[2024-01-24 11:05:25,246] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:25,250] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:25,250] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c9d58c0-83fe-4bad-a857-c4bc447fa937/dqc_reference
[2024-01-24 11:05:26,790] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:26,791] [INFO] Task started: Prodigal
[2024-01-24 11:05:26,791] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d38055d-f747-4fca-be82-dbc313ddea74/GCF_007745175.1_ASM774517v1_genomic.fna.gz | prodigal -d GCF_007745175.1_ASM774517v1_genomic.fna/cds.fna -a GCF_007745175.1_ASM774517v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:46,297] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:46,298] [INFO] Task started: HMMsearch
[2024-01-24 11:05:46,298] [INFO] Running command: hmmsearch --tblout GCF_007745175.1_ASM774517v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c9d58c0-83fe-4bad-a857-c4bc447fa937/dqc_reference/reference_markers.hmm GCF_007745175.1_ASM774517v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:46,633] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:46,635] [INFO] Found 6/6 markers.
[2024-01-24 11:05:46,689] [INFO] Query marker FASTA was written to GCF_007745175.1_ASM774517v1_genomic.fna/markers.fasta
[2024-01-24 11:05:46,689] [INFO] Task started: Blastn
[2024-01-24 11:05:46,689] [INFO] Running command: blastn -query GCF_007745175.1_ASM774517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c9d58c0-83fe-4bad-a857-c4bc447fa937/dqc_reference/reference_markers.fasta -out GCF_007745175.1_ASM774517v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:47,427] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:47,431] [INFO] Selected 31 target genomes.
[2024-01-24 11:05:47,432] [INFO] Target genome list was writen to GCF_007745175.1_ASM774517v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:47,446] [INFO] Task started: fastANI
[2024-01-24 11:05:47,447] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d38055d-f747-4fca-be82-dbc313ddea74/GCF_007745175.1_ASM774517v1_genomic.fna.gz --refList GCF_007745175.1_ASM774517v1_genomic.fna/target_genomes.txt --output GCF_007745175.1_ASM774517v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:15,519] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:15,520] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c9d58c0-83fe-4bad-a857-c4bc447fa937/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:15,521] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c9d58c0-83fe-4bad-a857-c4bc447fa937/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:15,540] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:15,540] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:15,541] [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
Caulifigura coniformis	strain=Pan44	GCA_007745175.1	2527983	2527983	type	True	100.0	2253	2253	95	conclusive
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	76.2638	254	2253	95	below_threshold
Planctomicrobium piriforme	strain=DSM 26348	GCA_900113665.1	1576369	1576369	type	True	76.0819	182	2253	95	below_threshold
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	76.0561	88	2253	95	below_threshold
Alienimonas chondri	strain=LzC2	GCA_013036045.1	2681879	2681879	type	True	75.9305	114	2253	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	75.8239	103	2253	95	below_threshold
Calycomorphotria hydatis	strain=V22	GCA_007745435.1	2528027	2528027	type	True	75.7521	61	2253	95	below_threshold
Rubinisphaera brasiliensis	strain=DSM 5305	GCA_000165715.3	119	119	type	True	75.6952	76	2253	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	75.6777	127	2253	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.6729	119	2253	95	below_threshold
Schlesneria paludicola	strain=DSM 18645	GCA_000255655.1	360056	360056	type	True	75.4191	78	2253	95	below_threshold
Blastopirellula retiformator	strain=Enr8	GCA_007859755.1	2527970	2527970	type	True	75.3186	68	2253	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	75.2051	145	2253	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.037	66	2253	95	below_threshold
Sphingopyxis macrogoltabida	strain=203	GCA_001314325.1	33050	33050	type	True	74.7292	50	2253	95	below_threshold
Lentzea cavernae	strain=CGMCC 4.7367	GCA_014653695.1	2020703	2020703	type	True	74.7289	85	2253	95	below_threshold
Lentzea atacamensis	strain=DSM 45479	GCA_003269295.1	531938	531938	type	True	74.7249	82	2253	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	74.7087	67	2253	95	below_threshold
Aeromicrobium endophyticum	strain=M2KJ-4	GCA_003586285.1	2292704	2292704	type	True	74.6895	55	2253	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:15,543] [INFO] DFAST Taxonomy check result was written to GCF_007745175.1_ASM774517v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:15,544] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:15,544] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:15,544] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c9d58c0-83fe-4bad-a857-c4bc447fa937/dqc_reference/checkm_data
[2024-01-24 11:06:15,545] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:15,610] [INFO] Task started: CheckM
[2024-01-24 11:06:15,611] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007745175.1_ASM774517v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007745175.1_ASM774517v1_genomic.fna/checkm_input GCF_007745175.1_ASM774517v1_genomic.fna/checkm_result
[2024-01-24 11:07:25,225] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:25,227] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:25,250] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:25,250] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:25,251] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007745175.1_ASM774517v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:25,251] [INFO] Task started: Blastn
[2024-01-24 11:07:25,251] [INFO] Running command: blastn -query GCF_007745175.1_ASM774517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c9d58c0-83fe-4bad-a857-c4bc447fa937/dqc_reference/reference_markers_gtdb.fasta -out GCF_007745175.1_ASM774517v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:26,187] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:26,194] [INFO] Selected 26 target genomes.
[2024-01-24 11:07:26,194] [INFO] Target genome list was writen to GCF_007745175.1_ASM774517v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:26,216] [INFO] Task started: fastANI
[2024-01-24 11:07:26,216] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d38055d-f747-4fca-be82-dbc313ddea74/GCF_007745175.1_ASM774517v1_genomic.fna.gz --refList GCF_007745175.1_ASM774517v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007745175.1_ASM774517v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:49,819] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:49,838] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:49,838] [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_007745175.1	s__Caulifigura coniformis	100.0	2253	2253	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Caulifigura	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001610835.1	s__Planctomyces_A sp001610835	76.6513	313	2253	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctomyces_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003671275.1	s__TH-plancto1 sp003671275	76.5485	116	2253	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__TH-plancto1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007747795.1	s__Maioricimonas rarisocia	76.3023	257	2253	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Maioricimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113665.1	s__Planctomicrobium piriforme	76.0663	184	2253	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795125.1	s__JAEUIG01 sp016795125	76.0653	205	2253	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JAEUIG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003388505.1	s__MB-PLM-1 sp003388505	76.0146	206	2253	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__MB-PLM-1	95.0	99.82	99.66	0.97	0.95	4	-
GCA_013813775.1	s__JACCRE01 sp013813775	75.8269	158	2253	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JACCRE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017795105.1	s__Rubinisphaera sp017795105	75.8147	114	2253	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Rubinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970605.1	s__QWPN01 sp018970605	75.7062	67	2253	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859765.1	s__Posidoniimonas corsicana	75.6777	127	2253	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859935.1	s__Posidoniimonas polymericola	75.6736	121	2253	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007747215.1	s__Urbifossiella limnaea	75.3773	154	2253	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Urbifossiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002197845.1	s__Fimbriiglobus ruber	75.3408	110	2253	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Fimbriiglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859755.1	s__Blastopirellula retiformator	75.3104	69	2253	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Blastopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903831155.1	s__QWPN01 sp903831155	75.1209	87	2253	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016184365.1	s__AR8 sp016184365	74.6947	64	2253	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__AR8	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:49,840] [INFO] GTDB search result was written to GCF_007745175.1_ASM774517v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:49,840] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:49,844] [INFO] DFAST_QC result json was written to GCF_007745175.1_ASM774517v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:49,844] [INFO] DFAST_QC completed!
[2024-01-24 11:07:49,845] [INFO] Total running time: 0h2m25s