[2024-01-24 13:21:10,949] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:10,952] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:10,952] [INFO] DQC Reference Directory: /var/lib/cwl/stg2bdc1da1-f0a7-40a6-bf26-b46c3b87cd24/dqc_reference
[2024-01-24 13:21:12,518] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:12,519] [INFO] Task started: Prodigal
[2024-01-24 13:21:12,520] [INFO] Running command: gunzip -c /var/lib/cwl/stgc2a11e0a-7b70-4bee-bd60-6d192d4324cd/GCF_000332355.1_ASM33235v1_genomic.fna.gz | prodigal -d GCF_000332355.1_ASM33235v1_genomic.fna/cds.fna -a GCF_000332355.1_ASM33235v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:21:28,549] [INFO] Task succeeded: Prodigal
[2024-01-24 13:21:28,550] [INFO] Task started: HMMsearch
[2024-01-24 13:21:28,550] [INFO] Running command: hmmsearch --tblout GCF_000332355.1_ASM33235v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2bdc1da1-f0a7-40a6-bf26-b46c3b87cd24/dqc_reference/reference_markers.hmm GCF_000332355.1_ASM33235v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:21:28,897] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:21:28,899] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc2a11e0a-7b70-4bee-bd60-6d192d4324cd/GCF_000332355.1_ASM33235v1_genomic.fna.gz]
[2024-01-24 13:21:28,950] [INFO] Query marker FASTA was written to GCF_000332355.1_ASM33235v1_genomic.fna/markers.fasta
[2024-01-24 13:21:28,951] [INFO] Task started: Blastn
[2024-01-24 13:21:28,951] [INFO] Running command: blastn -query GCF_000332355.1_ASM33235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bdc1da1-f0a7-40a6-bf26-b46c3b87cd24/dqc_reference/reference_markers.fasta -out GCF_000332355.1_ASM33235v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:29,612] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:29,616] [INFO] Selected 18 target genomes.
[2024-01-24 13:21:29,617] [INFO] Target genome list was writen to GCF_000332355.1_ASM33235v1_genomic.fna/target_genomes.txt
[2024-01-24 13:21:29,640] [INFO] Task started: fastANI
[2024-01-24 13:21:29,640] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2a11e0a-7b70-4bee-bd60-6d192d4324cd/GCF_000332355.1_ASM33235v1_genomic.fna.gz --refList GCF_000332355.1_ASM33235v1_genomic.fna/target_genomes.txt --output GCF_000332355.1_ASM33235v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:21:56,588] [INFO] Task succeeded: fastANI
[2024-01-24 13:21:56,588] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2bdc1da1-f0a7-40a6-bf26-b46c3b87cd24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:21:56,588] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2bdc1da1-f0a7-40a6-bf26-b46c3b87cd24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:21:56,598] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:21:56,598] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:21:56,598] [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
Baaleninema simplex	strain=PCC 7105	GCA_000332355.1	2862350	2862350	type	True	99.9999	2036	2047	95	conclusive
Kovacikia minuta	strain=CCNU0001	GCA_020091585.1	2931930	2931930	type	True	75.8941	52	2047	95	below_threshold
Argonema antarcticum	strain=A004/B2	GCA_023333585.1	2942763	2942763	type	True	75.6791	57	2047	95	below_threshold
Argonema galeatum	strain=A003/A1	GCA_023333595.1	2942762	2942762	type	True	75.5515	70	2047	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:21:56,603] [INFO] DFAST Taxonomy check result was written to GCF_000332355.1_ASM33235v1_genomic.fna/tc_result.tsv
[2024-01-24 13:21:56,604] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:21:56,604] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:21:56,604] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2bdc1da1-f0a7-40a6-bf26-b46c3b87cd24/dqc_reference/checkm_data
[2024-01-24 13:21:56,607] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:21:56,677] [INFO] Task started: CheckM
[2024-01-24 13:21:56,677] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000332355.1_ASM33235v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000332355.1_ASM33235v1_genomic.fna/checkm_input GCF_000332355.1_ASM33235v1_genomic.fna/checkm_result
[2024-01-24 13:22:45,367] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:45,368] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:45,395] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:45,395] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:45,396] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000332355.1_ASM33235v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:45,396] [INFO] Task started: Blastn
[2024-01-24 13:22:45,396] [INFO] Running command: blastn -query GCF_000332355.1_ASM33235v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bdc1da1-f0a7-40a6-bf26-b46c3b87cd24/dqc_reference/reference_markers_gtdb.fasta -out GCF_000332355.1_ASM33235v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:46,221] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:46,225] [INFO] Selected 15 target genomes.
[2024-01-24 13:22:46,225] [INFO] Target genome list was writen to GCF_000332355.1_ASM33235v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:46,253] [INFO] Task started: fastANI
[2024-01-24 13:22:46,253] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2a11e0a-7b70-4bee-bd60-6d192d4324cd/GCF_000332355.1_ASM33235v1_genomic.fna.gz --refList GCF_000332355.1_ASM33235v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000332355.1_ASM33235v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:10,889] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:10,902] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:10,902] [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_000332355.1	s__Geitlerinema sp000332355	99.9999	2037	2047	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__Geitlerinema	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001657325.1	s__Geitlerinema sp001657325	79.0578	814	2047	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__Geitlerinema	95.0	99.83	99.73	0.96	0.95	3	-
GCF_009846485.1	s__Phormidium_A sp009846485	77.6515	259	2047	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__Phormidium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001637315.1	s__Phormidium_A willei_A	77.5456	242	2047	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__Phormidium_A	95.0	95.56	95.56	0.82	0.82	2	-
GCA_004299065.1	s__Phormidium_A sp004299065	77.5329	232	2047	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__Phormidium_A	95.0	99.50	99.50	0.89	0.89	2	-
GCF_012911965.1	s__Phormidium_A sp007126595	77.3477	223	2047	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__Phormidium_A	95.0	99.08	98.97	0.85	0.76	4	-
GCA_001314905.1	s__Phormidium_A sp001314905	77.0826	277	2047	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__Phormidium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693465.1	s__Phormidium_A sp007693465	76.9648	218	2047	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__Phormidium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000972705.2	s__Lyngbya robusta	76.3232	55	2047	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Lyngbya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014697025.1	s__MUGG01 sp014697025	76.261	57	2047	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__MUGG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015207075.1	s__LEGE-11467 sp015207075	76.0533	105	2047	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Geitlerinemaceae;g__LEGE-11467	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014695715.1	s__FACHB-68 sp014695715	75.8213	51	2047	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae_A;g__FACHB-68	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012034575.1	s__Microcoleus sp012034575	75.7329	82	2047	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	98.56	98.27	0.85	0.83	4	-
GCF_000478195.2	s__Lyngbya aestuarii	75.6181	70	2047	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Lyngbya	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012031415.1	s__JAAUTN01 sp012031415	75.4827	61	2047	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__JAAUTN01	95.0	99.26	99.26	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:10,904] [INFO] GTDB search result was written to GCF_000332355.1_ASM33235v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:10,905] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:10,908] [INFO] DFAST_QC result json was written to GCF_000332355.1_ASM33235v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:10,908] [INFO] DFAST_QC completed!
[2024-01-24 13:23:10,908] [INFO] Total running time: 0h1m60s