[2024-01-24 12:47:14,086] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:14,088] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:14,088] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9157beb-9561-4b5b-8e47-8c9879977f19/dqc_reference
[2024-01-24 12:47:15,466] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:15,467] [INFO] Task started: Prodigal
[2024-01-24 12:47:15,467] [INFO] Running command: gunzip -c /var/lib/cwl/stg1eba346d-0b41-4588-ab2d-363ce0d12617/GCF_007751035.1_ASM775103v1_genomic.fna.gz | prodigal -d GCF_007751035.1_ASM775103v1_genomic.fna/cds.fna -a GCF_007751035.1_ASM775103v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:44,731] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:44,731] [INFO] Task started: HMMsearch
[2024-01-24 12:47:44,731] [INFO] Running command: hmmsearch --tblout GCF_007751035.1_ASM775103v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9157beb-9561-4b5b-8e47-8c9879977f19/dqc_reference/reference_markers.hmm GCF_007751035.1_ASM775103v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:45,138] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:45,139] [INFO] Found 6/6 markers.
[2024-01-24 12:47:45,207] [INFO] Query marker FASTA was written to GCF_007751035.1_ASM775103v1_genomic.fna/markers.fasta
[2024-01-24 12:47:45,208] [INFO] Task started: Blastn
[2024-01-24 12:47:45,208] [INFO] Running command: blastn -query GCF_007751035.1_ASM775103v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9157beb-9561-4b5b-8e47-8c9879977f19/dqc_reference/reference_markers.fasta -out GCF_007751035.1_ASM775103v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:45,837] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:45,841] [INFO] Selected 21 target genomes.
[2024-01-24 12:47:45,841] [INFO] Target genome list was writen to GCF_007751035.1_ASM775103v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:45,850] [INFO] Task started: fastANI
[2024-01-24 12:47:45,851] [INFO] Running command: fastANI --query /var/lib/cwl/stg1eba346d-0b41-4588-ab2d-363ce0d12617/GCF_007751035.1_ASM775103v1_genomic.fna.gz --refList GCF_007751035.1_ASM775103v1_genomic.fna/target_genomes.txt --output GCF_007751035.1_ASM775103v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:11,293] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:11,294] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9157beb-9561-4b5b-8e47-8c9879977f19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:11,294] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9157beb-9561-4b5b-8e47-8c9879977f19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:11,306] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:48:11,307] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:48:11,307] [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
Lignipirellula cremea	strain=Pla85_3_4	GCA_007751035.1	2528010	2528010	type	True	100.0	3186	3188	95	conclusive
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	75.8727	124	3188	95	below_threshold
Roseimaritima ulvae	strain=DSM 25454	GCA_001642915.1	980254	980254	type	True	75.8362	120	3188	95	below_threshold
Roseimaritima ulvae	strain=UC8	GCA_008065135.1	980254	980254	type	True	75.8346	120	3188	95	below_threshold
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	75.8318	122	3188	95	below_threshold
Blastopirellula retiformator	strain=Enr8	GCA_007859755.1	2527970	2527970	type	True	75.6293	143	3188	95	below_threshold
Roseiconus nitratireducens	strain=JC645	GCA_008629675.1	2605748	2605748	type	True	75.5783	99	3188	95	below_threshold
Stieleria maiorica	strain=Mal15	GCA_008035925.1	2795974	2795974	type	True	75.5698	105	3188	95	below_threshold
Crateriforma conspicua	strain=Mal65	GCA_007752935.1	2527996	2527996	type	True	75.5417	91	3188	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	75.4882	133	3188	95	below_threshold
Stieleria varia	strain=Pla52n	GCA_007860045.1	2528005	2528005	type	True	75.4749	95	3188	95	below_threshold
Rhodopirellula solitaria	strain=CA85	GCA_007859855.1	2527987	2527987	type	True	75.4694	71	3188	95	below_threshold
Crateriforma spongiae	strain=JC647	GCA_012290005.1	2724528	2724528	type	True	75.4508	79	3188	95	below_threshold
Stieleria neptunia	strain=Enr13	GCA_007754155.1	2527979	2527979	type	True	75.3406	99	3188	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:48:11,315] [INFO] DFAST Taxonomy check result was written to GCF_007751035.1_ASM775103v1_genomic.fna/tc_result.tsv
[2024-01-24 12:48:11,316] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:11,316] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:11,316] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9157beb-9561-4b5b-8e47-8c9879977f19/dqc_reference/checkm_data
[2024-01-24 12:48:11,318] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:11,408] [INFO] Task started: CheckM
[2024-01-24 12:48:11,408] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007751035.1_ASM775103v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007751035.1_ASM775103v1_genomic.fna/checkm_input GCF_007751035.1_ASM775103v1_genomic.fna/checkm_result
[2024-01-24 12:49:24,922] [INFO] Task succeeded: CheckM
[2024-01-24 12:49:24,924] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:49:24,947] [INFO] ===== Completeness check finished =====
[2024-01-24 12:49:24,947] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:49:24,947] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007751035.1_ASM775103v1_genomic.fna/markers.fasta)
[2024-01-24 12:49:24,947] [INFO] Task started: Blastn
[2024-01-24 12:49:24,948] [INFO] Running command: blastn -query GCF_007751035.1_ASM775103v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9157beb-9561-4b5b-8e47-8c9879977f19/dqc_reference/reference_markers_gtdb.fasta -out GCF_007751035.1_ASM775103v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:49:25,817] [INFO] Task succeeded: Blastn
[2024-01-24 12:49:25,821] [INFO] Selected 27 target genomes.
[2024-01-24 12:49:25,821] [INFO] Target genome list was writen to GCF_007751035.1_ASM775103v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:49:25,878] [INFO] Task started: fastANI
[2024-01-24 12:49:25,879] [INFO] Running command: fastANI --query /var/lib/cwl/stg1eba346d-0b41-4588-ab2d-363ce0d12617/GCF_007751035.1_ASM775103v1_genomic.fna.gz --refList GCF_007751035.1_ASM775103v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007751035.1_ASM775103v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:56,113] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:56,132] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:49:56,132] [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_007751035.1	s__Lignipirellula cremea	100.0	3186	3188	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Lignipirellula	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007859945.1	s__Pseudobythopirellula maris	75.8806	123	3188	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Pseudobythopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007746075.1	s__Lacipirellula limnantheis	75.8395	121	3188	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	97.19	97.19	0.90	0.90	2	-
GCA_003389325.1	s__LB-PLM-3 sp003389325	75.8341	153	3188	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__PALSA-1355;g__LB-PLM-3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007745835.1	s__Botrimarina sp007745835	75.7984	100	3188	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Botrimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859755.1	s__Blastopirellula retiformator	75.6521	140	3188	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Blastopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008629675.1	s__Stieleria nitratireducens	75.5894	98	3188	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010367455.1	s__Laterigemmans baculatus	75.5752	108	3188	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Laterigemmans	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014154935.1	s__Stieleria sp014154935	75.5604	111	3188	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016784735.1	s__JADHUC01 sp016784735	75.5199	105	3188	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__JADHUC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016191115.1	s__JACPPG01 sp016191115	75.4919	125	3188	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__JACPPG01;g__JACPPG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007750855.1	s__Pirellulimonas nuda	75.4801	134	3188	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Pirellulimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012290005.1	s__Crateriforma spongiae	75.4579	78	3188	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.43	98.43	0.93	0.93	2	-
GCA_011772275.1	s__CS4-C045 sp011772275	75.4189	64	3188	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA7805;g__CS4-C045	95.0	100.00	100.00	0.98	0.98	5	-
GCF_007754155.1	s__Stieleria neptunia	75.3539	97	3188	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003153375.1	s__PALSA-1355 sp003153375	75.3214	124	3188	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_005778405.1	s__SXOA01 sp005778405	75.3138	113	3188	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__SXOA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007121535.1	s__SKKK01 sp007121535	75.2839	91	3188	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__SKKK01	95.0	99.67	99.63	0.89	0.86	4	-
GCA_007122045.1	s__PWXP01 sp007122045	75.2517	66	3188	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__PWXP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012729315.1	s__JAAYDI01 sp012729315	75.2401	93	3188	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__JAAYDI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016933425.1	s__UBA11386 sp016933425	74.943	63	3188	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__UBA11386	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:49:56,134] [INFO] GTDB search result was written to GCF_007751035.1_ASM775103v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:56,135] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:56,139] [INFO] DFAST_QC result json was written to GCF_007751035.1_ASM775103v1_genomic.fna/dqc_result.json
[2024-01-24 12:49:56,139] [INFO] DFAST_QC completed!
[2024-01-24 12:49:56,139] [INFO] Total running time: 0h2m42s