[2024-01-24 13:37:12,954] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:12,957] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:12,957] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf1e2d3b-6684-45ea-9151-d133c2dae0fa/dqc_reference
[2024-01-24 13:37:14,210] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:14,211] [INFO] Task started: Prodigal
[2024-01-24 13:37:14,211] [INFO] Running command: gunzip -c /var/lib/cwl/stg00decf11-525e-4400-8f19-95cec4519ba8/GCF_007860185.1_ASM786018v1_genomic.fna.gz | prodigal -d GCF_007860185.1_ASM786018v1_genomic.fna/cds.fna -a GCF_007860185.1_ASM786018v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:39,406] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:39,407] [INFO] Task started: HMMsearch
[2024-01-24 13:37:39,407] [INFO] Running command: hmmsearch --tblout GCF_007860185.1_ASM786018v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf1e2d3b-6684-45ea-9151-d133c2dae0fa/dqc_reference/reference_markers.hmm GCF_007860185.1_ASM786018v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:39,781] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:39,782] [INFO] Found 6/6 markers.
[2024-01-24 13:37:39,835] [INFO] Query marker FASTA was written to GCF_007860185.1_ASM786018v1_genomic.fna/markers.fasta
[2024-01-24 13:37:39,836] [INFO] Task started: Blastn
[2024-01-24 13:37:39,836] [INFO] Running command: blastn -query GCF_007860185.1_ASM786018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf1e2d3b-6684-45ea-9151-d133c2dae0fa/dqc_reference/reference_markers.fasta -out GCF_007860185.1_ASM786018v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:40,446] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:40,449] [INFO] Selected 24 target genomes.
[2024-01-24 13:37:40,450] [INFO] Target genome list was writen to GCF_007860185.1_ASM786018v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:40,460] [INFO] Task started: fastANI
[2024-01-24 13:37:40,460] [INFO] Running command: fastANI --query /var/lib/cwl/stg00decf11-525e-4400-8f19-95cec4519ba8/GCF_007860185.1_ASM786018v1_genomic.fna.gz --refList GCF_007860185.1_ASM786018v1_genomic.fna/target_genomes.txt --output GCF_007860185.1_ASM786018v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:38:13,708] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:13,709] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf1e2d3b-6684-45ea-9151-d133c2dae0fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:38:13,709] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf1e2d3b-6684-45ea-9151-d133c2dae0fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:38:13,724] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:38:13,724] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:38:13,725] [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
Novipirellula aureliae	strain=Q31b	GCA_007860185.1	2527966	2527966	type	True	100.0	2402	2403	95	conclusive
Rhodopirellula aestuarii	strain=ICT_H3.1	GCA_023701485.1	2950107	2950107	type	True	78.1938	155	2403	95	below_threshold
Novipirellula artificiosorum	strain=Poly41	GCA_007860135.1	2528016	2528016	type	True	78.086	338	2403	95	below_threshold
Crateriforma conspicua	strain=Mal65	GCA_007752935.1	2527996	2527996	type	True	77.592	107	2403	95	below_threshold
Rubripirellula obstinata	strain=LF1	GCA_008374075.1	406547	406547	type	True	77.4572	137	2403	95	below_threshold
Rubripirellula obstinata	strain=CECT 8602	GCA_001642955.1	406547	406547	type	True	77.4091	131	2403	95	below_threshold
Crateriforma spongiae	strain=JC647	GCA_012290005.1	2724528	2724528	type	True	77.2518	129	2403	95	below_threshold
Rhodopirellula maiorica	strain=SM1	GCA_000346295.1	1265734	1265734	type	True	77.1309	199	2403	95	below_threshold
Rubripirellula lacrimiformis	strain=K22.7	GCA_007741535.1	1930273	1930273	type	True	77.0115	158	2403	95	below_threshold
Novipirellula galeiformis	strain=Pla52o	GCA_007860095.1	2528004	2528004	type	True	76.8108	193	2403	95	below_threshold
Rhodopirellula solitaria	strain=CA85	GCA_007859855.1	2527987	2527987	type	True	76.4833	118	2403	95	below_threshold
Roseiconus lacunae	strain=JC635	GCA_008312935.1	2605694	2605694	type	True	76.0584	100	2403	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:38:13,726] [INFO] DFAST Taxonomy check result was written to GCF_007860185.1_ASM786018v1_genomic.fna/tc_result.tsv
[2024-01-24 13:38:13,727] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:38:13,727] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:38:13,727] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf1e2d3b-6684-45ea-9151-d133c2dae0fa/dqc_reference/checkm_data
[2024-01-24 13:38:13,728] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:38:13,795] [INFO] Task started: CheckM
[2024-01-24 13:38:13,795] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007860185.1_ASM786018v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007860185.1_ASM786018v1_genomic.fna/checkm_input GCF_007860185.1_ASM786018v1_genomic.fna/checkm_result
[2024-01-24 13:39:26,906] [INFO] Task succeeded: CheckM
[2024-01-24 13:39:26,907] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:39:26,925] [INFO] ===== Completeness check finished =====
[2024-01-24 13:39:26,925] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:39:26,926] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007860185.1_ASM786018v1_genomic.fna/markers.fasta)
[2024-01-24 13:39:26,926] [INFO] Task started: Blastn
[2024-01-24 13:39:26,926] [INFO] Running command: blastn -query GCF_007860185.1_ASM786018v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf1e2d3b-6684-45ea-9151-d133c2dae0fa/dqc_reference/reference_markers_gtdb.fasta -out GCF_007860185.1_ASM786018v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:39:27,681] [INFO] Task succeeded: Blastn
[2024-01-24 13:39:27,685] [INFO] Selected 23 target genomes.
[2024-01-24 13:39:27,686] [INFO] Target genome list was writen to GCF_007860185.1_ASM786018v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:39:27,724] [INFO] Task started: fastANI
[2024-01-24 13:39:27,724] [INFO] Running command: fastANI --query /var/lib/cwl/stg00decf11-525e-4400-8f19-95cec4519ba8/GCF_007860185.1_ASM786018v1_genomic.fna.gz --refList GCF_007860185.1_ASM786018v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007860185.1_ASM786018v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:53,040] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:53,051] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:39:53,051] [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_007860185.1	s__Novipirellula aureliae	100.0	2402	2403	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007860135.1	s__Novipirellula artificiosorum	78.1063	336	2403	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007859835.1	s__Novipirellula sp007859835	77.4361	332	2403	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001642955.1	s__Rubripirellula obstinata	77.3876	132	2403	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	99.93	99.93	1.00	1.00	2	-
GCF_012290005.1	s__Crateriforma spongiae	77.2522	129	2403	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.43	98.43	0.93	0.93	2	-
GCA_007741535.1	s__Rubripirellula sp007741535	77.1423	154	2403	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000346295.1	s__Novipirellula maiorica	77.1332	198	2403	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860095.1	s__Novipirellula galeiformis	76.8225	190	2403	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859855.1	s__Rhodopirellula solitaria	76.5079	112	2403	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000346505.1	s__Rhodopirellula sallentina	76.4954	110	2403	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008312935.1	s__Stieleria lacunae	76.0735	99	2403	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	99.99	99.99	1.00	1.00	2	-
GCA_007694185.1	s__UBA6163 sp007694185	75.8558	71	2403	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA6163	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007127095.1	s__UBA6163 sp007127095	75.6599	69	2403	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA6163	95.0	99.08	99.08	0.89	0.86	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:39:53,053] [INFO] GTDB search result was written to GCF_007860185.1_ASM786018v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:53,053] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:53,059] [INFO] DFAST_QC result json was written to GCF_007860185.1_ASM786018v1_genomic.fna/dqc_result.json
[2024-01-24 13:39:53,059] [INFO] DFAST_QC completed!
[2024-01-24 13:39:53,059] [INFO] Total running time: 0h2m40s