[2024-01-24 11:26:27,821] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:27,825] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:27,826] [INFO] DQC Reference Directory: /var/lib/cwl/stgf000254d-b22f-469f-8fc1-d89602fc0482/dqc_reference
[2024-01-24 11:26:29,309] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:29,310] [INFO] Task started: Prodigal
[2024-01-24 11:26:29,310] [INFO] Running command: gunzip -c /var/lib/cwl/stged01530a-4d9d-420d-9b0f-3196951c5579/GCF_003315205.1_ASM331520v1_genomic.fna.gz | prodigal -d GCF_003315205.1_ASM331520v1_genomic.fna/cds.fna -a GCF_003315205.1_ASM331520v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:33,687] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:33,687] [INFO] Task started: HMMsearch
[2024-01-24 11:27:33,687] [INFO] Running command: hmmsearch --tblout GCF_003315205.1_ASM331520v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf000254d-b22f-469f-8fc1-d89602fc0482/dqc_reference/reference_markers.hmm GCF_003315205.1_ASM331520v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:34,065] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:34,067] [INFO] Found 6/6 markers.
[2024-01-24 11:27:34,125] [INFO] Query marker FASTA was written to GCF_003315205.1_ASM331520v1_genomic.fna/markers.fasta
[2024-01-24 11:27:34,126] [INFO] Task started: Blastn
[2024-01-24 11:27:34,126] [INFO] Running command: blastn -query GCF_003315205.1_ASM331520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf000254d-b22f-469f-8fc1-d89602fc0482/dqc_reference/reference_markers.fasta -out GCF_003315205.1_ASM331520v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:34,728] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:34,732] [INFO] Selected 16 target genomes.
[2024-01-24 11:27:34,733] [INFO] Target genome list was writen to GCF_003315205.1_ASM331520v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:34,741] [INFO] Task started: fastANI
[2024-01-24 11:27:34,741] [INFO] Running command: fastANI --query /var/lib/cwl/stged01530a-4d9d-420d-9b0f-3196951c5579/GCF_003315205.1_ASM331520v1_genomic.fna.gz --refList GCF_003315205.1_ASM331520v1_genomic.fna/target_genomes.txt --output GCF_003315205.1_ASM331520v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:53,428] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:53,429] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf000254d-b22f-469f-8fc1-d89602fc0482/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:53,429] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf000254d-b22f-469f-8fc1-d89602fc0482/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:53,442] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:53,442] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:53,443] [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
Roseimicrobium gellanilyticum	strain=DSM 25532	GCA_003315205.1	748857	748857	type	True	100.0	2627	2628	95	conclusive
Verrucomicrobium spinosum	strain=DSM 4136	GCA_000172155.1	2736	2736	type	True	77.6207	508	2628	95	below_threshold
Verrucomicrobium spinosum	strain=JCM 18804	GCA_001313125.1	2736	2736	type	True	77.6047	488	2628	95	below_threshold
Prosthecobacter vanneervenii	strain=DSM 12252	GCA_014203095.1	48466	48466	type	True	77.0867	282	2628	95	below_threshold
Brevifollis gellanilyticus	strain=NBRC 108608	GCA_007992435.1	748831	748831	type	True	76.9076	306	2628	95	below_threshold
Prosthecobacter debontii	strain=ATCC 700200	GCA_900167535.1	48467	48467	type	True	76.8636	200	2628	95	below_threshold
Prosthecobacter dejongeii	strain=DSM 12251	GCA_014203045.1	48465	48465	type	True	76.6214	157	2628	95	below_threshold
Prosthecobacter fusiformis	strain=ATCC 25309	GCA_004364345.1	48464	48464	type	True	76.4571	178	2628	95	below_threshold
Phragmitibacter flavus	strain=MG-N-17	GCA_005780165.1	2576071	2576071	type	True	76.4546	167	2628	95	below_threshold
Luteolibacter luteus	strain=G-1-1-1	GCA_012913485.1	2728835	2728835	type	True	76.4364	112	2628	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:53,444] [INFO] DFAST Taxonomy check result was written to GCF_003315205.1_ASM331520v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:53,445] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:53,445] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:53,445] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf000254d-b22f-469f-8fc1-d89602fc0482/dqc_reference/checkm_data
[2024-01-24 11:27:53,446] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:53,524] [INFO] Task started: CheckM
[2024-01-24 11:27:53,525] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003315205.1_ASM331520v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003315205.1_ASM331520v1_genomic.fna/checkm_input GCF_003315205.1_ASM331520v1_genomic.fna/checkm_result
[2024-01-24 11:30:51,607] [INFO] Task succeeded: CheckM
[2024-01-24 11:30:51,608] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:30:51,632] [INFO] ===== Completeness check finished =====
[2024-01-24 11:30:51,633] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:30:51,633] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003315205.1_ASM331520v1_genomic.fna/markers.fasta)
[2024-01-24 11:30:51,634] [INFO] Task started: Blastn
[2024-01-24 11:30:51,634] [INFO] Running command: blastn -query GCF_003315205.1_ASM331520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf000254d-b22f-469f-8fc1-d89602fc0482/dqc_reference/reference_markers_gtdb.fasta -out GCF_003315205.1_ASM331520v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:30:52,443] [INFO] Task succeeded: Blastn
[2024-01-24 11:30:52,448] [INFO] Selected 14 target genomes.
[2024-01-24 11:30:52,448] [INFO] Target genome list was writen to GCF_003315205.1_ASM331520v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:30:52,460] [INFO] Task started: fastANI
[2024-01-24 11:30:52,461] [INFO] Running command: fastANI --query /var/lib/cwl/stged01530a-4d9d-420d-9b0f-3196951c5579/GCF_003315205.1_ASM331520v1_genomic.fna.gz --refList GCF_003315205.1_ASM331520v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003315205.1_ASM331520v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:31:10,993] [INFO] Task succeeded: fastANI
[2024-01-24 11:31:11,007] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:31:11,007] [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_003315205.1	s__Roseimicrobium gellanilyticum	100.0	2627	2628	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Roseimicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011044495.1	s__Roseimicrobium sp011044495	83.9081	1868	2628	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Roseimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000739655.1	s__Verrucomicrobium sp000739655	77.8544	557	2628	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Verrucomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000739635.1	s__Verrucomicrobium sp000739635	77.6469	549	2628	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Verrucomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000172155.1	s__Verrucomicrobium spinosum	77.6225	507	2628	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Verrucomicrobium	95.0	99.88	99.88	1.00	1.00	2	-
GCA_002336895.1	s__Prosthecobacter sp002336895	77.1482	301	2628	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203095.1	s__Prosthecobacter vanneervenii	77.095	282	2628	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167535.1	s__Prosthecobacter debontii	76.8982	198	2628	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015075365.1	s__Prosthecobacter sp015075365	76.753	266	2628	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879935.1	s__Prosthecobacter sp014879935	76.6288	294	2628	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795365.1	s__JAEUHN01 sp016795365	76.578	241	2628	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__JAEUHN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713245.1	s__Prosthecobacter sp016713245	76.5016	277	2628	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364345.1	s__Prosthecobacter fusiformis	76.446	179	2628	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:31:11,009] [INFO] GTDB search result was written to GCF_003315205.1_ASM331520v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:31:11,010] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:31:11,013] [INFO] DFAST_QC result json was written to GCF_003315205.1_ASM331520v1_genomic.fna/dqc_result.json
[2024-01-24 11:31:11,013] [INFO] DFAST_QC completed!
[2024-01-24 11:31:11,013] [INFO] Total running time: 0h4m43s