[2024-01-24 12:29:27,462] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:27,465] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:27,466] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc8e4ff0-0d63-4f86-9dcc-373f7d036195/dqc_reference
[2024-01-24 12:29:28,844] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:28,845] [INFO] Task started: Prodigal
[2024-01-24 12:29:28,845] [INFO] Running command: gunzip -c /var/lib/cwl/stgad9b3f7d-c45d-4f26-8262-756b974996f4/GCF_008087625.1_ASM808762v1_genomic.fna.gz | prodigal -d GCF_008087625.1_ASM808762v1_genomic.fna/cds.fna -a GCF_008087625.1_ASM808762v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:56,633] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:56,633] [INFO] Task started: HMMsearch
[2024-01-24 12:29:56,633] [INFO] Running command: hmmsearch --tblout GCF_008087625.1_ASM808762v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc8e4ff0-0d63-4f86-9dcc-373f7d036195/dqc_reference/reference_markers.hmm GCF_008087625.1_ASM808762v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:57,128] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:57,130] [INFO] Found 6/6 markers.
[2024-01-24 12:29:57,203] [INFO] Query marker FASTA was written to GCF_008087625.1_ASM808762v1_genomic.fna/markers.fasta
[2024-01-24 12:29:57,204] [INFO] Task started: Blastn
[2024-01-24 12:29:57,204] [INFO] Running command: blastn -query GCF_008087625.1_ASM808762v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc8e4ff0-0d63-4f86-9dcc-373f7d036195/dqc_reference/reference_markers.fasta -out GCF_008087625.1_ASM808762v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:57,897] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:57,901] [INFO] Selected 15 target genomes.
[2024-01-24 12:29:57,901] [INFO] Target genome list was writen to GCF_008087625.1_ASM808762v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:57,907] [INFO] Task started: fastANI
[2024-01-24 12:29:57,907] [INFO] Running command: fastANI --query /var/lib/cwl/stgad9b3f7d-c45d-4f26-8262-756b974996f4/GCF_008087625.1_ASM808762v1_genomic.fna.gz --refList GCF_008087625.1_ASM808762v1_genomic.fna/target_genomes.txt --output GCF_008087625.1_ASM808762v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:21,935] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:21,935] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc8e4ff0-0d63-4f86-9dcc-373f7d036195/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:21,936] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc8e4ff0-0d63-4f86-9dcc-373f7d036195/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:21,947] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:21,947] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:21,948] [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
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	100.0	3506	3506	95	conclusive
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	78.5708	1212	3506	95	below_threshold
Paludisphaera borealis	strain=PX4	GCA_001956985.1	1387353	1387353	type	True	78.4856	1038	3506	95	below_threshold
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	78.0497	983	3506	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	76.8841	976	3506	95	below_threshold
Singulisphaera acidiphila	strain=DSM 18658	GCA_000242455.3	466153	466153	type	True	76.8329	557	3506	95	below_threshold
Singulisphaera acidiphila	strain=DSM 18658	GCA_000255675.1	466153	466153	type	True	76.7349	529	3506	95	below_threshold
Sphingomonas arenae	strain=SYSU D00720	GCA_016924655.1	2812555	2812555	type	True	75.3062	67	3506	95	below_threshold
Geothrix fermentans	strain=DSM 14018	GCA_000428885.1	44676	44676	type	True	74.9856	144	3506	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	74.8223	434	3506	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	74.8192	318	3506	95	below_threshold
Salsipaludibacter albus	strain=AS10	GCA_019798055.1	2849650	2849650	type	True	74.7561	230	3506	95	below_threshold
Streptoalloteichus hindustanus	strain=DSM 44523	GCA_900129375.1	2017	2017	type	True	74.7429	372	3506	95	below_threshold
Cohnella nanjingensis	strain=DSM 28246	GCA_014212125.1	1387779	1387779	type	True	74.6883	94	3506	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:21,949] [INFO] DFAST Taxonomy check result was written to GCF_008087625.1_ASM808762v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:21,950] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:21,950] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:21,950] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc8e4ff0-0d63-4f86-9dcc-373f7d036195/dqc_reference/checkm_data
[2024-01-24 12:30:21,951] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:22,045] [INFO] Task started: CheckM
[2024-01-24 12:30:22,045] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008087625.1_ASM808762v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008087625.1_ASM808762v1_genomic.fna/checkm_input GCF_008087625.1_ASM808762v1_genomic.fna/checkm_result
[2024-01-24 12:31:55,091] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:55,092] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:55,119] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:55,120] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:55,120] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008087625.1_ASM808762v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:55,121] [INFO] Task started: Blastn
[2024-01-24 12:31:55,121] [INFO] Running command: blastn -query GCF_008087625.1_ASM808762v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc8e4ff0-0d63-4f86-9dcc-373f7d036195/dqc_reference/reference_markers_gtdb.fasta -out GCF_008087625.1_ASM808762v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:56,125] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:56,131] [INFO] Selected 6 target genomes.
[2024-01-24 12:31:56,131] [INFO] Target genome list was writen to GCF_008087625.1_ASM808762v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:56,144] [INFO] Task started: fastANI
[2024-01-24 12:31:56,144] [INFO] Running command: fastANI --query /var/lib/cwl/stgad9b3f7d-c45d-4f26-8262-756b974996f4/GCF_008087625.1_ASM808762v1_genomic.fna.gz --refList GCF_008087625.1_ASM808762v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008087625.1_ASM808762v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:11,847] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:11,859] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:11,859] [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_008087625.1	s__Aquisphaera giovannonii	100.0	3506	3506	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Aquisphaera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011064615.1	s__Aquisphaera sp011064615	83.2612	2189	3506	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Aquisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011064595.1	s__Paludisphaera soli	78.6061	1202	3506	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	78.589	1058	3506	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	78.4649	1045	3506	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898385.1	s__Paludisphaera sp001898385	78.4364	1213	3506	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:11,861] [INFO] GTDB search result was written to GCF_008087625.1_ASM808762v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:11,862] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:11,867] [INFO] DFAST_QC result json was written to GCF_008087625.1_ASM808762v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:11,867] [INFO] DFAST_QC completed!
[2024-01-24 12:32:11,867] [INFO] Total running time: 0h2m44s