[2024-01-24 11:34:42,005] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:42,009] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:42,009] [INFO] DQC Reference Directory: /var/lib/cwl/stg47d8c892-afb9-4f81-a9c6-dee2e6ae31c3/dqc_reference
[2024-01-24 11:34:43,472] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:43,473] [INFO] Task started: Prodigal
[2024-01-24 11:34:43,474] [INFO] Running command: gunzip -c /var/lib/cwl/stge33de120-5d65-4b3a-9642-0c7821cdb912/GCF_020640915.1_ASM2064091v1_genomic.fna.gz | prodigal -d GCF_020640915.1_ASM2064091v1_genomic.fna/cds.fna -a GCF_020640915.1_ASM2064091v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:52,655] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:52,655] [INFO] Task started: HMMsearch
[2024-01-24 11:34:52,655] [INFO] Running command: hmmsearch --tblout GCF_020640915.1_ASM2064091v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47d8c892-afb9-4f81-a9c6-dee2e6ae31c3/dqc_reference/reference_markers.hmm GCF_020640915.1_ASM2064091v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:53,011] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:53,013] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge33de120-5d65-4b3a-9642-0c7821cdb912/GCF_020640915.1_ASM2064091v1_genomic.fna.gz]
[2024-01-24 11:34:53,068] [INFO] Query marker FASTA was written to GCF_020640915.1_ASM2064091v1_genomic.fna/markers.fasta
[2024-01-24 11:34:53,069] [INFO] Task started: Blastn
[2024-01-24 11:34:53,069] [INFO] Running command: blastn -query GCF_020640915.1_ASM2064091v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47d8c892-afb9-4f81-a9c6-dee2e6ae31c3/dqc_reference/reference_markers.fasta -out GCF_020640915.1_ASM2064091v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:53,689] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:53,692] [INFO] Selected 17 target genomes.
[2024-01-24 11:34:53,692] [INFO] Target genome list was writen to GCF_020640915.1_ASM2064091v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:53,699] [INFO] Task started: fastANI
[2024-01-24 11:34:53,699] [INFO] Running command: fastANI --query /var/lib/cwl/stge33de120-5d65-4b3a-9642-0c7821cdb912/GCF_020640915.1_ASM2064091v1_genomic.fna.gz --refList GCF_020640915.1_ASM2064091v1_genomic.fna/target_genomes.txt --output GCF_020640915.1_ASM2064091v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:08,172] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:08,172] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47d8c892-afb9-4f81-a9c6-dee2e6ae31c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:08,173] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47d8c892-afb9-4f81-a9c6-dee2e6ae31c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:08,180] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:08,180] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:08,181] [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
Waterburya agarophytonicola	strain=KI4	GCA_020640915.1	2886916	2886916	type	True	100.0	1622	1628	95	conclusive
Stanieria cyanosphaera	strain=PCC 7437	GCA_000317575.1	102116	102116	type	True	76.5357	242	1628	95	below_threshold
Gloeothece citriformis	strain=PCC 7424	GCA_000021825.1	2546356	2546356	type	True	75.384	82	1628	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	75.1239	55	1628	95	below_threshold
Anabaena cylindrica	strain=PCC 7122	GCA_000317695.1	1165	1165	type	True	75.1156	55	1628	95	below_threshold
Nostoc favosum	strain=CHAB 5714	GCA_020829495.1	2907819	2907819	type	True	75.0814	51	1628	95	below_threshold
Fischerella thermalis	strain=PCC 7521	GCA_000317225.1	372787	372787	type	True	74.9946	50	1628	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:08,182] [INFO] DFAST Taxonomy check result was written to GCF_020640915.1_ASM2064091v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:08,183] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:08,183] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:08,183] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47d8c892-afb9-4f81-a9c6-dee2e6ae31c3/dqc_reference/checkm_data
[2024-01-24 11:35:08,184] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:08,233] [INFO] Task started: CheckM
[2024-01-24 11:35:08,234] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020640915.1_ASM2064091v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020640915.1_ASM2064091v1_genomic.fna/checkm_input GCF_020640915.1_ASM2064091v1_genomic.fna/checkm_result
[2024-01-24 11:35:41,253] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:41,255] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:41,268] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:41,269] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:41,269] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020640915.1_ASM2064091v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:41,269] [INFO] Task started: Blastn
[2024-01-24 11:35:41,269] [INFO] Running command: blastn -query GCF_020640915.1_ASM2064091v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47d8c892-afb9-4f81-a9c6-dee2e6ae31c3/dqc_reference/reference_markers_gtdb.fasta -out GCF_020640915.1_ASM2064091v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:42,095] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:42,100] [INFO] Selected 14 target genomes.
[2024-01-24 11:35:42,100] [INFO] Target genome list was writen to GCF_020640915.1_ASM2064091v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:42,127] [INFO] Task started: fastANI
[2024-01-24 11:35:42,128] [INFO] Running command: fastANI --query /var/lib/cwl/stge33de120-5d65-4b3a-9642-0c7821cdb912/GCF_020640915.1_ASM2064091v1_genomic.fna.gz --refList GCF_020640915.1_ASM2064091v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020640915.1_ASM2064091v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:56,064] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:56,076] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:35:56,077] [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_015207195.1	s__Pleurocapsa sp015207195	78.3754	540	1628	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000332195.1	s__Pleurocapsa sp000332195	77.9145	580	1628	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003995.1	s__Pleurocapsa sp003003995	77.5792	426	1628	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002368355.1	s__Pleurocapsa sp002368355	77.4761	455	1628	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012034765.1	s__Pleurocapsa sp012034765	77.3897	424	1628	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Pleurocapsa	95.0	99.36	99.13	0.90	0.87	3	-
GCF_900659865.1	s__Hyella patelloides	76.7022	298	1628	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Hyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317575.1	s__Stanieria cyanosphaera	76.5436	241	1628	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Stanieria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932785.1	s__Hyella disjuncta	76.4018	222	1628	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Hyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000332055.1	s__Xenococcus sp000332055	76.2862	146	1628	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__Xenococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169335.1	s__Crocosphaera chwakensis	76.0101	77	1628	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Crocosphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000734895.2	s__Calothrix sp000734895	75.3501	59	1628	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Calothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015207205.1	s__Sphaerospermopsis sp015207205	75.0235	68	1628	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Sphaerospermopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:35:56,078] [INFO] GTDB search result was written to GCF_020640915.1_ASM2064091v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:56,079] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:56,081] [INFO] DFAST_QC result json was written to GCF_020640915.1_ASM2064091v1_genomic.fna/dqc_result.json
[2024-01-24 11:35:56,082] [INFO] DFAST_QC completed!
[2024-01-24 11:35:56,082] [INFO] Total running time: 0h1m14s