[2023-06-30 17:54:05,034] [INFO] DFAST_QC pipeline started.
[2023-06-30 17:54:05,035] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 17:54:05,036] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ecaedc4-48ce-434b-bbfd-f3dea1489f51/dqc_reference
[2023-06-30 17:54:06,321] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 17:54:06,322] [INFO] Task started: Prodigal
[2023-06-30 17:54:06,322] [INFO] Running command: gunzip -c /var/lib/cwl/stg39a30b36-97af-4413-925f-502ea5218d56/GCA_016784735.1_ASM1678473v1_genomic.fna.gz | prodigal -d GCA_016784735.1_ASM1678473v1_genomic.fna/cds.fna -a GCA_016784735.1_ASM1678473v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 17:54:44,932] [INFO] Task succeeded: Prodigal
[2023-06-30 17:54:44,932] [INFO] Task started: HMMsearch
[2023-06-30 17:54:44,932] [INFO] Running command: hmmsearch --tblout GCA_016784735.1_ASM1678473v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ecaedc4-48ce-434b-bbfd-f3dea1489f51/dqc_reference/reference_markers.hmm GCA_016784735.1_ASM1678473v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 17:54:45,308] [INFO] Task succeeded: HMMsearch
[2023-06-30 17:54:45,309] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg39a30b36-97af-4413-925f-502ea5218d56/GCA_016784735.1_ASM1678473v1_genomic.fna.gz]
[2023-06-30 17:54:45,384] [INFO] Query marker FASTA was written to GCA_016784735.1_ASM1678473v1_genomic.fna/markers.fasta
[2023-06-30 17:54:45,384] [INFO] Task started: Blastn
[2023-06-30 17:54:45,384] [INFO] Running command: blastn -query GCA_016784735.1_ASM1678473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ecaedc4-48ce-434b-bbfd-f3dea1489f51/dqc_reference/reference_markers.fasta -out GCA_016784735.1_ASM1678473v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:54:45,951] [INFO] Task succeeded: Blastn
[2023-06-30 17:54:45,955] [INFO] Selected 24 target genomes.
[2023-06-30 17:54:45,956] [INFO] Target genome list was writen to GCA_016784735.1_ASM1678473v1_genomic.fna/target_genomes.txt
[2023-06-30 17:54:45,957] [INFO] Task started: fastANI
[2023-06-30 17:54:45,957] [INFO] Running command: fastANI --query /var/lib/cwl/stg39a30b36-97af-4413-925f-502ea5218d56/GCA_016784735.1_ASM1678473v1_genomic.fna.gz --refList GCA_016784735.1_ASM1678473v1_genomic.fna/target_genomes.txt --output GCA_016784735.1_ASM1678473v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 17:55:08,277] [INFO] Task succeeded: fastANI
[2023-06-30 17:55:08,278] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ecaedc4-48ce-434b-bbfd-f3dea1489f51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 17:55:08,278] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ecaedc4-48ce-434b-bbfd-f3dea1489f51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 17:55:08,288] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 17:55:08,288] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 17:55:08,288] [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
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.808	76	3667	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	75.7134	76	3667	95	below_threshold
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	75.6238	56	3667	95	below_threshold
Lignipirellula cremea	strain=Pla85_3_4	GCA_007751035.1	2528010	2528010	type	True	75.4892	102	3667	95	below_threshold
Bremerella volcania	strain=Pan97	GCA_007748115.1	2527984	2527984	type	True	75.4801	57	3667	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	75.4205	65	3667	95	below_threshold
Blastopirellula retiformator	strain=Enr8	GCA_007859755.1	2527970	2527970	type	True	75.411	52	3667	95	below_threshold
Rosistilla oblonga	strain=CA51	GCA_007751715.1	2527990	2527990	type	True	75.4094	60	3667	95	below_threshold
Stieleria neptunia	strain=Enr13	GCA_007754155.1	2527979	2527979	type	True	75.368	72	3667	95	below_threshold
Roseimaritima sediminicola	strain=JC651	GCA_009618275.1	2662066	2662066	type	True	75.3445	67	3667	95	below_threshold
Anatilimnocola aggregata	strain=ETA_A8	GCA_007747655.1	2528021	2528021	type	True	75.191	68	3667	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 17:55:08,290] [INFO] DFAST Taxonomy check result was written to GCA_016784735.1_ASM1678473v1_genomic.fna/tc_result.tsv
[2023-06-30 17:55:08,291] [INFO] ===== Taxonomy check completed =====
[2023-06-30 17:55:08,291] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 17:55:08,291] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ecaedc4-48ce-434b-bbfd-f3dea1489f51/dqc_reference/checkm_data
[2023-06-30 17:55:08,292] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 17:55:08,391] [INFO] Task started: CheckM
[2023-06-30 17:55:08,392] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016784735.1_ASM1678473v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016784735.1_ASM1678473v1_genomic.fna/checkm_input GCA_016784735.1_ASM1678473v1_genomic.fna/checkm_result
[2023-06-30 17:56:50,095] [INFO] Task succeeded: CheckM
[2023-06-30 17:56:50,096] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 17:56:50,117] [INFO] ===== Completeness check finished =====
[2023-06-30 17:56:50,117] [INFO] ===== Start GTDB Search =====
[2023-06-30 17:56:50,118] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016784735.1_ASM1678473v1_genomic.fna/markers.fasta)
[2023-06-30 17:56:50,118] [INFO] Task started: Blastn
[2023-06-30 17:56:50,118] [INFO] Running command: blastn -query GCA_016784735.1_ASM1678473v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ecaedc4-48ce-434b-bbfd-f3dea1489f51/dqc_reference/reference_markers_gtdb.fasta -out GCA_016784735.1_ASM1678473v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:56:50,876] [INFO] Task succeeded: Blastn
[2023-06-30 17:56:50,880] [INFO] Selected 20 target genomes.
[2023-06-30 17:56:50,880] [INFO] Target genome list was writen to GCA_016784735.1_ASM1678473v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 17:56:50,885] [INFO] Task started: fastANI
[2023-06-30 17:56:50,885] [INFO] Running command: fastANI --query /var/lib/cwl/stg39a30b36-97af-4413-925f-502ea5218d56/GCA_016784735.1_ASM1678473v1_genomic.fna.gz --refList GCA_016784735.1_ASM1678473v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016784735.1_ASM1678473v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 17:57:12,548] [INFO] Task succeeded: fastANI
[2023-06-30 17:57:12,559] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 17:57:12,559] [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_016784735.1	s__JADHUC01 sp016784735	100.0	3622	3667	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__JADHUC01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002726245.1	s__GCA-2726245 sp002726245	76.2684	86	3667	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__GCA-2726245	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012728855.1	s__JABWBD01 sp012728855	76.0035	167	3667	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JABWBD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012515235.1	s__Anammoximicrobium sp012515235	75.9069	255	3667	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Anammoximicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859935.1	s__Posidoniimonas polymericola	75.808	76	3667	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007121535.1	s__SKKK01 sp007121535	75.6955	134	3667	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__SKKK01	95.0	99.67	99.63	0.89	0.86	4	-
GCF_010367455.1	s__Laterigemmans baculatus	75.379	62	3667	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Laterigemmans	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016191115.1	s__JACPPG01 sp016191115	75.3495	86	3667	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__JACPPG01;g__JACPPG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016931075.1	s__JAFGFF01 sp016931075	75.1606	75	3667	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAFGFF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872555.1	s__F1-20-MAGs016 sp016872555	75.1406	55	3667	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__F1-20-MAGs016	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576845.1	s__PLA5 sp003576845	75.0789	103	3667	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__PLA5;g__PLA5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007119795.1	s__SKOZ01 sp007119795	75.0706	52	3667	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__SKOZ01	95.0	99.25	99.25	0.71	0.71	2	-
GCA_016872605.1	s__SIAQ01 sp016872605	75.0071	54	3667	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Gemmatales;f__Gemmataceae;g__SIAQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 17:57:12,564] [INFO] GTDB search result was written to GCA_016784735.1_ASM1678473v1_genomic.fna/result_gtdb.tsv
[2023-06-30 17:57:12,564] [INFO] ===== GTDB Search completed =====
[2023-06-30 17:57:12,568] [INFO] DFAST_QC result json was written to GCA_016784735.1_ASM1678473v1_genomic.fna/dqc_result.json
[2023-06-30 17:57:12,568] [INFO] DFAST_QC completed!
[2023-06-30 17:57:12,569] [INFO] Total running time: 0h3m8s