[2024-01-24 13:46:55,743] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:55,744] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:55,745] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a31d59d-8c63-46a7-ba99-f78a2f7387cb/dqc_reference
[2024-01-24 13:46:57,144] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:57,145] [INFO] Task started: Prodigal
[2024-01-24 13:46:57,145] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4183d08-65fe-4773-8b5c-3a828d5ff284/GCF_007860175.1_ASM786017v1_genomic.fna.gz | prodigal -d GCF_007860175.1_ASM786017v1_genomic.fna/cds.fna -a GCF_007860175.1_ASM786017v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:31,819] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:31,819] [INFO] Task started: HMMsearch
[2024-01-24 13:47:31,819] [INFO] Running command: hmmsearch --tblout GCF_007860175.1_ASM786017v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a31d59d-8c63-46a7-ba99-f78a2f7387cb/dqc_reference/reference_markers.hmm GCF_007860175.1_ASM786017v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:32,186] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:32,189] [INFO] Found 6/6 markers.
[2024-01-24 13:47:32,255] [INFO] Query marker FASTA was written to GCF_007860175.1_ASM786017v1_genomic.fna/markers.fasta
[2024-01-24 13:47:32,255] [INFO] Task started: Blastn
[2024-01-24 13:47:32,255] [INFO] Running command: blastn -query GCF_007860175.1_ASM786017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a31d59d-8c63-46a7-ba99-f78a2f7387cb/dqc_reference/reference_markers.fasta -out GCF_007860175.1_ASM786017v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:32,863] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:32,867] [INFO] Selected 20 target genomes.
[2024-01-24 13:47:32,868] [INFO] Target genome list was writen to GCF_007860175.1_ASM786017v1_genomic.fna/target_genomes.txt
[2024-01-24 13:47:32,894] [INFO] Task started: fastANI
[2024-01-24 13:47:32,894] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4183d08-65fe-4773-8b5c-3a828d5ff284/GCF_007860175.1_ASM786017v1_genomic.fna.gz --refList GCF_007860175.1_ASM786017v1_genomic.fna/target_genomes.txt --output GCF_007860175.1_ASM786017v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:56,422] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:56,423] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a31d59d-8c63-46a7-ba99-f78a2f7387cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:56,424] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a31d59d-8c63-46a7-ba99-f78a2f7387cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:56,436] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:56,436] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:56,436] [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 reticaptiva	strain=Poly59	GCA_007860175.1	2528013	2528013	type	True	100.0	2610	2610	95	conclusive
Rubripirellula tenax	strain=Poly51	GCA_007860125.1	2528015	2528015	type	True	79.6106	827	2610	95	below_threshold
Rubripirellula lacrimiformis	strain=K22.7	GCA_007741535.1	1930273	1930273	type	True	78.5399	640	2610	95	below_threshold
Rubripirellula amarantea	strain=Pla22	GCA_007859865.1	2527999	2527999	type	True	78.0999	265	2610	95	below_threshold
Crateriforma conspicua	strain=Mal65	GCA_007752935.1	2527996	2527996	type	True	77.3765	215	2610	95	below_threshold
Rhodopirellula baltica	strain=1	GCA_000196115.1	265606	265606	type	True	77.3735	214	2610	95	below_threshold
Rubripirellula obstinata	strain=CECT 8602	GCA_001642955.1	406547	406547	type	True	77.2311	263	2610	95	below_threshold
Rhodopirellula bahusiensis	strain=SWK21	GCA_002727185.1	2014065	2014065	type	True	77.1186	220	2610	95	below_threshold
Rhodopirellula maiorica	strain=SM1	GCA_000346295.1	1265734	1265734	type	True	76.9569	241	2610	95	below_threshold
Rhodopirellula europaea	strain=6C	GCA_000338295.1	1263866	1263866	type	True	76.9396	216	2610	95	below_threshold
Novipirellula galeiformis	strain=Pla52o	GCA_007860095.1	2528004	2528004	type	True	76.5031	209	2610	95	below_threshold
Stieleria neptunia	strain=Enr13	GCA_007754155.1	2527979	2527979	type	True	76.5024	246	2610	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:56,438] [INFO] DFAST Taxonomy check result was written to GCF_007860175.1_ASM786017v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:56,438] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:56,439] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:56,439] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a31d59d-8c63-46a7-ba99-f78a2f7387cb/dqc_reference/checkm_data
[2024-01-24 13:47:56,440] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:56,512] [INFO] Task started: CheckM
[2024-01-24 13:47:56,512] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007860175.1_ASM786017v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007860175.1_ASM786017v1_genomic.fna/checkm_input GCF_007860175.1_ASM786017v1_genomic.fna/checkm_result
[2024-01-24 13:49:32,799] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:32,800] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:32,822] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:32,823] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:32,823] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007860175.1_ASM786017v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:32,823] [INFO] Task started: Blastn
[2024-01-24 13:49:32,824] [INFO] Running command: blastn -query GCF_007860175.1_ASM786017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a31d59d-8c63-46a7-ba99-f78a2f7387cb/dqc_reference/reference_markers_gtdb.fasta -out GCF_007860175.1_ASM786017v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:33,618] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:33,621] [INFO] Selected 18 target genomes.
[2024-01-24 13:49:33,621] [INFO] Target genome list was writen to GCF_007860175.1_ASM786017v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:33,634] [INFO] Task started: fastANI
[2024-01-24 13:49:33,634] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4183d08-65fe-4773-8b5c-3a828d5ff284/GCF_007860175.1_ASM786017v1_genomic.fna.gz --refList GCF_007860175.1_ASM786017v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007860175.1_ASM786017v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:57,948] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:57,964] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:57,964] [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_007860175.1	s__Rubripirellula reticaptiva	100.0	2610	2610	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	79.6041	833	2610	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007741535.1	s__Rubripirellula sp007741535	78.5428	639	2610	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	78.0999	265	2610	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	77.3837	209	2610	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.43	98.43	0.93	0.93	2	-
GCF_001642955.1	s__Rubripirellula obstinata	77.2379	264	2610	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	99.93	99.93	1.00	1.00	2	-
GCF_002727185.1	s__Rhodopirellula bahusiensis	77.1297	219	2610	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000346295.1	s__Novipirellula maiorica	76.953	239	2610	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000338295.1	s__Rhodopirellula europaea	76.9399	216	2610	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	96.18	96.16	0.87	0.86	3	-
GCF_007860045.1	s__Stieleria varia	76.6376	217	2610	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	76.5093	245	2610	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860095.1	s__Novipirellula galeiformis	76.4934	210	2610	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	76.4044	253	2610	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	76.1027	240	2610	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	75.8106	94	2610	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Laterigemmans	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002428205.1	s__UBA6163 sp002428205	75.746	96	2610	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 13:49:57,966] [INFO] GTDB search result was written to GCF_007860175.1_ASM786017v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:57,966] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:57,974] [INFO] DFAST_QC result json was written to GCF_007860175.1_ASM786017v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:57,974] [INFO] DFAST_QC completed!
[2024-01-24 13:49:57,975] [INFO] Total running time: 0h3m2s