[2024-01-24 13:28:01,813] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:01,815] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:01,815] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d820e65-6cd6-4f74-b055-048691dc9f87/dqc_reference
[2024-01-24 13:28:03,208] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:03,209] [INFO] Task started: Prodigal
[2024-01-24 13:28:03,209] [INFO] Running command: gunzip -c /var/lib/cwl/stg35dcc09f-bb0f-442f-a08c-6680227d2d94/GCF_000353285.1_ASM35328v1_genomic.fna.gz | prodigal -d GCF_000353285.1_ASM35328v1_genomic.fna/cds.fna -a GCF_000353285.1_ASM35328v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:21,426] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:21,427] [INFO] Task started: HMMsearch
[2024-01-24 13:28:21,427] [INFO] Running command: hmmsearch --tblout GCF_000353285.1_ASM35328v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d820e65-6cd6-4f74-b055-048691dc9f87/dqc_reference/reference_markers.hmm GCF_000353285.1_ASM35328v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:21,776] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:21,777] [INFO] Found 6/6 markers.
[2024-01-24 13:28:21,843] [INFO] Query marker FASTA was written to GCF_000353285.1_ASM35328v1_genomic.fna/markers.fasta
[2024-01-24 13:28:21,843] [INFO] Task started: Blastn
[2024-01-24 13:28:21,844] [INFO] Running command: blastn -query GCF_000353285.1_ASM35328v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d820e65-6cd6-4f74-b055-048691dc9f87/dqc_reference/reference_markers.fasta -out GCF_000353285.1_ASM35328v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:22,445] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:22,448] [INFO] Selected 23 target genomes.
[2024-01-24 13:28:22,449] [INFO] Target genome list was writen to GCF_000353285.1_ASM35328v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:22,468] [INFO] Task started: fastANI
[2024-01-24 13:28:22,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg35dcc09f-bb0f-442f-a08c-6680227d2d94/GCF_000353285.1_ASM35328v1_genomic.fna.gz --refList GCF_000353285.1_ASM35328v1_genomic.fna/target_genomes.txt --output GCF_000353285.1_ASM35328v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:43,514] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:43,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d820e65-6cd6-4f74-b055-048691dc9f87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:43,515] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d820e65-6cd6-4f74-b055-048691dc9f87/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:43,522] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:43,522] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:43,522] [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
Leptolyngbya boryana	strain=PCC 6306	GCA_000353285.1	1184	1184	type	True	100.0	2419	2419	95	conclusive
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	76.9275	65	2419	95	below_threshold
Kovacikia minuta	strain=CCNU0001	GCA_020091585.1	2931930	2931930	type	True	76.8732	111	2419	95	below_threshold
Leptothermofonsia sichuanensis	strain=PKUAC-SCTE412	GCA_019891175.1	2917832	2917832	type	True	76.4207	68	2419	95	below_threshold
Allocoleopsis franciscana	strain=PCC 7113	GCA_000317515.1	2886352	2886352	type	True	76.2587	72	2419	95	below_threshold
Leptodesmis sichuanensis	strain=PKUAC-SCTA121	GCA_021379005.1	2906798	2906798	type	True	75.8903	88	2419	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:43,524] [INFO] DFAST Taxonomy check result was written to GCF_000353285.1_ASM35328v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:43,525] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:43,525] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:43,525] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d820e65-6cd6-4f74-b055-048691dc9f87/dqc_reference/checkm_data
[2024-01-24 13:28:43,526] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:43,596] [INFO] Task started: CheckM
[2024-01-24 13:28:43,596] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000353285.1_ASM35328v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000353285.1_ASM35328v1_genomic.fna/checkm_input GCF_000353285.1_ASM35328v1_genomic.fna/checkm_result
[2024-01-24 13:29:39,860] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:39,861] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:39,880] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:39,881] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:39,881] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000353285.1_ASM35328v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:39,881] [INFO] Task started: Blastn
[2024-01-24 13:29:39,881] [INFO] Running command: blastn -query GCF_000353285.1_ASM35328v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d820e65-6cd6-4f74-b055-048691dc9f87/dqc_reference/reference_markers_gtdb.fasta -out GCF_000353285.1_ASM35328v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:40,648] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:40,651] [INFO] Selected 12 target genomes.
[2024-01-24 13:29:40,652] [INFO] Target genome list was writen to GCF_000353285.1_ASM35328v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:40,700] [INFO] Task started: fastANI
[2024-01-24 13:29:40,700] [INFO] Running command: fastANI --query /var/lib/cwl/stg35dcc09f-bb0f-442f-a08c-6680227d2d94/GCF_000353285.1_ASM35328v1_genomic.fna.gz --refList GCF_000353285.1_ASM35328v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000353285.1_ASM35328v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:54,899] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:54,910] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:54,910] [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_000353285.1	s__Leptolyngbya boryana	100.0	2419	2419	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__Leptolyngbya	95.0	99.54	97.95	0.96	0.83	10	conclusive
GCA_014695255.1	s__Leptolyngbya sp014695255	78.8558	712	2419	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__Leptolyngbya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001485215.1	s__Leptolyngbya sp001485215	78.8472	792	2419	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__Leptolyngbya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001548435.1	s__Leptolyngbya sp001548435	78.7639	744	2419	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__Leptolyngbya	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014695195.1	s__Leptolyngbya sp014695195	78.6507	637	2419	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__Leptolyngbya	95.0	97.20	97.20	0.87	0.87	2	-
GCA_016743235.1	s__Pantanalinema sp016743235	76.606	115	2419	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__Pantanalinema	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000309945.1	s__JSC-12 sp000309945	76.3043	71	2419	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__JSC-12	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016208305.1	s__JAAUOQ01 sp016208305	76.2563	91	2419	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__JAAUOQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698505.1	s__Nostoc foliaceum_A	76.0887	53	2419	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	98.20	96.44	0.93	0.87	3	-
GCA_015272515.1	s__JSC-12 sp015272515	76.0643	83	2419	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__JSC-12	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650195.1	s__Phormidesmis_A priestleyi_B	76.0266	155	2419	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__Phormidesmis_A	95.0	98.71	98.71	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:54,912] [INFO] GTDB search result was written to GCF_000353285.1_ASM35328v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:54,912] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:54,916] [INFO] DFAST_QC result json was written to GCF_000353285.1_ASM35328v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:54,916] [INFO] DFAST_QC completed!
[2024-01-24 13:29:54,916] [INFO] Total running time: 0h1m53s