[2023-06-29 12:58:41,870] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:58:41,873] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:58:41,873] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e6d59fe-a21a-4790-b718-2c5d1c9dccaf/dqc_reference
[2023-06-29 12:58:43,294] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:58:43,295] [INFO] Task started: Prodigal
[2023-06-29 12:58:43,296] [INFO] Running command: gunzip -c /var/lib/cwl/stg864e79c6-ca1a-4182-8223-dac68d170463/GCA_012728855.1_ASM1272885v1_genomic.fna.gz | prodigal -d GCA_012728855.1_ASM1272885v1_genomic.fna/cds.fna -a GCA_012728855.1_ASM1272885v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:59:19,615] [INFO] Task succeeded: Prodigal
[2023-06-29 12:59:19,615] [INFO] Task started: HMMsearch
[2023-06-29 12:59:19,616] [INFO] Running command: hmmsearch --tblout GCA_012728855.1_ASM1272885v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e6d59fe-a21a-4790-b718-2c5d1c9dccaf/dqc_reference/reference_markers.hmm GCA_012728855.1_ASM1272885v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:59:20,025] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:59:20,026] [INFO] Found 6/6 markers.
[2023-06-29 12:59:20,104] [INFO] Query marker FASTA was written to GCA_012728855.1_ASM1272885v1_genomic.fna/markers.fasta
[2023-06-29 12:59:20,105] [INFO] Task started: Blastn
[2023-06-29 12:59:20,105] [INFO] Running command: blastn -query GCA_012728855.1_ASM1272885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e6d59fe-a21a-4790-b718-2c5d1c9dccaf/dqc_reference/reference_markers.fasta -out GCA_012728855.1_ASM1272885v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:59:20,713] [INFO] Task succeeded: Blastn
[2023-06-29 12:59:20,718] [INFO] Selected 26 target genomes.
[2023-06-29 12:59:20,719] [INFO] Target genome list was writen to GCA_012728855.1_ASM1272885v1_genomic.fna/target_genomes.txt
[2023-06-29 12:59:20,726] [INFO] Task started: fastANI
[2023-06-29 12:59:20,726] [INFO] Running command: fastANI --query /var/lib/cwl/stg864e79c6-ca1a-4182-8223-dac68d170463/GCA_012728855.1_ASM1272885v1_genomic.fna.gz --refList GCA_012728855.1_ASM1272885v1_genomic.fna/target_genomes.txt --output GCA_012728855.1_ASM1272885v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:59:44,389] [INFO] Task succeeded: fastANI
[2023-06-29 12:59:44,389] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e6d59fe-a21a-4790-b718-2c5d1c9dccaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:59:44,390] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e6d59fe-a21a-4790-b718-2c5d1c9dccaf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:59:44,412] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:59:44,412] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 12:59:44,412] [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
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	75.6999	116	3385	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	75.5702	134	3385	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	75.5328	137	3385	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.4501	152	3385	95	below_threshold
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	75.4106	106	3385	95	below_threshold
Aeoliella mucimassa	strain=Pan181	GCA_007748035.1	2527972	2527972	type	True	75.296	50	3385	95	below_threshold
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	75.2509	103	3385	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	75.2186	107	3385	95	below_threshold
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	75.0861	136	3385	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	75.0693	161	3385	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.0656	139	3385	95	below_threshold
Roseimaritima sediminicola	strain=JC651	GCA_009618275.1	2662066	2662066	type	True	75.054	81	3385	95	below_threshold
Tautonia sociabilis	strain=GM2012	GCA_003977685.1	2080755	2080755	type	True	74.9855	104	3385	95	below_threshold
Pseudoroseicyclus tamaricis	strain=CLL3-39	GCA_010435925.1	2705421	2705421	type	True	74.8086	59	3385	95	below_threshold
Deinococcus metallilatus	strain=MA1002	GCA_004758605.1	1211322	1211322	type	True	74.7328	53	3385	95	below_threshold
Pleomorphomonas diazotrophica	strain=R5-392	GCA_002844595.1	1166257	1166257	type	True	74.7217	52	3385	95	below_threshold
Pleomorphomonas diazotrophica	strain=R5-392	GCA_900114935.1	1166257	1166257	type	True	74.7207	52	3385	95	below_threshold
Pseudoroseicyclus tamaricis	strain=CLL3-39	GCA_012070395.1	2705421	2705421	type	True	74.7176	58	3385	95	below_threshold
Deinococcus metallilatus	strain=DSM 105434	GCA_014202095.1	1211322	1211322	type	True	74.6526	53	3385	95	below_threshold
Kibdelosporangium banguiense	strain=DSM 46670	GCA_017876405.1	1365924	1365924	type	True	74.6305	101	3385	95	below_threshold
Deinococcus metallilatus	strain=MA1002	GCA_004115945.1	1211322	1211322	type	True	74.6075	52	3385	95	below_threshold
Nocardia iowensis	strain=NRRL 5646	GCA_019222765.1	204891	204891	type	True	74.5884	83	3385	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:59:44,414] [INFO] DFAST Taxonomy check result was written to GCA_012728855.1_ASM1272885v1_genomic.fna/tc_result.tsv
[2023-06-29 12:59:44,415] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:59:44,415] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:59:44,415] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e6d59fe-a21a-4790-b718-2c5d1c9dccaf/dqc_reference/checkm_data
[2023-06-29 12:59:44,416] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:59:44,523] [INFO] Task started: CheckM
[2023-06-29 12:59:44,523] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_012728855.1_ASM1272885v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_012728855.1_ASM1272885v1_genomic.fna/checkm_input GCA_012728855.1_ASM1272885v1_genomic.fna/checkm_result
[2023-06-29 13:01:20,313] [INFO] Task succeeded: CheckM
[2023-06-29 13:01:20,315] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-29 13:01:20,344] [INFO] ===== Completeness check finished =====
[2023-06-29 13:01:20,344] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:01:20,344] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_012728855.1_ASM1272885v1_genomic.fna/markers.fasta)
[2023-06-29 13:01:20,345] [INFO] Task started: Blastn
[2023-06-29 13:01:20,345] [INFO] Running command: blastn -query GCA_012728855.1_ASM1272885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e6d59fe-a21a-4790-b718-2c5d1c9dccaf/dqc_reference/reference_markers_gtdb.fasta -out GCA_012728855.1_ASM1272885v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:01:21,322] [INFO] Task succeeded: Blastn
[2023-06-29 13:01:21,328] [INFO] Selected 23 target genomes.
[2023-06-29 13:01:21,328] [INFO] Target genome list was writen to GCA_012728855.1_ASM1272885v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:01:21,340] [INFO] Task started: fastANI
[2023-06-29 13:01:21,340] [INFO] Running command: fastANI --query /var/lib/cwl/stg864e79c6-ca1a-4182-8223-dac68d170463/GCA_012728855.1_ASM1272885v1_genomic.fna.gz --refList GCA_012728855.1_ASM1272885v1_genomic.fna/target_genomes_gtdb.txt --output GCA_012728855.1_ASM1272885v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:01:47,086] [INFO] Task succeeded: fastANI
[2023-06-29 13:01:47,105] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 13:01:47,105] [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_012728855.1	s__JABWBD01 sp012728855	100.0	3365	3385	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JABWBD01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013360685.1	s__JABWBD01 sp013360685	78.6786	873	3385	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JABWBD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012744395.1	s__JAAYCB01 sp012744395	76.8912	339	3385	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAAYCB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012719125.1	s__JAAYAY01 sp012719125	76.7236	385	3385	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAAYAY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018897395.1	s__JAHIKV01 sp018897395	76.2616	167	3385	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAHIKV01	95.0	99.63	99.63	0.95	0.95	2	-
GCA_011367845.1	s__DSXL01 sp011367845	76.199	268	3385	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__DSXL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016935315.1	s__JAFGRD01 sp016935315	76.1935	267	3385	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAFGRD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016936015.1	s__JAFGPV01 sp016936015	76.102	194	3385	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAFGPV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007119795.1	s__SKOZ01 sp007119795	76.0744	133	3385	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__SKOZ01	95.0	99.25	99.25	0.71	0.71	2	-
GCA_016931995.1	s__JAFGDS01 sp016931995	76.0175	230	3385	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAFGDS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007122045.1	s__PWXP01 sp007122045	75.8875	137	3385	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__PWXP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016928165.1	s__JAHIKV01 sp016928165	75.8766	151	3385	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAHIKV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016929515.1	s__UBA11386 sp016929515	75.655	110	3385	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__UBA11386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011332595.1	s__DSXM01 sp011332595	75.5669	93	3385	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__DSXM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859935.1	s__Posidoniimonas polymericola	75.4679	149	3385	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303535.1	s__PNKZ01 sp017303535	75.3759	107	3385	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__PNKZ01;g__PNKZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576845.1	s__PLA5 sp003576845	75.1765	135	3385	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__PLA5;g__PLA5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200205.1	s__PALSA-1355 sp016200205	75.1182	89	3385	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__PALSA-1355;g__PALSA-1355	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308215.1	s__Urbifossiella sp017308215	74.9181	129	3385	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__Urbifossiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014154935.1	s__Stieleria sp014154935	74.7656	82	3385	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 13:01:47,109] [INFO] GTDB search result was written to GCA_012728855.1_ASM1272885v1_genomic.fna/result_gtdb.tsv
[2023-06-29 13:01:47,110] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:01:47,115] [INFO] DFAST_QC result json was written to GCA_012728855.1_ASM1272885v1_genomic.fna/dqc_result.json
[2023-06-29 13:01:47,116] [INFO] DFAST_QC completed!
[2023-06-29 13:01:47,116] [INFO] Total running time: 0h3m5s