[2024-01-24 12:36:24,831] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:24,833] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:24,833] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9d144d8-ab2b-4a89-ac90-49d4a831eab5/dqc_reference
[2024-01-24 12:36:26,137] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:26,138] [INFO] Task started: Prodigal
[2024-01-24 12:36:26,138] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0523e5a-ea2b-4f62-a0be-103fe5ff1b9a/GCF_003977685.1_ASM397768v1_genomic.fna.gz | prodigal -d GCF_003977685.1_ASM397768v1_genomic.fna/cds.fna -a GCF_003977685.1_ASM397768v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:41,899] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:41,899] [INFO] Task started: HMMsearch
[2024-01-24 12:36:41,899] [INFO] Running command: hmmsearch --tblout GCF_003977685.1_ASM397768v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9d144d8-ab2b-4a89-ac90-49d4a831eab5/dqc_reference/reference_markers.hmm GCF_003977685.1_ASM397768v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:42,261] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:42,263] [INFO] Found 6/6 markers.
[2024-01-24 12:36:42,311] [INFO] Query marker FASTA was written to GCF_003977685.1_ASM397768v1_genomic.fna/markers.fasta
[2024-01-24 12:36:42,311] [INFO] Task started: Blastn
[2024-01-24 12:36:42,311] [INFO] Running command: blastn -query GCF_003977685.1_ASM397768v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9d144d8-ab2b-4a89-ac90-49d4a831eab5/dqc_reference/reference_markers.fasta -out GCF_003977685.1_ASM397768v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:42,957] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:42,962] [INFO] Selected 11 target genomes.
[2024-01-24 12:36:42,962] [INFO] Target genome list was writen to GCF_003977685.1_ASM397768v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:42,971] [INFO] Task started: fastANI
[2024-01-24 12:36:42,971] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0523e5a-ea2b-4f62-a0be-103fe5ff1b9a/GCF_003977685.1_ASM397768v1_genomic.fna.gz --refList GCF_003977685.1_ASM397768v1_genomic.fna/target_genomes.txt --output GCF_003977685.1_ASM397768v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:36:58,774] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:58,774] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9d144d8-ab2b-4a89-ac90-49d4a831eab5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:36:58,775] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9d144d8-ab2b-4a89-ac90-49d4a831eab5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:36:58,790] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:36:58,790] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:36:58,790] [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 sociabilis	strain=GM2012	GCA_003977685.1	2080755	2080755	type	True	100.0	2180	2190	95	conclusive
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	82.2662	1517	2190	95	below_threshold
Tautonia marina	strain=JC650	GCA_009177065.1	2653855	2653855	type	True	79.0407	935	2190	95	below_threshold
Tautonia rosea	strain=JC657	GCA_012958305.1	2728037	2728037	type	True	78.78	844	2190	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	76.9955	674	2190	95	below_threshold
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	76.8774	508	2190	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	76.5639	701	2190	95	below_threshold
Geodermatophilus tzadiensis	strain=DSM 45416	GCA_003002915.1	1137988	1137988	type	True	74.8339	251	2190	95	below_threshold
Thermaerobacter marianensis	strain=DSM 12885	GCA_000184705.1	73919	73919	type	True	74.7575	92	2190	95	below_threshold
Amycolatopsis acididurans	strain=K13G38	GCA_012328925.1	2724524	2724524	type	True	74.7368	168	2190	95	below_threshold
Amycolatopsis sacchari	strain=DSM 44468	GCA_900114035.1	115433	115433	type	True	74.681	180	2190	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:36:58,793] [INFO] DFAST Taxonomy check result was written to GCF_003977685.1_ASM397768v1_genomic.fna/tc_result.tsv
[2024-01-24 12:36:58,794] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:36:58,794] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:36:58,795] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9d144d8-ab2b-4a89-ac90-49d4a831eab5/dqc_reference/checkm_data
[2024-01-24 12:36:58,796] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:36:58,866] [INFO] Task started: CheckM
[2024-01-24 12:36:58,866] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003977685.1_ASM397768v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003977685.1_ASM397768v1_genomic.fna/checkm_input GCF_003977685.1_ASM397768v1_genomic.fna/checkm_result
[2024-01-24 12:37:48,837] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:48,838] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:48,861] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:48,861] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:48,862] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003977685.1_ASM397768v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:48,862] [INFO] Task started: Blastn
[2024-01-24 12:37:48,862] [INFO] Running command: blastn -query GCF_003977685.1_ASM397768v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9d144d8-ab2b-4a89-ac90-49d4a831eab5/dqc_reference/reference_markers_gtdb.fasta -out GCF_003977685.1_ASM397768v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:49,747] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:49,752] [INFO] Selected 10 target genomes.
[2024-01-24 12:37:49,753] [INFO] Target genome list was writen to GCF_003977685.1_ASM397768v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:49,763] [INFO] Task started: fastANI
[2024-01-24 12:37:49,764] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0523e5a-ea2b-4f62-a0be-103fe5ff1b9a/GCF_003977685.1_ASM397768v1_genomic.fna.gz --refList GCF_003977685.1_ASM397768v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003977685.1_ASM397768v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:03,229] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:03,243] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:03,244] [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_003977685.1	s__Tautonia sociabilis	100.0	2180	2190	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_007752535.1	s__Tautonia plasticadhaerens	82.2828	1512	2190	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Tautonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009177065.1	s__Tautonia marina	79.0413	937	2190	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Tautonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012958305.1	s__Tautonia rosea	78.7683	847	2190	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Tautonia	95.0	100.00	100.00	1.00	1.00	3	-
GCA_019232645.1	s__JAFANO01 sp019232645	77.466	320	2190	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__JAFANO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011064595.1	s__Paludisphaera soli	77.0029	672	2190	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	76.7738	548	2190	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	76.565	703	2190	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Aquisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903891325.1	s__Palsa-1447 sp903891325	74.8427	82	2190	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Palsa-1447	95.0	99.85	99.79	0.96	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:03,246] [INFO] GTDB search result was written to GCF_003977685.1_ASM397768v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:03,247] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:03,253] [INFO] DFAST_QC result json was written to GCF_003977685.1_ASM397768v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:03,253] [INFO] DFAST_QC completed!
[2024-01-24 12:38:03,253] [INFO] Total running time: 0h1m38s