[2023-06-30 10:57:31,625] [INFO] DFAST_QC pipeline started.
[2023-06-30 10:57:31,627] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 10:57:31,627] [INFO] DQC Reference Directory: /var/lib/cwl/stg77649ebb-a58e-406a-8a86-504c1483291e/dqc_reference
[2023-06-30 10:57:33,379] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 10:57:33,379] [INFO] Task started: Prodigal
[2023-06-30 10:57:33,380] [INFO] Running command: gunzip -c /var/lib/cwl/stg25faf2f3-db9f-4156-aeb5-87043e06ed0c/GCA_024320855.1_ASM2432085v1_genomic.fna.gz | prodigal -d GCA_024320855.1_ASM2432085v1_genomic.fna/cds.fna -a GCA_024320855.1_ASM2432085v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 10:57:41,281] [INFO] Task succeeded: Prodigal
[2023-06-30 10:57:41,281] [INFO] Task started: HMMsearch
[2023-06-30 10:57:41,281] [INFO] Running command: hmmsearch --tblout GCA_024320855.1_ASM2432085v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77649ebb-a58e-406a-8a86-504c1483291e/dqc_reference/reference_markers.hmm GCA_024320855.1_ASM2432085v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 10:57:41,544] [INFO] Task succeeded: HMMsearch
[2023-06-30 10:57:41,545] [INFO] Found 6/6 markers.
[2023-06-30 10:57:41,580] [INFO] Query marker FASTA was written to GCA_024320855.1_ASM2432085v1_genomic.fna/markers.fasta
[2023-06-30 10:57:41,581] [INFO] Task started: Blastn
[2023-06-30 10:57:41,581] [INFO] Running command: blastn -query GCA_024320855.1_ASM2432085v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77649ebb-a58e-406a-8a86-504c1483291e/dqc_reference/reference_markers.fasta -out GCA_024320855.1_ASM2432085v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:57:42,131] [INFO] Task succeeded: Blastn
[2023-06-30 10:57:42,135] [INFO] Selected 21 target genomes.
[2023-06-30 10:57:42,136] [INFO] Target genome list was writen to GCA_024320855.1_ASM2432085v1_genomic.fna/target_genomes.txt
[2023-06-30 10:57:42,181] [INFO] Task started: fastANI
[2023-06-30 10:57:42,181] [INFO] Running command: fastANI --query /var/lib/cwl/stg25faf2f3-db9f-4156-aeb5-87043e06ed0c/GCA_024320855.1_ASM2432085v1_genomic.fna.gz --refList GCA_024320855.1_ASM2432085v1_genomic.fna/target_genomes.txt --output GCA_024320855.1_ASM2432085v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 10:58:04,142] [INFO] Task succeeded: fastANI
[2023-06-30 10:58:04,142] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77649ebb-a58e-406a-8a86-504c1483291e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 10:58:04,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77649ebb-a58e-406a-8a86-504c1483291e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 10:58:04,154] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2023-06-30 10:58:04,154] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-30 10:58:04,154] [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
Planktothrix agardhii	strain=NIES-204	GCA_003609755.1	1160	1160	type	True	99.1569	1434	1527	95	conclusive
Planktothrix tepida	strain=PCC9214	GCA_904830955.1	1678309	1678309	type	True	83.0217	1167	1527	95	below_threshold
Argonema antarcticum	strain=A004/B2	GCA_023333585.1	2942763	2942763	type	True	75.9047	94	1527	95	below_threshold
Gloeothece citriformis	strain=PCC 7424	GCA_000021825.1	2546356	2546356	type	True	75.6702	126	1527	95	below_threshold
Oscillatoria acuminata	strain=PCC 6304	GCA_000317105.1	118323	118323	type	True	75.6663	100	1527	95	below_threshold
Euhalothece natronophila	strain=Z-M001	GCA_007904085.1	577489	577489	type	True	75.6629	55	1527	95	below_threshold
Rippkaea orientalis	strain=PCC 8801	GCA_000021805.1	2546366	2546366	type	True	75.394	101	1527	95	below_threshold
Crocosphaera chwakensis	strain=CCY0110	GCA_000169335.1	2546361	2546361	type	True	75.3093	83	1527	95	below_threshold
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	75.2752	78	1527	95	below_threshold
Iningainema tapete	strain=BLCC-T55	GCA_014698965.1	2806730	2806730	type	True	75.074	54	1527	95	below_threshold
Nostoc favosum	strain=CHAB 5714	GCA_020829495.1	2907819	2907819	type	True	75.0716	74	1527	95	below_threshold
Dulcicalothrix desertica	strain=PCC 7102	GCA_003991905.1	32056	32056	type	True	75.0158	51	1527	95	below_threshold
Dulcicalothrix desertica	strain=PCC 7102	GCA_007830875.1	32056	32056	type	True	74.9876	56	1527	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 10:58:04,156] [INFO] DFAST Taxonomy check result was written to GCA_024320855.1_ASM2432085v1_genomic.fna/tc_result.tsv
[2023-06-30 10:58:04,157] [INFO] ===== Taxonomy check completed =====
[2023-06-30 10:58:04,157] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 10:58:04,157] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77649ebb-a58e-406a-8a86-504c1483291e/dqc_reference/checkm_data
[2023-06-30 10:58:04,158] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 10:58:04,202] [INFO] Task started: CheckM
[2023-06-30 10:58:04,202] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024320855.1_ASM2432085v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024320855.1_ASM2432085v1_genomic.fna/checkm_input GCA_024320855.1_ASM2432085v1_genomic.fna/checkm_result
[2023-06-30 10:58:33,052] [INFO] Task succeeded: CheckM
[2023-06-30 10:58:33,055] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 10:58:33,076] [INFO] ===== Completeness check finished =====
[2023-06-30 10:58:33,077] [INFO] ===== Start GTDB Search =====
[2023-06-30 10:58:33,077] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024320855.1_ASM2432085v1_genomic.fna/markers.fasta)
[2023-06-30 10:58:33,077] [INFO] Task started: Blastn
[2023-06-30 10:58:33,078] [INFO] Running command: blastn -query GCA_024320855.1_ASM2432085v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77649ebb-a58e-406a-8a86-504c1483291e/dqc_reference/reference_markers_gtdb.fasta -out GCA_024320855.1_ASM2432085v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:58:33,808] [INFO] Task succeeded: Blastn
[2023-06-30 10:58:33,812] [INFO] Selected 6 target genomes.
[2023-06-30 10:58:33,812] [INFO] Target genome list was writen to GCA_024320855.1_ASM2432085v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 10:58:33,815] [INFO] Task started: fastANI
[2023-06-30 10:58:33,815] [INFO] Running command: fastANI --query /var/lib/cwl/stg25faf2f3-db9f-4156-aeb5-87043e06ed0c/GCA_024320855.1_ASM2432085v1_genomic.fna.gz --refList GCA_024320855.1_ASM2432085v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024320855.1_ASM2432085v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 10:58:44,468] [INFO] Task succeeded: fastANI
[2023-06-30 10:58:44,475] [INFO] Found 6 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-30 10:58:44,476] [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_003609755.1	s__Planktothrix agardhii	99.1569	1434	1527	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Planktothrix	96.6657	99.00	98.84	0.93	0.89	4	inconclusive
GCF_900009275.2	s__Planktothrix rubescens	96.8738	1382	1527	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Planktothrix	96.6657	98.32	97.64	0.92	0.88	11	inconclusive
GCF_900009135.1	s__Planktothrix sp900009135	90.8998	1262	1527	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Planktothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900009265.2	s__Planktothrix paucivesiculata	90.0089	1236	1527	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Planktothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001873365.1	s__Planktothrix sp001873365	89.7794	1167	1527	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Planktothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003456035.1	s__Planktothrix sp003456035	88.9816	812	1527	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Planktothrix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 10:58:44,480] [INFO] GTDB search result was written to GCA_024320855.1_ASM2432085v1_genomic.fna/result_gtdb.tsv
[2023-06-30 10:58:44,481] [INFO] ===== GTDB Search completed =====
[2023-06-30 10:58:44,487] [INFO] DFAST_QC result json was written to GCA_024320855.1_ASM2432085v1_genomic.fna/dqc_result.json
[2023-06-30 10:58:44,488] [INFO] DFAST_QC completed!
[2023-06-30 10:58:44,488] [INFO] Total running time: 0h1m13s