[2024-01-24 13:19:01,360] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:01,363] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:01,364] [INFO] DQC Reference Directory: /var/lib/cwl/stgf8203ec8-7e08-40b1-a84a-509993a9dc53/dqc_reference
[2024-01-24 13:19:02,724] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:02,725] [INFO] Task started: Prodigal
[2024-01-24 13:19:02,725] [INFO] Running command: gunzip -c /var/lib/cwl/stg21861107-7683-4d3d-8653-864b5268d6a5/GCF_007904085.1_ASM790408v1_genomic.fna.gz | prodigal -d GCF_007904085.1_ASM790408v1_genomic.fna/cds.fna -a GCF_007904085.1_ASM790408v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:09,895] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:09,896] [INFO] Task started: HMMsearch
[2024-01-24 13:19:09,896] [INFO] Running command: hmmsearch --tblout GCF_007904085.1_ASM790408v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf8203ec8-7e08-40b1-a84a-509993a9dc53/dqc_reference/reference_markers.hmm GCF_007904085.1_ASM790408v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:10,224] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:10,231] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg21861107-7683-4d3d-8653-864b5268d6a5/GCF_007904085.1_ASM790408v1_genomic.fna.gz]
[2024-01-24 13:19:10,281] [INFO] Query marker FASTA was written to GCF_007904085.1_ASM790408v1_genomic.fna/markers.fasta
[2024-01-24 13:19:10,281] [INFO] Task started: Blastn
[2024-01-24 13:19:10,281] [INFO] Running command: blastn -query GCF_007904085.1_ASM790408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8203ec8-7e08-40b1-a84a-509993a9dc53/dqc_reference/reference_markers.fasta -out GCF_007904085.1_ASM790408v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:11,016] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:11,019] [INFO] Selected 15 target genomes.
[2024-01-24 13:19:11,020] [INFO] Target genome list was writen to GCF_007904085.1_ASM790408v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:11,044] [INFO] Task started: fastANI
[2024-01-24 13:19:11,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg21861107-7683-4d3d-8653-864b5268d6a5/GCF_007904085.1_ASM790408v1_genomic.fna.gz --refList GCF_007904085.1_ASM790408v1_genomic.fna/target_genomes.txt --output GCF_007904085.1_ASM790408v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:26,659] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:26,659] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf8203ec8-7e08-40b1-a84a-509993a9dc53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:26,660] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf8203ec8-7e08-40b1-a84a-509993a9dc53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:26,667] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:26,667] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:26,668] [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
Euhalothece natronophila	strain=Z-M001	GCA_007904085.1	577489	577489	type	True	100.0	1169	1172	95	conclusive
Dactylococcopsis salina	strain=PCC 8305	GCA_000317615.1	292566	292566	type	True	78.54	408	1172	95	below_threshold
Planktothrix agardhii	strain=NIES-204	GCA_003609755.1	1160	1160	type	True	76.5475	59	1172	95	below_threshold
Anabaena cylindrica	strain=PCC 7122	GCA_000317695.1	1165	1165	type	True	75.8838	52	1172	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	75.8818	52	1172	95	below_threshold
Planktothrix tepida	strain=PCC9214	GCA_904830955.1	1678309	1678309	type	True	75.6163	73	1172	95	below_threshold
Fischerella muscicola	strain=PCC 7414	GCA_000317205.1	92938	92938	type	True	75.1587	54	1172	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:26,669] [INFO] DFAST Taxonomy check result was written to GCF_007904085.1_ASM790408v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:26,670] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:26,670] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:26,670] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf8203ec8-7e08-40b1-a84a-509993a9dc53/dqc_reference/checkm_data
[2024-01-24 13:19:26,671] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:26,711] [INFO] Task started: CheckM
[2024-01-24 13:19:26,711] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007904085.1_ASM790408v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007904085.1_ASM790408v1_genomic.fna/checkm_input GCF_007904085.1_ASM790408v1_genomic.fna/checkm_result
[2024-01-24 13:19:55,609] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:55,610] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:55,648] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:55,648] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:55,649] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007904085.1_ASM790408v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:55,649] [INFO] Task started: Blastn
[2024-01-24 13:19:55,649] [INFO] Running command: blastn -query GCF_007904085.1_ASM790408v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8203ec8-7e08-40b1-a84a-509993a9dc53/dqc_reference/reference_markers_gtdb.fasta -out GCF_007904085.1_ASM790408v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:56,621] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:56,624] [INFO] Selected 19 target genomes.
[2024-01-24 13:19:56,624] [INFO] Target genome list was writen to GCF_007904085.1_ASM790408v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:56,694] [INFO] Task started: fastANI
[2024-01-24 13:19:56,695] [INFO] Running command: fastANI --query /var/lib/cwl/stg21861107-7683-4d3d-8653-864b5268d6a5/GCF_007904085.1_ASM790408v1_genomic.fna.gz --refList GCF_007904085.1_ASM790408v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007904085.1_ASM790408v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:16,648] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:16,663] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:16,663] [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_007904085.1	s__Halothece natronophila	100.0	1169	1172	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Rubidibacteraceae;g__Halothece	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000317615.1	s__Halothece salina	78.5508	409	1172	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Rubidibacteraceae;g__Halothece	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317635.1	s__Halothece sp000317635	78.3353	473	1172	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Rubidibacteraceae;g__Halothece	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009909085.1	s__Halothece sp009909085	77.7814	382	1172	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Rubidibacteraceae;g__Halothece	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021905.1	s__Halothece sp003021905	77.1375	311	1172	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Rubidibacteraceae;g__Halothece	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900009275.2	s__Planktothrix rubescens	76.0475	65	1172	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Planktothrix	96.6657	98.32	97.64	0.92	0.88	11	-
GCA_002110465.1	s__Rippkaea sp002110465	75.9122	66	1172	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Rippkaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001298445.1	s__Nostoc_B piscinale	75.5014	69	1172	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698045.1	s__Nostoc_B sp014698045	75.3485	56	1172	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc_B	95.0	98.36	98.34	0.86	0.85	4	-
GCF_014698475.1	s__Nostoc_B spongiaeforme	75.1313	52	1172	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc_B	95.0	97.27	97.27	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:16,664] [INFO] GTDB search result was written to GCF_007904085.1_ASM790408v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:16,665] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:16,667] [INFO] DFAST_QC result json was written to GCF_007904085.1_ASM790408v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:16,668] [INFO] DFAST_QC completed!
[2024-01-24 13:20:16,668] [INFO] Total running time: 0h1m15s