[2024-01-24 15:27:20,825] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:20,827] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:20,827] [INFO] DQC Reference Directory: /var/lib/cwl/stge62cf631-f701-4aa5-8b72-174e68675d4a/dqc_reference
[2024-01-24 15:27:23,292] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:23,293] [INFO] Task started: Prodigal
[2024-01-24 15:27:23,293] [INFO] Running command: gunzip -c /var/lib/cwl/stg1733f4b7-53f5-4a58-91d5-fd59703c4e0a/GCF_009177065.1_ASM917706v1_genomic.fna.gz | prodigal -d GCF_009177065.1_ASM917706v1_genomic.fna/cds.fna -a GCF_009177065.1_ASM917706v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:43,019] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:43,020] [INFO] Task started: HMMsearch
[2024-01-24 15:27:43,020] [INFO] Running command: hmmsearch --tblout GCF_009177065.1_ASM917706v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge62cf631-f701-4aa5-8b72-174e68675d4a/dqc_reference/reference_markers.hmm GCF_009177065.1_ASM917706v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:43,345] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:43,347] [INFO] Found 6/6 markers.
[2024-01-24 15:27:43,400] [INFO] Query marker FASTA was written to GCF_009177065.1_ASM917706v1_genomic.fna/markers.fasta
[2024-01-24 15:27:43,400] [INFO] Task started: Blastn
[2024-01-24 15:27:43,401] [INFO] Running command: blastn -query GCF_009177065.1_ASM917706v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge62cf631-f701-4aa5-8b72-174e68675d4a/dqc_reference/reference_markers.fasta -out GCF_009177065.1_ASM917706v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:44,059] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:44,063] [INFO] Selected 19 target genomes.
[2024-01-24 15:27:44,063] [INFO] Target genome list was writen to GCF_009177065.1_ASM917706v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:44,070] [INFO] Task started: fastANI
[2024-01-24 15:27:44,071] [INFO] Running command: fastANI --query /var/lib/cwl/stg1733f4b7-53f5-4a58-91d5-fd59703c4e0a/GCF_009177065.1_ASM917706v1_genomic.fna.gz --refList GCF_009177065.1_ASM917706v1_genomic.fna/target_genomes.txt --output GCF_009177065.1_ASM917706v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:05,899] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:05,900] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge62cf631-f701-4aa5-8b72-174e68675d4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:05,900] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge62cf631-f701-4aa5-8b72-174e68675d4a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:05,912] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:28:05,913] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:28:05,913] [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
Tautonia marina	strain=JC650	GCA_009177065.1	2653855	2653855	type	True	100.0	2322	2326	95	conclusive
Tautonia rosea	strain=JC657	GCA_012958305.1	2728037	2728037	type	True	85.7956	1830	2326	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	79.2598	1080	2326	95	below_threshold
Tautonia sociabilis	strain=GM2012	GCA_003977685.1	2080755	2080755	type	True	79.0666	940	2326	95	below_threshold
Paludisphaera borealis	strain=PX4	GCA_001956985.1	1387353	1387353	type	True	76.5366	353	2326	95	below_threshold
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	76.5293	304	2326	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	76.4817	389	2326	95	below_threshold
Singulisphaera acidiphila	strain=DSM 18658	GCA_000255675.1	466153	466153	type	True	76.0474	266	2326	95	below_threshold
Microbispora rosea subsp. aerata	strain=JCM 3076	GCA_014647835.1	147065	58117	type	True	74.8252	99	2326	95	below_threshold
Microbispora rosea subsp. aerata	strain=NBRC 14624	GCA_016863075.1	147065	58117	type	True	74.8252	99	2326	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	74.777	86	2326	95	below_threshold
Microbispora sitophila	strain=NEAU-D428	GCA_014892245.1	2771537	2771537	type	True	74.7215	126	2326	95	below_threshold
Actinomadura atramentaria	strain=SF2197	GCA_000381885.1	1990	1990	type	True	74.6406	92	2326	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:05,915] [INFO] DFAST Taxonomy check result was written to GCF_009177065.1_ASM917706v1_genomic.fna/tc_result.tsv
[2024-01-24 15:28:05,915] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:05,916] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:05,916] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge62cf631-f701-4aa5-8b72-174e68675d4a/dqc_reference/checkm_data
[2024-01-24 15:28:05,917] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:05,992] [INFO] Task started: CheckM
[2024-01-24 15:28:05,992] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009177065.1_ASM917706v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009177065.1_ASM917706v1_genomic.fna/checkm_input GCF_009177065.1_ASM917706v1_genomic.fna/checkm_result
[2024-01-24 15:29:08,960] [INFO] Task succeeded: CheckM
[2024-01-24 15:29:08,961] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:29:08,985] [INFO] ===== Completeness check finished =====
[2024-01-24 15:29:08,986] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:29:08,987] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009177065.1_ASM917706v1_genomic.fna/markers.fasta)
[2024-01-24 15:29:08,987] [INFO] Task started: Blastn
[2024-01-24 15:29:08,987] [INFO] Running command: blastn -query GCF_009177065.1_ASM917706v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge62cf631-f701-4aa5-8b72-174e68675d4a/dqc_reference/reference_markers_gtdb.fasta -out GCF_009177065.1_ASM917706v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:29:09,983] [INFO] Task succeeded: Blastn
[2024-01-24 15:29:09,987] [INFO] Selected 11 target genomes.
[2024-01-24 15:29:09,987] [INFO] Target genome list was writen to GCF_009177065.1_ASM917706v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:29:09,997] [INFO] Task started: fastANI
[2024-01-24 15:29:09,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg1733f4b7-53f5-4a58-91d5-fd59703c4e0a/GCF_009177065.1_ASM917706v1_genomic.fna.gz --refList GCF_009177065.1_ASM917706v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009177065.1_ASM917706v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:29:24,741] [INFO] Task succeeded: fastANI
[2024-01-24 15:29:24,755] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:29:24,756] [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_009177065.1	s__Tautonia marina	100.0	2322	2326	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Tautonia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_012958305.1	s__Tautonia rosea	85.7878	1832	2326	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Tautonia	95.0	100.00	100.00	1.00	1.00	3	-
GCF_007752535.1	s__Tautonia plasticadhaerens	79.2598	1081	2326	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Tautonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003977685.1	s__Tautonia sociabilis	79.0602	940	2326	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Tautonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019232645.1	s__JAFANO01 sp019232645	76.9339	186	2326	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__JAFANO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898385.1	s__Paludisphaera sp001898385	76.5281	377	2326	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	76.5176	354	2326	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	76.4716	391	2326	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129635.1	s__Singulisphaera sp900129635	76.2989	288	2326	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Singulisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:29:24,758] [INFO] GTDB search result was written to GCF_009177065.1_ASM917706v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:29:24,759] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:29:24,762] [INFO] DFAST_QC result json was written to GCF_009177065.1_ASM917706v1_genomic.fna/dqc_result.json
[2024-01-24 15:29:24,763] [INFO] DFAST_QC completed!
[2024-01-24 15:29:24,763] [INFO] Total running time: 0h2m4s