[2023-07-01 01:12:38,033] [INFO] DFAST_QC pipeline started.
[2023-07-01 01:12:38,053] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 01:12:38,054] [INFO] DQC Reference Directory: /var/lib/cwl/stgba0ebdcc-57d2-4f8c-9402-89d8af55678a/dqc_reference
[2023-07-01 01:12:39,465] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 01:12:39,466] [INFO] Task started: Prodigal
[2023-07-01 01:12:39,466] [INFO] Running command: gunzip -c /var/lib/cwl/stg99bcfb6d-925c-4029-98b4-ec7c1e6c218d/GCA_025194985.1_ASM2519498v1_genomic.fna.gz | prodigal -d GCA_025194985.1_ASM2519498v1_genomic.fna/cds.fna -a GCA_025194985.1_ASM2519498v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 01:12:56,739] [INFO] Task succeeded: Prodigal
[2023-07-01 01:12:56,739] [INFO] Task started: HMMsearch
[2023-07-01 01:12:56,740] [INFO] Running command: hmmsearch --tblout GCA_025194985.1_ASM2519498v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba0ebdcc-57d2-4f8c-9402-89d8af55678a/dqc_reference/reference_markers.hmm GCA_025194985.1_ASM2519498v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 01:12:57,115] [INFO] Task succeeded: HMMsearch
[2023-07-01 01:12:57,117] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg99bcfb6d-925c-4029-98b4-ec7c1e6c218d/GCA_025194985.1_ASM2519498v1_genomic.fna.gz]
[2023-07-01 01:12:57,167] [INFO] Query marker FASTA was written to GCA_025194985.1_ASM2519498v1_genomic.fna/markers.fasta
[2023-07-01 01:12:57,167] [INFO] Task started: Blastn
[2023-07-01 01:12:57,167] [INFO] Running command: blastn -query GCA_025194985.1_ASM2519498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba0ebdcc-57d2-4f8c-9402-89d8af55678a/dqc_reference/reference_markers.fasta -out GCA_025194985.1_ASM2519498v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:12:57,966] [INFO] Task succeeded: Blastn
[2023-07-01 01:12:57,969] [INFO] Selected 24 target genomes.
[2023-07-01 01:12:57,970] [INFO] Target genome list was writen to GCA_025194985.1_ASM2519498v1_genomic.fna/target_genomes.txt
[2023-07-01 01:12:57,978] [INFO] Task started: fastANI
[2023-07-01 01:12:57,978] [INFO] Running command: fastANI --query /var/lib/cwl/stg99bcfb6d-925c-4029-98b4-ec7c1e6c218d/GCA_025194985.1_ASM2519498v1_genomic.fna.gz --refList GCA_025194985.1_ASM2519498v1_genomic.fna/target_genomes.txt --output GCA_025194985.1_ASM2519498v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 01:13:15,750] [INFO] Task succeeded: fastANI
[2023-07-01 01:13:15,751] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba0ebdcc-57d2-4f8c-9402-89d8af55678a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 01:13:15,751] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba0ebdcc-57d2-4f8c-9402-89d8af55678a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 01:13:15,757] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 01:13:15,757] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 01:13:15,757] [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
Parasynechococcus marenigrum	strain=WH 8102	GCA_000195975.1	2881428	2881428	type	True	77.8803	213	852	95	below_threshold
Synechococcus lacustris	strain=Tous	GCA_003011125.1	2116544	2116544	suspected-type	True	76.5739	97	852	95	below_threshold
Methylobacterium crusticola	strain=MIMD6	GCA_003574465.1	1697972	1697972	type	True	74.8523	57	852	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 01:13:15,759] [INFO] DFAST Taxonomy check result was written to GCA_025194985.1_ASM2519498v1_genomic.fna/tc_result.tsv
[2023-07-01 01:13:15,760] [INFO] ===== Taxonomy check completed =====
[2023-07-01 01:13:15,760] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 01:13:15,760] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba0ebdcc-57d2-4f8c-9402-89d8af55678a/dqc_reference/checkm_data
[2023-07-01 01:13:15,762] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 01:13:15,794] [INFO] Task started: CheckM
[2023-07-01 01:13:15,794] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025194985.1_ASM2519498v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025194985.1_ASM2519498v1_genomic.fna/checkm_input GCA_025194985.1_ASM2519498v1_genomic.fna/checkm_result
[2023-07-01 01:14:04,427] [INFO] Task succeeded: CheckM
[2023-07-01 01:14:04,428] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 01:14:04,448] [INFO] ===== Completeness check finished =====
[2023-07-01 01:14:04,449] [INFO] ===== Start GTDB Search =====
[2023-07-01 01:14:04,449] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025194985.1_ASM2519498v1_genomic.fna/markers.fasta)
[2023-07-01 01:14:04,449] [INFO] Task started: Blastn
[2023-07-01 01:14:04,449] [INFO] Running command: blastn -query GCA_025194985.1_ASM2519498v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba0ebdcc-57d2-4f8c-9402-89d8af55678a/dqc_reference/reference_markers_gtdb.fasta -out GCA_025194985.1_ASM2519498v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:14:05,338] [INFO] Task succeeded: Blastn
[2023-07-01 01:14:05,343] [INFO] Selected 15 target genomes.
[2023-07-01 01:14:05,343] [INFO] Target genome list was writen to GCA_025194985.1_ASM2519498v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 01:14:05,354] [INFO] Task started: fastANI
[2023-07-01 01:14:05,354] [INFO] Running command: fastANI --query /var/lib/cwl/stg99bcfb6d-925c-4029-98b4-ec7c1e6c218d/GCA_025194985.1_ASM2519498v1_genomic.fna.gz --refList GCA_025194985.1_ASM2519498v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025194985.1_ASM2519498v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 01:14:15,639] [INFO] Task succeeded: fastANI
[2023-07-01 01:14:15,656] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 01:14:15,656] [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_001885215.1	s__QBMD01 sp001885215	99.4674	819	852	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__QBMD01	95.0	99.98	99.98	0.98	0.98	2	conclusive
GCA_013203655.1	s__QBMD01 sp013203655	92.2902	524	852	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__QBMD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003249115.1	s__QBMD01 sp003249115	81.4607	518	852	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__QBMD01	95.0	98.24	98.24	0.84	0.84	2	-
GCF_014224355.1	s__WH-5701 sp014224355	80.6443	512	852	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__WH-5701	95.0	99.99	99.99	0.99	0.99	2	-
GCF_015841355.1	s__WH-5701 sp015841355	80.5729	510	852	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__WH-5701	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252635.1	s__MW101C3 sp002252635	80.545	492	852	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__MW101C3	95.0	97.20	97.20	0.89	0.89	2	-
GCF_002252625.1	s__WH-5701 sp002252625	80.5002	496	852	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__WH-5701	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252675.1	s__Cyanobium sp002252675	80.0657	464	852	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	97.52	95.99	0.91	0.88	5	-
GCA_016882315.1	s__Cyanobium sp016882315	79.9255	439	852	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002252705.1	s__Vulcanococcus limneticus	79.8946	457	852	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019038465.1	s__Cyanobium sp019038465	79.8652	446	852	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016882415.1	s__Vulcanococcus sp016882415	79.7485	213	852	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903917565.1	s__Cyanobium sp903917565	79.5079	439	852	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Cyanobium	95.0	100.00	99.99	0.99	0.98	6	-
GCF_000155635.1	s__NIES-981 sp000155635	79.203	441	852	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__NIES-981	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903934375.1	s__Vulcanococcus sp903934375	79.049	363	852	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-6307;f__Cyanobiaceae;g__Vulcanococcus	95.0	98.96	98.94	0.87	0.87	3	-
--------------------------------------------------------------------------------
[2023-07-01 01:14:15,658] [INFO] GTDB search result was written to GCA_025194985.1_ASM2519498v1_genomic.fna/result_gtdb.tsv
[2023-07-01 01:14:15,659] [INFO] ===== GTDB Search completed =====
[2023-07-01 01:14:15,665] [INFO] DFAST_QC result json was written to GCA_025194985.1_ASM2519498v1_genomic.fna/dqc_result.json
[2023-07-01 01:14:15,665] [INFO] DFAST_QC completed!
[2023-07-01 01:14:15,665] [INFO] Total running time: 0h1m38s