[2024-01-25 19:07:20,578] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:07:20,580] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:07:20,580] [INFO] DQC Reference Directory: /var/lib/cwl/stg0104dc70-fc6a-45d6-91ba-7f73dda24e7e/dqc_reference
[2024-01-25 19:07:21,737] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:07:21,737] [INFO] Task started: Prodigal
[2024-01-25 19:07:21,738] [INFO] Running command: gunzip -c /var/lib/cwl/stgd925d691-7f32-4b7b-8192-64e41b6353bf/GCF_011065895.1_ASM1106589v1_genomic.fna.gz | prodigal -d GCF_011065895.1_ASM1106589v1_genomic.fna/cds.fna -a GCF_011065895.1_ASM1106589v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:07:39,586] [INFO] Task succeeded: Prodigal
[2024-01-25 19:07:39,586] [INFO] Task started: HMMsearch
[2024-01-25 19:07:39,587] [INFO] Running command: hmmsearch --tblout GCF_011065895.1_ASM1106589v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0104dc70-fc6a-45d6-91ba-7f73dda24e7e/dqc_reference/reference_markers.hmm GCF_011065895.1_ASM1106589v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:07:39,917] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:07:39,918] [INFO] Found 6/6 markers.
[2024-01-25 19:07:39,976] [INFO] Query marker FASTA was written to GCF_011065895.1_ASM1106589v1_genomic.fna/markers.fasta
[2024-01-25 19:07:39,976] [INFO] Task started: Blastn
[2024-01-25 19:07:39,976] [INFO] Running command: blastn -query GCF_011065895.1_ASM1106589v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0104dc70-fc6a-45d6-91ba-7f73dda24e7e/dqc_reference/reference_markers.fasta -out GCF_011065895.1_ASM1106589v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:40,592] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:40,597] [INFO] Selected 12 target genomes.
[2024-01-25 19:07:40,598] [INFO] Target genome list was writen to GCF_011065895.1_ASM1106589v1_genomic.fna/target_genomes.txt
[2024-01-25 19:07:40,619] [INFO] Task started: fastANI
[2024-01-25 19:07:40,619] [INFO] Running command: fastANI --query /var/lib/cwl/stgd925d691-7f32-4b7b-8192-64e41b6353bf/GCF_011065895.1_ASM1106589v1_genomic.fna.gz --refList GCF_011065895.1_ASM1106589v1_genomic.fna/target_genomes.txt --output GCF_011065895.1_ASM1106589v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:07:59,440] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:59,441] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0104dc70-fc6a-45d6-91ba-7f73dda24e7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:07:59,441] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0104dc70-fc6a-45d6-91ba-7f73dda24e7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:07:59,449] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:07:59,449] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:07:59,450] [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
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	100.0	2629	2632	95	conclusive
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	81.4778	1485	2632	95	below_threshold
Paludisphaera borealis	strain=PX4	GCA_001956985.1	1387353	1387353	type	True	79.1984	1108	2632	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	78.1933	957	2632	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	76.8597	612	2632	95	below_threshold
Singulisphaera acidiphila	strain=DSM 18658	GCA_000255675.1	466153	466153	type	True	76.7052	460	2632	95	below_threshold
Tautonia marina	strain=JC650	GCA_009177065.1	2653855	2653855	type	True	76.545	312	2632	95	below_threshold
Tautonia rosea	strain=JC657	GCA_012958305.1	2728037	2728037	type	True	76.3406	263	2632	95	below_threshold
Egibacter rhizosphaerae	strain=EGI 80759	GCA_004322855.1	1670831	1670831	type	True	74.822	101	2632	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.8052	171	2632	95	below_threshold
Microbispora rosea subsp. aerata	strain=NBRC 14624	GCA_016863075.1	147065	58117	type	True	74.6855	181	2632	95	below_threshold
Microbispora rosea subsp. aerata	strain=JCM 3076	GCA_014647835.1	147065	58117	type	True	74.6846	182	2632	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:07:59,451] [INFO] DFAST Taxonomy check result was written to GCF_011065895.1_ASM1106589v1_genomic.fna/tc_result.tsv
[2024-01-25 19:07:59,452] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:07:59,452] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:07:59,452] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0104dc70-fc6a-45d6-91ba-7f73dda24e7e/dqc_reference/checkm_data
[2024-01-25 19:07:59,453] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:07:59,529] [INFO] Task started: CheckM
[2024-01-25 19:07:59,529] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011065895.1_ASM1106589v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011065895.1_ASM1106589v1_genomic.fna/checkm_input GCF_011065895.1_ASM1106589v1_genomic.fna/checkm_result
[2024-01-25 19:08:49,875] [INFO] Task succeeded: CheckM
[2024-01-25 19:08:49,884] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:08:49,914] [INFO] ===== Completeness check finished =====
[2024-01-25 19:08:49,914] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:08:49,915] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011065895.1_ASM1106589v1_genomic.fna/markers.fasta)
[2024-01-25 19:08:49,916] [INFO] Task started: Blastn
[2024-01-25 19:08:49,916] [INFO] Running command: blastn -query GCF_011065895.1_ASM1106589v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0104dc70-fc6a-45d6-91ba-7f73dda24e7e/dqc_reference/reference_markers_gtdb.fasta -out GCF_011065895.1_ASM1106589v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:08:50,910] [INFO] Task succeeded: Blastn
[2024-01-25 19:08:50,912] [INFO] Selected 6 target genomes.
[2024-01-25 19:08:50,913] [INFO] Target genome list was writen to GCF_011065895.1_ASM1106589v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:08:50,919] [INFO] Task started: fastANI
[2024-01-25 19:08:50,920] [INFO] Running command: fastANI --query /var/lib/cwl/stgd925d691-7f32-4b7b-8192-64e41b6353bf/GCF_011065895.1_ASM1106589v1_genomic.fna.gz --refList GCF_011065895.1_ASM1106589v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011065895.1_ASM1106589v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:09:03,831] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:03,836] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:09:03,836] [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_011065895.1	s__Paludisphaera sp011065895	100.0	2629	2632	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001898385.1	s__Paludisphaera sp001898385	81.8622	1480	2632	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011064595.1	s__Paludisphaera soli	81.4955	1481	2632	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001610895.1	s__Paludisphaera sp001610895	81.3572	1398	2632	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956985.1	s__Paludisphaera borealis	79.154	1119	2632	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008087625.1	s__Aquisphaera giovannonii	78.1567	967	2632	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Aquisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:09:03,838] [INFO] GTDB search result was written to GCF_011065895.1_ASM1106589v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:09:03,838] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:09:03,840] [INFO] DFAST_QC result json was written to GCF_011065895.1_ASM1106589v1_genomic.fna/dqc_result.json
[2024-01-25 19:09:03,841] [INFO] DFAST_QC completed!
[2024-01-25 19:09:03,841] [INFO] Total running time: 0h1m43s