[2024-01-24 15:18:27,441] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:27,442] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:27,443] [INFO] DQC Reference Directory: /var/lib/cwl/stg95ba83fa-d294-4140-9768-e7b8c79979fc/dqc_reference
[2024-01-24 15:18:28,940] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:28,941] [INFO] Task started: Prodigal
[2024-01-24 15:18:28,941] [INFO] Running command: gunzip -c /var/lib/cwl/stg5e0cc26c-0b44-4f5a-985c-9cc03db609af/GCF_028369095.1_ASM2836909v1_genomic.fna.gz | prodigal -d GCF_028369095.1_ASM2836909v1_genomic.fna/cds.fna -a GCF_028369095.1_ASM2836909v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:13,731] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:13,731] [INFO] Task started: HMMsearch
[2024-01-24 15:19:13,732] [INFO] Running command: hmmsearch --tblout GCF_028369095.1_ASM2836909v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95ba83fa-d294-4140-9768-e7b8c79979fc/dqc_reference/reference_markers.hmm GCF_028369095.1_ASM2836909v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:14,200] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:14,201] [INFO] Found 6/6 markers.
[2024-01-24 15:19:14,296] [INFO] Query marker FASTA was written to GCF_028369095.1_ASM2836909v1_genomic.fna/markers.fasta
[2024-01-24 15:19:14,296] [INFO] Task started: Blastn
[2024-01-24 15:19:14,297] [INFO] Running command: blastn -query GCF_028369095.1_ASM2836909v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95ba83fa-d294-4140-9768-e7b8c79979fc/dqc_reference/reference_markers.fasta -out GCF_028369095.1_ASM2836909v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:15,136] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:15,140] [INFO] Selected 32 target genomes.
[2024-01-24 15:19:15,140] [INFO] Target genome list was writen to GCF_028369095.1_ASM2836909v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:15,152] [INFO] Task started: fastANI
[2024-01-24 15:19:15,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e0cc26c-0b44-4f5a-985c-9cc03db609af/GCF_028369095.1_ASM2836909v1_genomic.fna.gz --refList GCF_028369095.1_ASM2836909v1_genomic.fna/target_genomes.txt --output GCF_028369095.1_ASM2836909v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:54,036] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:54,036] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95ba83fa-d294-4140-9768-e7b8c79979fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:54,037] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95ba83fa-d294-4140-9768-e7b8c79979fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:54,071] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:19:54,071] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:19:54,072] [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
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	88.7569	3148	4297	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	88.7465	3076	4297	95	below_threshold
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	76.1301	1204	4297	95	below_threshold
Vulgatibacter incomptus	strain=DSM 27710	GCA_001263175.1	1391653	1391653	type	True	75.4048	325	4297	95	below_threshold
Parolsenella massiliensis	strain=Marseille-P3237	GCA_900143685.1	1871022	1871022	type	True	75.2312	114	4297	95	below_threshold
Parolsenella catena	strain=JCM 31932	GCA_003966955.1	2003188	2003188	type	True	75.1858	94	4297	95	below_threshold
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	75.1504	947	4297	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.0979	701	4297	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	75.065	533	4297	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	75.0561	761	4297	95	below_threshold
Rhodocaloribacter litoris	strain=ISCAR-4553	GCA_011682235.2	2558931	2558931	type	True	75.0524	216	4297	95	below_threshold
Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis	strain=AM401	GCA_006636215.1	2590453	2590453	type	True	75.0244	461	4297	95	below_threshold
Thermophilibacter immobilis	strain=LZLJ-2	GCA_015277515.1	2779519	2779519	type	True	74.9987	113	4297	95	below_threshold
Agromyces badenianii	strain=MF30-A	GCA_003070885.1	2080742	2080742	type	True	74.977	324	4297	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	74.9664	533	4297	95	below_threshold
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	74.9624	224	4297	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	74.9555	290	4297	95	below_threshold
Olsenella intestinalis	strain=KCTC 25379	GCA_023276655.1	2930083	2930083	type	True	74.9484	191	4297	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	74.945	407	4297	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	74.9146	508	4297	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	74.9109	449	4297	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	74.9067	458	4297	95	below_threshold
Bifidobacterium santillanense	strain=MA2	GCA_018555385.1	2809028	2809028	type	True	74.903	195	4297	95	below_threshold
Sphingomonas yantingensis	strain=DSM 27244	GCA_014199325.1	1241761	1241761	type	True	74.8948	293	4297	95	below_threshold
Bifidobacterium rousetti	strain=RST9	GCA_008698235.1	2045439	2045439	type	True	74.886	176	4297	95	below_threshold
Agrococcus carbonis	strain=DSM 22965	GCA_900104705.1	684552	684552	type	True	74.8833	446	4297	95	below_threshold
Verminephrobacter eiseniae	strain=EF01-2	GCA_000015565.1	364317	364317	type	True	74.8752	219	4297	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	74.8493	418	4297	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	74.8185	393	4297	95	below_threshold
Agromyces hippuratus	strain=DSM 8598	GCA_013410355.1	286438	286438	type	True	74.8013	423	4297	95	below_threshold
Actinoplanes auranticolor	strain=NBRC 12245	GCA_018332655.1	47988	47988	type	True	74.8009	739	4297	95	below_threshold
Nocardioides jishulii	strain=dk3136	GCA_006007965.1	2575440	2575440	type	True	74.7915	279	4297	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:54,073] [INFO] DFAST Taxonomy check result was written to GCF_028369095.1_ASM2836909v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:54,074] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:54,074] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:54,074] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95ba83fa-d294-4140-9768-e7b8c79979fc/dqc_reference/checkm_data
[2024-01-24 15:19:54,075] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:54,187] [INFO] Task started: CheckM
[2024-01-24 15:19:54,187] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028369095.1_ASM2836909v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028369095.1_ASM2836909v1_genomic.fna/checkm_input GCF_028369095.1_ASM2836909v1_genomic.fna/checkm_result
[2024-01-24 15:23:00,400] [INFO] Task succeeded: CheckM
[2024-01-24 15:23:00,402] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:23:00,456] [INFO] ===== Completeness check finished =====
[2024-01-24 15:23:00,457] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:23:00,457] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028369095.1_ASM2836909v1_genomic.fna/markers.fasta)
[2024-01-24 15:23:00,457] [INFO] Task started: Blastn
[2024-01-24 15:23:00,457] [INFO] Running command: blastn -query GCF_028369095.1_ASM2836909v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg95ba83fa-d294-4140-9768-e7b8c79979fc/dqc_reference/reference_markers_gtdb.fasta -out GCF_028369095.1_ASM2836909v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:23:01,796] [INFO] Task succeeded: Blastn
[2024-01-24 15:23:01,800] [INFO] Selected 8 target genomes.
[2024-01-24 15:23:01,800] [INFO] Target genome list was writen to GCF_028369095.1_ASM2836909v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:23:01,806] [INFO] Task started: fastANI
[2024-01-24 15:23:01,807] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e0cc26c-0b44-4f5a-985c-9cc03db609af/GCF_028369095.1_ASM2836909v1_genomic.fna.gz --refList GCF_028369095.1_ASM2836909v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028369095.1_ASM2836909v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:23:27,430] [INFO] Task succeeded: fastANI
[2024-01-24 15:23:27,444] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 15:23:27,444] [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_002343915.1	s__Nannocystis exedens	88.759	3150	4297	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	99.98	99.98	1.00	1.00	2	-
GCA_013812955.1	s__Nannocystis sp013812955	79.793	1180	4297	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714285.1	s__Nannocystis sp016714285	79.4031	1728	4297	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	99.25	99.25	0.96	0.96	2	-
GCA_016793465.1	s__Nannocystis sp016793465	79.3287	2032	4297	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712315.1	s__JADJRG01 sp016712315	76.734	1178	4297	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__JADJRG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709225.1	s__Ga0077550 sp016709225	76.1517	1244	4297	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	99.66	99.17	0.98	0.94	4	-
GCF_000170895.1	s__Plesiocystis pacifica	76.1418	1200	4297	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Plesiocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464385.1	s__Ga0077550 sp001464385	76.0944	1360	4297	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:23:27,446] [INFO] GTDB search result was written to GCF_028369095.1_ASM2836909v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:23:27,446] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:23:27,451] [INFO] DFAST_QC result json was written to GCF_028369095.1_ASM2836909v1_genomic.fna/dqc_result.json
[2024-01-24 15:23:27,451] [INFO] DFAST_QC completed!
[2024-01-24 15:23:27,451] [INFO] Total running time: 0h5m0s