[2023-06-30 12:04:22,297] [INFO] DFAST_QC pipeline started.
[2023-06-30 12:04:22,300] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 12:04:22,300] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f7d7ee6-4eae-4571-a673-e572c45db387/dqc_reference
[2023-06-30 12:04:23,537] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 12:04:23,538] [INFO] Task started: Prodigal
[2023-06-30 12:04:23,539] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3412df1-a401-41f4-a3f6-2a193ac8f00c/GCA_016714285.1_ASM1671428v1_genomic.fna.gz | prodigal -d GCA_016714285.1_ASM1671428v1_genomic.fna/cds.fna -a GCA_016714285.1_ASM1671428v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 12:04:47,381] [INFO] Task succeeded: Prodigal
[2023-06-30 12:04:47,382] [INFO] Task started: HMMsearch
[2023-06-30 12:04:47,382] [INFO] Running command: hmmsearch --tblout GCA_016714285.1_ASM1671428v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f7d7ee6-4eae-4571-a673-e572c45db387/dqc_reference/reference_markers.hmm GCA_016714285.1_ASM1671428v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 12:04:47,710] [INFO] Task succeeded: HMMsearch
[2023-06-30 12:04:47,712] [INFO] Found 6/6 markers.
[2023-06-30 12:04:47,775] [INFO] Query marker FASTA was written to GCA_016714285.1_ASM1671428v1_genomic.fna/markers.fasta
[2023-06-30 12:04:47,776] [INFO] Task started: Blastn
[2023-06-30 12:04:47,776] [INFO] Running command: blastn -query GCA_016714285.1_ASM1671428v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f7d7ee6-4eae-4571-a673-e572c45db387/dqc_reference/reference_markers.fasta -out GCA_016714285.1_ASM1671428v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:04:48,546] [INFO] Task succeeded: Blastn
[2023-06-30 12:04:48,560] [INFO] Selected 29 target genomes.
[2023-06-30 12:04:48,561] [INFO] Target genome list was writen to GCA_016714285.1_ASM1671428v1_genomic.fna/target_genomes.txt
[2023-06-30 12:04:48,563] [INFO] Task started: fastANI
[2023-06-30 12:04:48,563] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3412df1-a401-41f4-a3f6-2a193ac8f00c/GCA_016714285.1_ASM1671428v1_genomic.fna.gz --refList GCA_016714285.1_ASM1671428v1_genomic.fna/target_genomes.txt --output GCA_016714285.1_ASM1671428v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 12:05:21,420] [INFO] Task succeeded: fastANI
[2023-06-30 12:05:21,420] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f7d7ee6-4eae-4571-a673-e572c45db387/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 12:05:21,420] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f7d7ee6-4eae-4571-a673-e572c45db387/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 12:05:21,440] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 12:05:21,440] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 12:05:21,441] [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	79.6637	1678	3006	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	79.6048	1664	3006	95	below_threshold
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	76.2858	978	3006	95	below_threshold
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	75.1742	695	3006	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	75.0739	277	3006	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	75.0616	277	3006	95	below_threshold
Myxococcus vastator	strain=AM301	GCA_010894475.1	2709664	2709664	type	True	75.058	317	3006	95	below_threshold
Corallococcus exercitus	strain=AB043A	GCA_003611585.1	2316736	2316736	type	True	75.0346	331	3006	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	75.0249	271	3006	95	below_threshold
Rhodocaloribacter litoris	strain=ISCAR-4553	GCA_011682235.2	2558931	2558931	type	True	75.0223	175	3006	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	75.0007	454	3006	95	below_threshold
Corallococcus aberystwythensis	strain=AB050A	GCA_003612165.1	2316722	2316722	type	True	75.0005	315	3006	95	below_threshold
Corallococcus praedator	strain=CA031B	GCA_003612125.1	2316724	2316724	type	True	74.9687	302	3006	95	below_threshold
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	74.9578	238	3006	95	below_threshold
Nocardioides szechwanensis	strain=NBRC 108562	GCA_007992395.1	1005944	1005944	type	True	74.9307	317	3006	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	74.9239	444	3006	95	below_threshold
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	74.9148	296	3006	95	below_threshold
Rubrivirga marina	strain=SAORIC-28	GCA_002283365.1	1196024	1196024	type	True	74.9132	369	3006	95	below_threshold
Nocardioides psychrotolerans	strain=CGMCC 1.11156	GCA_900113685.1	1005945	1005945	type	True	74.8987	280	3006	95	below_threshold
Nocardioides psychrotolerans	strain=NBRC 108563	GCA_007992415.1	1005945	1005945	type	True	74.893	283	3006	95	below_threshold
Acuticoccus kandeliae	strain=J103	GCA_003073115.1	2073160	2073160	type	True	74.8901	369	3006	95	below_threshold
Nocardioides szechwanensis	strain=CGMCC 1.11147	GCA_900103935.1	1005944	1005944	type	True	74.8828	335	3006	95	below_threshold
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	74.86	230	3006	95	below_threshold
Bifidobacterium margollesii	strain=Uis1B	GCA_002860355.1	2020964	2020964	type	True	74.8555	60	3006	95	below_threshold
Longimicrobium terrae	strain=CECT 8660	GCA_014198875.1	1639882	1639882	type	True	74.8519	234	3006	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	74.8277	556	3006	95	below_threshold
Herbaspirillum robiniae	strain=HZ10	GCA_002213415.1	2014887	2014887	type	True	74.7959	232	3006	95	below_threshold
Cellulomonas soli	strain=DSM 24484	GCA_013409305.1	931535	931535	type	True	74.7615	320	3006	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 12:05:21,443] [INFO] DFAST Taxonomy check result was written to GCA_016714285.1_ASM1671428v1_genomic.fna/tc_result.tsv
[2023-06-30 12:05:21,443] [INFO] ===== Taxonomy check completed =====
[2023-06-30 12:05:21,443] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 12:05:21,444] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f7d7ee6-4eae-4571-a673-e572c45db387/dqc_reference/checkm_data
[2023-06-30 12:05:21,445] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 12:05:21,525] [INFO] Task started: CheckM
[2023-06-30 12:05:21,525] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016714285.1_ASM1671428v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016714285.1_ASM1671428v1_genomic.fna/checkm_input GCA_016714285.1_ASM1671428v1_genomic.fna/checkm_result
[2023-06-30 12:06:40,231] [INFO] Task succeeded: CheckM
[2023-06-30 12:06:40,232] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.36%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 12:06:40,253] [INFO] ===== Completeness check finished =====
[2023-06-30 12:06:40,253] [INFO] ===== Start GTDB Search =====
[2023-06-30 12:06:40,253] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016714285.1_ASM1671428v1_genomic.fna/markers.fasta)
[2023-06-30 12:06:40,254] [INFO] Task started: Blastn
[2023-06-30 12:06:40,254] [INFO] Running command: blastn -query GCA_016714285.1_ASM1671428v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f7d7ee6-4eae-4571-a673-e572c45db387/dqc_reference/reference_markers_gtdb.fasta -out GCA_016714285.1_ASM1671428v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:06:41,503] [INFO] Task succeeded: Blastn
[2023-06-30 12:06:41,507] [INFO] Selected 10 target genomes.
[2023-06-30 12:06:41,507] [INFO] Target genome list was writen to GCA_016714285.1_ASM1671428v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 12:06:41,512] [INFO] Task started: fastANI
[2023-06-30 12:06:41,512] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3412df1-a401-41f4-a3f6-2a193ac8f00c/GCA_016714285.1_ASM1671428v1_genomic.fna.gz --refList GCA_016714285.1_ASM1671428v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016714285.1_ASM1671428v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 12:07:06,763] [INFO] Task succeeded: fastANI
[2023-06-30 12:07:06,772] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 12:07:06,772] [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
GCA_016714285.1	s__Nannocystis sp016714285	100.0	3003	3006	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	99.25	99.25	0.96	0.96	2	conclusive
GCA_013812955.1	s__Nannocystis sp013812955	83.3872	1254	3006	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793465.1	s__Nannocystis sp016793465	81.4016	1891	3006	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002343915.1	s__Nannocystis exedens	79.642	1683	3006	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	99.98	99.98	1.00	1.00	2	-
GCA_016712315.1	s__JADJRG01 sp016712315	77.457	1056	3006	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__JADJRG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002994615.1	s__Enhygromyxa salina_A	76.3218	871	3006	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Enhygromyxa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709225.1	s__Ga0077550 sp016709225	76.2789	942	3006	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	99.66	99.17	0.98	0.94	4	-
GCA_001464385.1	s__Ga0077550 sp001464385	76.1599	1054	3006	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737335.2	s__Enhygromyxa salina_C	75.996	699	3006	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Enhygromyxa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003612165.1	s__Corallococcus aberystwythensis	74.9973	316	3006	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Corallococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 12:07:06,774] [INFO] GTDB search result was written to GCA_016714285.1_ASM1671428v1_genomic.fna/result_gtdb.tsv
[2023-06-30 12:07:06,775] [INFO] ===== GTDB Search completed =====
[2023-06-30 12:07:06,780] [INFO] DFAST_QC result json was written to GCA_016714285.1_ASM1671428v1_genomic.fna/dqc_result.json
[2023-06-30 12:07:06,780] [INFO] DFAST_QC completed!
[2023-06-30 12:07:06,780] [INFO] Total running time: 0h2m44s