[2024-01-24 14:23:20,453] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:20,455] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:20,455] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ab0d9c2-4df1-4060-9f86-e3395012f6e2/dqc_reference
[2024-01-24 14:23:21,791] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:21,791] [INFO] Task started: Prodigal
[2024-01-24 14:23:21,792] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3405e8b-36e5-4ac2-b937-add1e00eedfb/GCF_028369105.1_ASM2836910v1_genomic.fna.gz | prodigal -d GCF_028369105.1_ASM2836910v1_genomic.fna/cds.fna -a GCF_028369105.1_ASM2836910v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:24:23,107] [INFO] Task succeeded: Prodigal
[2024-01-24 14:24:23,107] [INFO] Task started: HMMsearch
[2024-01-24 14:24:23,108] [INFO] Running command: hmmsearch --tblout GCF_028369105.1_ASM2836910v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ab0d9c2-4df1-4060-9f86-e3395012f6e2/dqc_reference/reference_markers.hmm GCF_028369105.1_ASM2836910v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:24:23,786] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:24:23,788] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgf3405e8b-36e5-4ac2-b937-add1e00eedfb/GCF_028369105.1_ASM2836910v1_genomic.fna.gz]
[2024-01-24 14:24:23,893] [INFO] Query marker FASTA was written to GCF_028369105.1_ASM2836910v1_genomic.fna/markers.fasta
[2024-01-24 14:24:23,893] [INFO] Task started: Blastn
[2024-01-24 14:24:23,893] [INFO] Running command: blastn -query GCF_028369105.1_ASM2836910v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ab0d9c2-4df1-4060-9f86-e3395012f6e2/dqc_reference/reference_markers.fasta -out GCF_028369105.1_ASM2836910v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:24,651] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:24,654] [INFO] Selected 20 target genomes.
[2024-01-24 14:24:24,654] [INFO] Target genome list was writen to GCF_028369105.1_ASM2836910v1_genomic.fna/target_genomes.txt
[2024-01-24 14:24:24,673] [INFO] Task started: fastANI
[2024-01-24 14:24:24,674] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3405e8b-36e5-4ac2-b937-add1e00eedfb/GCF_028369105.1_ASM2836910v1_genomic.fna.gz --refList GCF_028369105.1_ASM2836910v1_genomic.fna/target_genomes.txt --output GCF_028369105.1_ASM2836910v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:24:59,060] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:59,061] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ab0d9c2-4df1-4060-9f86-e3395012f6e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:24:59,061] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ab0d9c2-4df1-4060-9f86-e3395012f6e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:24:59,080] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:24:59,080] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:24:59,080] [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
Polyangium fumosum	strain=DSM 14668	GCA_005144585.1	889272	889272	neotype	True	94.3353	3710	4417	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	88.0122	2947	4417	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	80.5033	2188	4417	95	below_threshold
Chondromyces crocatus	strain=Cm c5	GCA_001189295.1	52	52	type	True	76.8382	883	4417	95	below_threshold
Labilithrix luteola	strain=DSM 27648	GCA_001263205.1	1391654	1391654	type	True	75.9508	668	4417	95	below_threshold
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	75.3822	1129	4417	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.2339	558	4417	95	below_threshold
Lutibaculum baratangense	strain=AMV1	GCA_000496075.1	1358440	1358440	type	True	75.065	224	4417	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	75.0351	272	4417	95	below_threshold
Halochromatium glycolicum	strain=DSM 11080	GCA_016584085.1	85075	85075	type	True	74.9716	143	4417	95	below_threshold
Salsipaludibacter albus	strain=AS10	GCA_019798055.1	2849650	2849650	type	True	74.9054	156	4417	95	below_threshold
Burkholderia thailandensis	strain=E264; ATCC 700388	GCA_000012365.1	57975	57975	type	True	74.895	528	4417	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	74.8721	436	4417	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	74.8521	436	4417	95	below_threshold
Agrococcus carbonis	strain=DSM 22965	GCA_900104705.1	684552	684552	type	True	74.8493	354	4417	95	below_threshold
Burkholderia thailandensis	strain=ATCC 700388	GCA_000152285.1	57975	57975	type	True	74.8468	491	4417	95	below_threshold
Aeromicrobium terrae	strain=CC-CFT486	GCA_008039565.1	2498846	2498846	type	True	74.8439	220	4417	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	74.8172	381	4417	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	74.7885	420	4417	95	below_threshold
Cellulomonas persica	strain=NBRC 101101	GCA_007989825.1	76861	76861	type	True	74.7849	335	4417	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:24:59,082] [INFO] DFAST Taxonomy check result was written to GCF_028369105.1_ASM2836910v1_genomic.fna/tc_result.tsv
[2024-01-24 14:24:59,083] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:24:59,083] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:24:59,083] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ab0d9c2-4df1-4060-9f86-e3395012f6e2/dqc_reference/checkm_data
[2024-01-24 14:24:59,084] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:24:59,203] [INFO] Task started: CheckM
[2024-01-24 14:24:59,203] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028369105.1_ASM2836910v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028369105.1_ASM2836910v1_genomic.fna/checkm_input GCF_028369105.1_ASM2836910v1_genomic.fna/checkm_result
[2024-01-24 14:29:20,313] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:20,314] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:20,342] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:20,342] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:20,343] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028369105.1_ASM2836910v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:20,343] [INFO] Task started: Blastn
[2024-01-24 14:29:20,343] [INFO] Running command: blastn -query GCF_028369105.1_ASM2836910v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ab0d9c2-4df1-4060-9f86-e3395012f6e2/dqc_reference/reference_markers_gtdb.fasta -out GCF_028369105.1_ASM2836910v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:21,704] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:21,708] [INFO] Selected 11 target genomes.
[2024-01-24 14:29:21,708] [INFO] Target genome list was writen to GCF_028369105.1_ASM2836910v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:21,767] [INFO] Task started: fastANI
[2024-01-24 14:29:21,768] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3405e8b-36e5-4ac2-b937-add1e00eedfb/GCF_028369105.1_ASM2836910v1_genomic.fna.gz --refList GCF_028369105.1_ASM2836910v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028369105.1_ASM2836910v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:30:04,374] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:04,392] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:30:04,392] [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_005144585.1	s__Polyangium fumosum	94.3272	3713	4417	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649845.1	s__Polyangium spumosum	88.0208	2946	4417	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144635.1	s__Polyangium sp005144635	80.4857	2162	4417	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016715885.1	s__Polyangium sp016715885	77.5257	804	4417	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135735.1	s__Sorangium cellulosum_F	77.3046	1382	4417	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000067165.1	s__Sorangium cellulosum_B	77.2401	1412	4417	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002950945.1	s__Sorangium cellulosum_E	77.2038	1527	4417	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000418325.1	s__Sorangium cellulosum_D	77.1834	1620	4417	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	95.45	95.45	0.82	0.82	2	-
GCA_903906315.1	s__CAIVJW01 sp903906315	77.1762	1144	4417	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAIVJW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001931535.1	s__Minicystis rosea	77.117	1460	4417	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Minicystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903893335.1	s__CAITLX01 sp903893335	76.3111	602	4417	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__CAITLX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:30:04,394] [INFO] GTDB search result was written to GCF_028369105.1_ASM2836910v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:30:04,395] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:30:04,399] [INFO] DFAST_QC result json was written to GCF_028369105.1_ASM2836910v1_genomic.fna/dqc_result.json
[2024-01-24 14:30:04,399] [INFO] DFAST_QC completed!
[2024-01-24 14:30:04,399] [INFO] Total running time: 0h6m44s