[2024-01-24 14:06:30,046] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:30,048] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:30,048] [INFO] DQC Reference Directory: /var/lib/cwl/stge6f6413a-74b9-445f-8ad0-395eff8959db/dqc_reference
[2024-01-24 14:06:31,390] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:31,391] [INFO] Task started: Prodigal
[2024-01-24 14:06:31,391] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9996638-f6c2-4273-a02f-5e2178551546/GCF_007747655.1_ASM774765v1_genomic.fna.gz | prodigal -d GCF_007747655.1_ASM774765v1_genomic.fna/cds.fna -a GCF_007747655.1_ASM774765v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:10,039] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:10,040] [INFO] Task started: HMMsearch
[2024-01-24 14:07:10,040] [INFO] Running command: hmmsearch --tblout GCF_007747655.1_ASM774765v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6f6413a-74b9-445f-8ad0-395eff8959db/dqc_reference/reference_markers.hmm GCF_007747655.1_ASM774765v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:10,524] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:10,526] [INFO] Found 6/6 markers.
[2024-01-24 14:07:10,597] [INFO] Query marker FASTA was written to GCF_007747655.1_ASM774765v1_genomic.fna/markers.fasta
[2024-01-24 14:07:10,597] [INFO] Task started: Blastn
[2024-01-24 14:07:10,597] [INFO] Running command: blastn -query GCF_007747655.1_ASM774765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6f6413a-74b9-445f-8ad0-395eff8959db/dqc_reference/reference_markers.fasta -out GCF_007747655.1_ASM774765v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:11,188] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:11,191] [INFO] Selected 23 target genomes.
[2024-01-24 14:07:11,191] [INFO] Target genome list was writen to GCF_007747655.1_ASM774765v1_genomic.fna/target_genomes.txt
[2024-01-24 14:07:11,208] [INFO] Task started: fastANI
[2024-01-24 14:07:11,208] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9996638-f6c2-4273-a02f-5e2178551546/GCF_007747655.1_ASM774765v1_genomic.fna.gz --refList GCF_007747655.1_ASM774765v1_genomic.fna/target_genomes.txt --output GCF_007747655.1_ASM774765v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:30,813] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:30,814] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6f6413a-74b9-445f-8ad0-395eff8959db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:30,815] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6f6413a-74b9-445f-8ad0-395eff8959db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:30,828] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:07:30,828] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:30,828] [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
Anatilimnocola aggregata	strain=ETA_A8	GCA_007747655.1	2528021	2528021	type	True	100.0	3001	3002	95	conclusive
Lignipirellula cremea	strain=Pla85_3_4	GCA_007751035.1	2528010	2528010	type	True	77.6358	163	3002	95	below_threshold
Pirellula staleyi	strain=DSM 6068	GCA_000025185.1	125	125	type	True	76.3736	227	3002	95	below_threshold
Crateriforma conspicua	strain=Mal65	GCA_007752935.1	2527996	2527996	type	True	75.8982	59	3002	95	below_threshold
Blastopirellula retiformator	strain=Enr8	GCA_007859755.1	2527970	2527970	type	True	75.8771	117	3002	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	75.7917	107	3002	95	below_threshold
Bremerella alba	strain=FF15	GCA_013618625.1	980252	980252	type	True	75.6778	74	3002	95	below_threshold
Rosistilla carotiformis	strain=Poly24	GCA_007753095.1	2528017	2528017	type	True	75.6746	68	3002	95	below_threshold
Blastopirellula marina	strain=DSM 3645	GCA_000153105.1	124	124	suspected-type	True	75.6729	108	3002	95	below_threshold
Bremerella volcania	strain=Pan97	GCA_007748115.1	2527984	2527984	type	True	75.6518	88	3002	95	below_threshold
Crateriforma spongiae	strain=JC647	GCA_012290005.1	2724528	2724528	type	True	75.6181	62	3002	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:30,830] [INFO] DFAST Taxonomy check result was written to GCF_007747655.1_ASM774765v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:30,830] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:30,830] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:30,831] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6f6413a-74b9-445f-8ad0-395eff8959db/dqc_reference/checkm_data
[2024-01-24 14:07:30,832] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:30,910] [INFO] Task started: CheckM
[2024-01-24 14:07:30,910] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007747655.1_ASM774765v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007747655.1_ASM774765v1_genomic.fna/checkm_input GCF_007747655.1_ASM774765v1_genomic.fna/checkm_result
[2024-01-24 14:09:14,585] [INFO] Task succeeded: CheckM
[2024-01-24 14:09:14,587] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:09:14,619] [INFO] ===== Completeness check finished =====
[2024-01-24 14:09:14,620] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:09:14,620] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007747655.1_ASM774765v1_genomic.fna/markers.fasta)
[2024-01-24 14:09:14,621] [INFO] Task started: Blastn
[2024-01-24 14:09:14,621] [INFO] Running command: blastn -query GCF_007747655.1_ASM774765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6f6413a-74b9-445f-8ad0-395eff8959db/dqc_reference/reference_markers_gtdb.fasta -out GCF_007747655.1_ASM774765v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:09:15,468] [INFO] Task succeeded: Blastn
[2024-01-24 14:09:15,472] [INFO] Selected 21 target genomes.
[2024-01-24 14:09:15,472] [INFO] Target genome list was writen to GCF_007747655.1_ASM774765v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:09:15,486] [INFO] Task started: fastANI
[2024-01-24 14:09:15,487] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9996638-f6c2-4273-a02f-5e2178551546/GCF_007747655.1_ASM774765v1_genomic.fna.gz --refList GCF_007747655.1_ASM774765v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007747655.1_ASM774765v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:09:34,768] [INFO] Task succeeded: fastANI
[2024-01-24 14:09:34,785] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:09:34,785] [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_007747655.1	s__Anatilimnocola aggregata	100.0	3001	3002	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Anatilimnocola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000025185.1	s__Pirellula staleyi	76.3629	227	3002	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Pirellula	95.0	98.27	98.27	0.94	0.94	2	-
GCA_013822725.1	s__Lacipirellula sp013822725	76.2117	85	3002	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009177095.1	s__Lacipirellula parvula	75.7917	107	3002	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Lacipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007753095.1	s__Rosistilla carotiformis	75.6903	67	3002	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rosistilla	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242585.1	s__JAFEBQ01 sp018242585	75.6698	127	3002	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__PNKZ01;g__JAFEBQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012290005.1	s__Crateriforma spongiae	75.6181	62	3002	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.43	98.43	0.93	0.93	2	-
GCA_003389325.1	s__LB-PLM-3 sp003389325	75.591	104	3002	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_003576845.1	s__PLA5 sp003576845	75.5204	103	3002	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__PLA5;g__PLA5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010367455.1	s__Laterigemmans baculatus	75.4574	74	3002	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Laterigemmans	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003153375.1	s__PALSA-1355 sp003153375	75.2979	105	3002	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_003455945.1	s__UBA11682 sp003455945	75.2728	72	3002	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA11682	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:09:34,787] [INFO] GTDB search result was written to GCF_007747655.1_ASM774765v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:09:34,788] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:09:34,791] [INFO] DFAST_QC result json was written to GCF_007747655.1_ASM774765v1_genomic.fna/dqc_result.json
[2024-01-24 14:09:34,791] [INFO] DFAST_QC completed!
[2024-01-24 14:09:34,791] [INFO] Total running time: 0h3m5s