[2023-06-14 01:07:36,078] [INFO] DFAST_QC pipeline started.
[2023-06-14 01:07:36,080] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 01:07:36,080] [INFO] DQC Reference Directory: /var/lib/cwl/stgfbe82c6e-603c-4b68-9169-1f0562c528ad/dqc_reference
[2023-06-14 01:07:37,934] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 01:07:37,936] [INFO] Task started: Prodigal
[2023-06-14 01:07:37,936] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b16eeae-5e8a-4552-9b23-bb7e8fd100ba/GCA_022841245.1_ASM2284124v1_genomic.fna.gz | prodigal -d GCA_022841245.1_ASM2284124v1_genomic.fna/cds.fna -a GCA_022841245.1_ASM2284124v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 01:07:53,658] [INFO] Task succeeded: Prodigal
[2023-06-14 01:07:53,659] [INFO] Task started: HMMsearch
[2023-06-14 01:07:53,660] [INFO] Running command: hmmsearch --tblout GCA_022841245.1_ASM2284124v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfbe82c6e-603c-4b68-9169-1f0562c528ad/dqc_reference/reference_markers.hmm GCA_022841245.1_ASM2284124v1_genomic.fna/protein.faa > /dev/null
[2023-06-14 01:07:53,966] [INFO] Task succeeded: HMMsearch
[2023-06-14 01:07:53,968] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8b16eeae-5e8a-4552-9b23-bb7e8fd100ba/GCA_022841245.1_ASM2284124v1_genomic.fna.gz]
[2023-06-14 01:07:54,018] [INFO] Query marker FASTA was written to GCA_022841245.1_ASM2284124v1_genomic.fna/markers.fasta
[2023-06-14 01:07:54,019] [INFO] Task started: Blastn
[2023-06-14 01:07:54,019] [INFO] Running command: blastn -query GCA_022841245.1_ASM2284124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbe82c6e-603c-4b68-9169-1f0562c528ad/dqc_reference/reference_markers.fasta -out GCA_022841245.1_ASM2284124v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:07:54,797] [INFO] Task succeeded: Blastn
[2023-06-14 01:07:54,802] [INFO] Selected 26 target genomes.
[2023-06-14 01:07:54,802] [INFO] Target genome list was writen to GCA_022841245.1_ASM2284124v1_genomic.fna/target_genomes.txt
[2023-06-14 01:07:54,840] [INFO] Task started: fastANI
[2023-06-14 01:07:54,840] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b16eeae-5e8a-4552-9b23-bb7e8fd100ba/GCA_022841245.1_ASM2284124v1_genomic.fna.gz --refList GCA_022841245.1_ASM2284124v1_genomic.fna/target_genomes.txt --output GCA_022841245.1_ASM2284124v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 01:08:13,818] [INFO] Task succeeded: fastANI
[2023-06-14 01:08:13,819] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfbe82c6e-603c-4b68-9169-1f0562c528ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 01:08:13,819] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfbe82c6e-603c-4b68-9169-1f0562c528ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 01:08:13,842] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-14 01:08:13,842] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-14 01:08:13,843] [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
Mucisphaera calidilacus	strain=Pan265	GCA_007748075.1	2527982	2527982	type	True	75.4783	64	1627	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.4322	111	1627	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	75.2121	146	1627	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	75.2089	147	1627	95	below_threshold
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	75.1767	170	1627	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	75.1393	176	1627	95	below_threshold
Phenylobacterium parvum	strain=HYN0004	GCA_003150835.1	2201350	2201350	type	True	75.1345	71	1627	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	75.106	105	1627	95	below_threshold
Methylobacterium bullatum	strain=DSM 21893	GCA_022179105.1	570505	570505	type	True	74.9661	116	1627	95	below_threshold
Rhodobacter flagellatus	strain=SYSU G03088	GCA_008271465.1	2593021	2593021	type	True	74.9481	65	1627	95	below_threshold
Allgaiera indica	strain=DSM 24802	GCA_900106675.1	765699	765699	type	True	74.9319	91	1627	95	below_threshold
Paracoccus suum	strain=SC2-6	GCA_003324675.1	2259340	2259340	type	True	74.9194	63	1627	95	below_threshold
Allgaiera indica	strain=CGMCC 1.10859	GCA_014653075.1	765699	765699	type	True	74.9141	94	1627	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	74.9037	238	1627	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	74.8839	78	1627	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	74.8695	150	1627	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	74.8619	152	1627	95	below_threshold
Roseomonas lacus	strain=CGMCC 1.3617	GCA_014644535.1	287609	287609	type	True	74.8442	161	1627	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.8257	160	1627	95	below_threshold
Micromonospora carbonacea	strain=DSM 43168	GCA_900091535.1	47853	47853	type	True	74.7804	225	1627	95	below_threshold
Micromonospora rubida	strain=NEAU-HG-1	GCA_009908295.1	2697657	2697657	type	True	74.7732	202	1627	95	below_threshold
Micromonospora carbonacea	strain=aurantiaca	GCA_013389765.1	47853	47853	type	True	74.7559	231	1627	95	below_threshold
Micromonospora fulviviridis	strain=JCM 3259	GCA_014648395.1	47860	47860	type	True	74.733	233	1627	95	below_threshold
Micromonospora avicenniae	strain=DSM 45758	GCA_900156065.1	1198245	1198245	type	True	74.6477	166	1627	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-14 01:08:13,845] [INFO] DFAST Taxonomy check result was written to GCA_022841245.1_ASM2284124v1_genomic.fna/tc_result.tsv
[2023-06-14 01:08:13,846] [INFO] ===== Taxonomy check completed =====
[2023-06-14 01:08:13,846] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 01:08:13,846] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfbe82c6e-603c-4b68-9169-1f0562c528ad/dqc_reference/checkm_data
[2023-06-14 01:08:13,848] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 01:08:13,903] [INFO] Task started: CheckM
[2023-06-14 01:08:13,903] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022841245.1_ASM2284124v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022841245.1_ASM2284124v1_genomic.fna/checkm_input GCA_022841245.1_ASM2284124v1_genomic.fna/checkm_result
[2023-06-14 01:09:04,254] [INFO] Task succeeded: CheckM
[2023-06-14 01:09:04,256] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 01:09:04,278] [INFO] ===== Completeness check finished =====
[2023-06-14 01:09:04,279] [INFO] ===== Start GTDB Search =====
[2023-06-14 01:09:04,279] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022841245.1_ASM2284124v1_genomic.fna/markers.fasta)
[2023-06-14 01:09:04,279] [INFO] Task started: Blastn
[2023-06-14 01:09:04,280] [INFO] Running command: blastn -query GCA_022841245.1_ASM2284124v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbe82c6e-603c-4b68-9169-1f0562c528ad/dqc_reference/reference_markers_gtdb.fasta -out GCA_022841245.1_ASM2284124v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:09:05,522] [INFO] Task succeeded: Blastn
[2023-06-14 01:09:05,527] [INFO] Selected 13 target genomes.
[2023-06-14 01:09:05,527] [INFO] Target genome list was writen to GCA_022841245.1_ASM2284124v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 01:09:05,611] [INFO] Task started: fastANI
[2023-06-14 01:09:05,611] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b16eeae-5e8a-4552-9b23-bb7e8fd100ba/GCA_022841245.1_ASM2284124v1_genomic.fna.gz --refList GCA_022841245.1_ASM2284124v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022841245.1_ASM2284124v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 01:09:15,920] [INFO] Task succeeded: fastANI
[2023-06-14 01:09:15,930] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-14 01:09:15,930] [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_017302815.1	s__UBA11346 sp017302815	82.9663	615	1627	d__Bacteria;p__Planctomycetota;c__UBA11346;o__UBA11346;f__UBA11346;g__UBA11346	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003482625.1	s__UBA11346 sp003482625	82.2434	492	1627	d__Bacteria;p__Planctomycetota;c__UBA11346;o__UBA11346;f__UBA11346;g__UBA11346	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013821615.1	s__BOG-1363 sp013821615	78.3664	276	1627	d__Bacteria;p__Planctomycetota;c__UBA11346;o__UBA11346;f__UBA11346;g__BOG-1363	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013816645.1	s__JACDEC01 sp013816645	77.9101	247	1627	d__Bacteria;p__Planctomycetota;c__UBA11346;o__UBA11346;f__UBA11346;g__JACDEC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903902515.1	s__CAIUVD01 sp903902515	77.5439	184	1627	d__Bacteria;p__Planctomycetota;c__UBA11346;o__UBA11346;f__UBA11346;g__CAIUVD01	95.0	99.75	99.70	0.91	0.90	3	-
GCA_013816415.1	s__JACCZE01 sp013816415	77.5195	216	1627	d__Bacteria;p__Planctomycetota;c__UBA11346;o__UBA11346;f__UBA11346;g__JACCZE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013696105.1	s__JACCZE01 sp013696105	77.2647	242	1627	d__Bacteria;p__Planctomycetota;c__UBA11346;o__UBA11346;f__UBA11346;g__JACCZE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003136555.1	s__BOG-1363 sp003136555	77.0269	294	1627	d__Bacteria;p__Planctomycetota;c__UBA11346;o__UBA11346;f__UBA11346;g__BOG-1363	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872755.1	s__GW928-bin9 sp016872755	75.3591	106	1627	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GW928-bin9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003434305.1	s__Micromonospora sp003434305	74.7668	221	1627	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648395.1	s__Micromonospora fulviviridis	74.7297	241	1627	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	95.01	95.01	0.74	0.74	2	-
--------------------------------------------------------------------------------
[2023-06-14 01:09:15,932] [INFO] GTDB search result was written to GCA_022841245.1_ASM2284124v1_genomic.fna/result_gtdb.tsv
[2023-06-14 01:09:15,933] [INFO] ===== GTDB Search completed =====
[2023-06-14 01:09:15,937] [INFO] DFAST_QC result json was written to GCA_022841245.1_ASM2284124v1_genomic.fna/dqc_result.json
[2023-06-14 01:09:15,937] [INFO] DFAST_QC completed!
[2023-06-14 01:09:15,937] [INFO] Total running time: 0h1m40s