[2024-01-24 13:13:08,333] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:08,336] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:08,336] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f7111cf-8522-41b6-bce4-ac82563aaaad/dqc_reference
[2024-01-24 13:13:09,592] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:09,592] [INFO] Task started: Prodigal
[2024-01-24 13:13:09,593] [INFO] Running command: gunzip -c /var/lib/cwl/stg1ef09250-1891-4383-8c80-922ef66f2b0c/GCF_007741535.1_ASM774153v1_genomic.fna.gz | prodigal -d GCF_007741535.1_ASM774153v1_genomic.fna/cds.fna -a GCF_007741535.1_ASM774153v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:53,021] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:53,021] [INFO] Task started: HMMsearch
[2024-01-24 13:13:53,021] [INFO] Running command: hmmsearch --tblout GCF_007741535.1_ASM774153v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f7111cf-8522-41b6-bce4-ac82563aaaad/dqc_reference/reference_markers.hmm GCF_007741535.1_ASM774153v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:53,421] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:53,422] [INFO] Found 6/6 markers.
[2024-01-24 13:13:53,485] [INFO] Query marker FASTA was written to GCF_007741535.1_ASM774153v1_genomic.fna/markers.fasta
[2024-01-24 13:13:53,486] [INFO] Task started: Blastn
[2024-01-24 13:13:53,486] [INFO] Running command: blastn -query GCF_007741535.1_ASM774153v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f7111cf-8522-41b6-bce4-ac82563aaaad/dqc_reference/reference_markers.fasta -out GCF_007741535.1_ASM774153v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:54,133] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:54,136] [INFO] Selected 18 target genomes.
[2024-01-24 13:13:54,136] [INFO] Target genome list was writen to GCF_007741535.1_ASM774153v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:54,221] [INFO] Task started: fastANI
[2024-01-24 13:13:54,221] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ef09250-1891-4383-8c80-922ef66f2b0c/GCF_007741535.1_ASM774153v1_genomic.fna.gz --refList GCF_007741535.1_ASM774153v1_genomic.fna/target_genomes.txt --output GCF_007741535.1_ASM774153v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:18,180] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:18,181] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f7111cf-8522-41b6-bce4-ac82563aaaad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:18,181] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f7111cf-8522-41b6-bce4-ac82563aaaad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:18,190] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:14:18,191] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:18,191] [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
Rubripirellula lacrimiformis	strain=K22.7	GCA_007741535.1	1930273	1930273	type	True	100.0	2847	2847	95	conclusive
Rubripirellula tenax	strain=Poly51	GCA_007860125.1	2528015	2528015	type	True	78.34	635	2847	95	below_threshold
Rubripirellula reticaptiva	strain=Poly59	GCA_007860175.1	2528013	2528013	type	True	78.3164	673	2847	95	below_threshold
Crateriforma conspicua	strain=Mal65	GCA_007752935.1	2527996	2527996	type	True	77.5459	297	2847	95	below_threshold
Crateriforma spongiae	strain=JC647	GCA_012290005.1	2724528	2724528	type	True	77.5374	286	2847	95	below_threshold
Rubripirellula obstinata	strain=CECT 8602	GCA_001642955.1	406547	406547	type	True	77.1951	314	2847	95	below_threshold
Rubripirellula obstinata	strain=LF1	GCA_008374075.1	406547	406547	type	True	77.1855	328	2847	95	below_threshold
Stieleria neptunia	strain=Enr13	GCA_007754155.1	2527979	2527979	type	True	76.3986	343	2847	95	below_threshold
Stieleria maiorica	strain=Mal15	GCA_008035925.1	2795974	2795974	type	True	76.3645	343	2847	95	below_threshold
Roseimaritima sediminicola	strain=JC651	GCA_009618275.1	2662066	2662066	type	True	76.2965	213	2847	95	below_threshold
Rhodopirellula sallentina	strain=SM41	GCA_000346505.1	1263869	1263869	type	True	76.1617	177	2847	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:18,192] [INFO] DFAST Taxonomy check result was written to GCF_007741535.1_ASM774153v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:18,193] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:18,193] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:18,193] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f7111cf-8522-41b6-bce4-ac82563aaaad/dqc_reference/checkm_data
[2024-01-24 13:14:18,194] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:18,275] [INFO] Task started: CheckM
[2024-01-24 13:14:18,275] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007741535.1_ASM774153v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007741535.1_ASM774153v1_genomic.fna/checkm_input GCF_007741535.1_ASM774153v1_genomic.fna/checkm_result
[2024-01-24 13:16:13,297] [INFO] Task succeeded: CheckM
[2024-01-24 13:16:13,298] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:16:13,318] [INFO] ===== Completeness check finished =====
[2024-01-24 13:16:13,318] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:16:13,319] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007741535.1_ASM774153v1_genomic.fna/markers.fasta)
[2024-01-24 13:16:13,319] [INFO] Task started: Blastn
[2024-01-24 13:16:13,319] [INFO] Running command: blastn -query GCF_007741535.1_ASM774153v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f7111cf-8522-41b6-bce4-ac82563aaaad/dqc_reference/reference_markers_gtdb.fasta -out GCF_007741535.1_ASM774153v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:16:14,135] [INFO] Task succeeded: Blastn
[2024-01-24 13:16:14,138] [INFO] Selected 17 target genomes.
[2024-01-24 13:16:14,138] [INFO] Target genome list was writen to GCF_007741535.1_ASM774153v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:16:14,152] [INFO] Task started: fastANI
[2024-01-24 13:16:14,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ef09250-1891-4383-8c80-922ef66f2b0c/GCF_007741535.1_ASM774153v1_genomic.fna.gz --refList GCF_007741535.1_ASM774153v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007741535.1_ASM774153v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:16:39,527] [INFO] Task succeeded: fastANI
[2024-01-24 13:16:39,550] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:16:39,551] [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_007741535.1	s__Rubripirellula sp007741535	100.0	2847	2847	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007860125.1	s__Rubripirellula tenax	78.3551	634	2847	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860175.1	s__Rubripirellula reticaptiva	78.3308	672	2847	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859865.1	s__Rubripirellula amarantea	77.5925	257	2847	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012290005.1	s__Crateriforma spongiae	77.5484	285	2847	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.43	98.43	0.93	0.93	2	-
GCF_007752935.1	s__Crateriforma conspicua	77.5352	298	2847	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.96	98.96	0.93	0.93	2	-
GCF_001642955.1	s__Rubripirellula obstinata	77.1965	315	2847	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	99.93	99.93	1.00	1.00	2	-
GCA_007753675.1	s__Stieleria sp007753675	76.7865	349	2847	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000346295.1	s__Novipirellula maiorica	76.6022	259	2847	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014154935.1	s__Stieleria sp014154935	76.5087	329	2847	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007754155.1	s__Stieleria neptunia	76.4013	341	2847	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008035925.1	s__Stieleria maiorica	76.3045	344	2847	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009618275.1	s__Roseimaritima sp009618275	76.2849	213	2847	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Roseimaritima	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002289565.1	s__Stieleria sp002289565	76.2055	293	2847	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000346505.1	s__Rhodopirellula sallentina	76.1519	178	2847	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422955.1	s__UBA6163 sp002422955	75.7417	97	2847	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__UBA6163	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:16:39,552] [INFO] GTDB search result was written to GCF_007741535.1_ASM774153v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:16:39,556] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:16:39,561] [INFO] DFAST_QC result json was written to GCF_007741535.1_ASM774153v1_genomic.fna/dqc_result.json
[2024-01-24 13:16:39,562] [INFO] DFAST_QC completed!
[2024-01-24 13:16:39,562] [INFO] Total running time: 0h3m31s