilinea antarctica	76.1605	54	1936	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	98.34	98.34	0.86	0.86	2	-
GCA_012032525.1	s__JAAUSV01 sp012032525	76.1372	81	1936	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__JAAUSV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016208305.1	s__JAAUOQ01 sp016208305	76.1078	123	1936	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__JAAUOQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317285.1	s__Chlorogloeopsis fritschii	76.0474	58	1936	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Chlorogloeopsis	95.0	99.29	97.93	0.97	0.93	4	-
GCA_012034615.1	s__JAAUPA01 sp012034615	76.006	83	1936	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__JAAUPA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014695325.1	s__Leptolyngbya_A sp014695325	75.9062	138	1936	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__Leptolyngbya_A	95.0	99.45	99.45	0.94	0.94	2	-
GCA_014695345.1	s__JAAUTN01 sp014695345	75.8947	111	1936	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__JAAUTN01	95.0	97.27	96.86	0.89	0.88	4	-
GCA_016743235.1	s__Pantanalinema sp016743235	75.7135	97	1936	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__Pantanalinema	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012031475.1	s__JAAUTJ01 sp012031475	75.4962	62	1936	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__JAAUTJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014380065.1	s__Stenomitos sp014380065	75.4764	66	1936	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__Stenomitos	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015272155.1	s__JACYME01 sp015272155	75.2636	51	1936	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__JACYME01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:42:50,340] [INFO] GTDB search result was written to GCF_026802175.1_ASM2680217v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:42:50,341] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:42:50,343] [INFO] DFAST_QC result json was written to GCF_026802175.1_ASM2680217v1_genomic.fna/dqc_result.json
[2024-01-25 18:42:50,344] [INFO] DFAST_QC completed!
[2024-01-25 18:42:50,344] [INFO] Total running time: 0h1m44s