[2024-01-24 13:55:18,516] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:18,519] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:18,519] [INFO] DQC Reference Directory: /var/lib/cwl/stga5207ebb-ac2c-44d6-89a9-bb22927b1b7e/dqc_reference
[2024-01-24 13:55:19,888] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:19,889] [INFO] Task started: Prodigal
[2024-01-24 13:55:19,889] [INFO] Running command: gunzip -c /var/lib/cwl/stg868c9be0-1d54-4512-9529-64157b357be5/GCF_007859865.1_ASM785986v1_genomic.fna.gz | prodigal -d GCF_007859865.1_ASM785986v1_genomic.fna/cds.fna -a GCF_007859865.1_ASM785986v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:00,990] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:00,991] [INFO] Task started: HMMsearch
[2024-01-24 13:56:00,991] [INFO] Running command: hmmsearch --tblout GCF_007859865.1_ASM785986v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5207ebb-ac2c-44d6-89a9-bb22927b1b7e/dqc_reference/reference_markers.hmm GCF_007859865.1_ASM785986v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:01,364] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:01,366] [INFO] Found 6/6 markers.
[2024-01-24 13:56:01,420] [INFO] Query marker FASTA was written to GCF_007859865.1_ASM785986v1_genomic.fna/markers.fasta
[2024-01-24 13:56:01,421] [INFO] Task started: Blastn
[2024-01-24 13:56:01,421] [INFO] Running command: blastn -query GCF_007859865.1_ASM785986v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5207ebb-ac2c-44d6-89a9-bb22927b1b7e/dqc_reference/reference_markers.fasta -out GCF_007859865.1_ASM785986v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:02,043] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:02,047] [INFO] Selected 24 target genomes.
[2024-01-24 13:56:02,047] [INFO] Target genome list was writen to GCF_007859865.1_ASM785986v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:02,068] [INFO] Task started: fastANI
[2024-01-24 13:56:02,069] [INFO] Running command: fastANI --query /var/lib/cwl/stg868c9be0-1d54-4512-9529-64157b357be5/GCF_007859865.1_ASM785986v1_genomic.fna.gz --refList GCF_007859865.1_ASM785986v1_genomic.fna/target_genomes.txt --output GCF_007859865.1_ASM785986v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:31,480] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:31,481] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5207ebb-ac2c-44d6-89a9-bb22927b1b7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:31,482] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5207ebb-ac2c-44d6-89a9-bb22927b1b7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:31,502] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:31,502] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:31,502] [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 amarantea	strain=Pla22	GCA_007859865.1	2527999	2527999	type	True	100.0	2309	2309	95	conclusive
Rhodopirellula rubra	strain=CECT 8075	GCA_014192335.1	980271	980271	type	True	79.2646	156	2309	95	below_threshold
Rosistilla carotiformis	strain=Poly24	GCA_007753095.1	2528017	2528017	type	True	78.5978	100	2309	95	below_threshold
Rubripirellula obstinata	strain=CECT 8602	GCA_001642955.1	406547	406547	type	True	78.1123	262	2309	95	below_threshold
Rubripirellula obstinata	strain=LF1	GCA_008374075.1	406547	406547	type	True	78.0297	272	2309	95	below_threshold
Rubripirellula reticaptiva	strain=Poly59	GCA_007860175.1	2528013	2528013	type	True	77.983	263	2309	95	below_threshold
Rhodopirellula pilleata	strain=Pla100	GCA_007859915.1	2714738	2714738	type	True	77.6844	167	2309	95	below_threshold
Rubripirellula lacrimiformis	strain=K22.7	GCA_007741535.1	1930273	1930273	type	True	77.5647	248	2309	95	below_threshold
Rubripirellula tenax	strain=Poly51	GCA_007860125.1	2528015	2528015	type	True	77.4281	271	2309	95	below_threshold
Rhodopirellula islandica	strain=K833	GCA_001027925.1	595434	595434	type	True	77.0647	141	2309	95	below_threshold
Rhodopirellula solitaria	strain=CA85	GCA_007859855.1	2527987	2527987	type	True	76.9172	91	2309	95	below_threshold
Rhodopirellula sallentina	strain=SM41	GCA_000346505.1	1263869	1263869	type	True	76.8982	117	2309	95	below_threshold
Rhodopirellula maiorica	strain=SM1	GCA_000346295.1	1265734	1265734	type	True	76.8521	161	2309	95	below_threshold
Stieleria varia	strain=Pla52n	GCA_007860045.1	2528005	2528005	type	True	76.6778	144	2309	95	below_threshold
Stieleria neptunia	strain=Enr13	GCA_007754155.1	2527979	2527979	type	True	76.5188	156	2309	95	below_threshold
Stieleria maiorica	strain=Mal15	GCA_008035925.1	2795974	2795974	type	True	76.3859	142	2309	95	below_threshold
Roseimaritima sediminicola	strain=JC651	GCA_009618275.1	2662066	2662066	type	True	76.0768	81	2309	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:31,504] [INFO] DFAST Taxonomy check result was written to GCF_007859865.1_ASM785986v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:31,505] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:31,505] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:31,505] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5207ebb-ac2c-44d6-89a9-bb22927b1b7e/dqc_reference/checkm_data
[2024-01-24 13:56:31,507] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:31,578] [INFO] Task started: CheckM
[2024-01-24 13:56:31,579] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007859865.1_ASM785986v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007859865.1_ASM785986v1_genomic.fna/checkm_input GCF_007859865.1_ASM785986v1_genomic.fna/checkm_result
[2024-01-24 13:58:22,164] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:22,166] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:22,186] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:22,186] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:22,187] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007859865.1_ASM785986v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:22,187] [INFO] Task started: Blastn
[2024-01-24 13:58:22,187] [INFO] Running command: blastn -query GCF_007859865.1_ASM785986v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5207ebb-ac2c-44d6-89a9-bb22927b1b7e/dqc_reference/reference_markers_gtdb.fasta -out GCF_007859865.1_ASM785986v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:23,071] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:23,075] [INFO] Selected 24 target genomes.
[2024-01-24 13:58:23,075] [INFO] Target genome list was writen to GCF_007859865.1_ASM785986v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:23,107] [INFO] Task started: fastANI
[2024-01-24 13:58:23,107] [INFO] Running command: fastANI --query /var/lib/cwl/stg868c9be0-1d54-4512-9529-64157b357be5/GCF_007859865.1_ASM785986v1_genomic.fna.gz --refList GCF_007859865.1_ASM785986v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007859865.1_ASM785986v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:54,820] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:54,845] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:54,846] [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_007859865.1	s__Rubripirellula amarantea	100.0	2309	2309	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_014192335.1	s__Rhodopirellula rubra	79.2646	156	2309	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	95.37	95.37	0.86	0.86	2	-
GCF_007753095.1	s__Rosistilla carotiformis	78.5978	100	2309	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rosistilla	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007741555.1	s__K23-9 sp007741555	78.1401	164	2309	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__K23-9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001642955.1	s__Rubripirellula obstinata	78.1401	260	2309	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	99.93	99.93	1.00	1.00	2	-
GCF_007860175.1	s__Rubripirellula reticaptiva	77.9693	264	2309	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007752935.1	s__Crateriforma conspicua	77.9408	149	2309	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.96	98.96	0.93	0.93	2	-
GCA_007741535.1	s__Rubripirellula sp007741535	77.5647	248	2309	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860125.1	s__Rubripirellula tenax	77.4277	271	2309	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	77.3629	156	2309	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.43	98.43	0.93	0.93	2	-
GCF_001027925.1	s__Rhodopirellula islandica	77.089	138	2309	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	76.9161	116	2309	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859855.1	s__Rhodopirellula solitaria	76.9128	90	2309	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	76.8517	162	2309	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860045.1	s__Stieleria varia	76.6778	144	2309	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	76.5782	153	2309	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Novipirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008312935.1	s__Stieleria lacunae	76.5692	106	2309	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	99.99	99.99	1.00	1.00	2	-
GCF_007754155.1	s__Stieleria neptunia	76.4975	154	2309	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014154935.1	s__Stieleria sp014154935	76.496	154	2309	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	76.4003	141	2309	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002289565.1	s__Stieleria sp002289565	76.3475	139	2309	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	76.0591	82	2309	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Roseimaritima	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862205.1	s__Rubripirellula sp002862205	75.755	76	2309	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:54,847] [INFO] GTDB search result was written to GCF_007859865.1_ASM785986v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:54,848] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:54,854] [INFO] DFAST_QC result json was written to GCF_007859865.1_ASM785986v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:54,854] [INFO] DFAST_QC completed!
[2024-01-24 13:58:54,854] [INFO] Total running time: 0h3m36s