[2024-01-24 14:22:17,469] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:17,471] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:17,471] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ab486b3-4a30-4d6c-9a97-a5753785238a/dqc_reference
[2024-01-24 14:22:18,792] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:18,793] [INFO] Task started: Prodigal
[2024-01-24 14:22:18,793] [INFO] Running command: gunzip -c /var/lib/cwl/stg16319168-2c5d-4ddd-bd59-5916021e7883/GCF_007754155.1_ASM775415v1_genomic.fna.gz | prodigal -d GCF_007754155.1_ASM775415v1_genomic.fna/cds.fna -a GCF_007754155.1_ASM775415v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:48,447] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:48,447] [INFO] Task started: HMMsearch
[2024-01-24 14:23:48,447] [INFO] Running command: hmmsearch --tblout GCF_007754155.1_ASM775415v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ab486b3-4a30-4d6c-9a97-a5753785238a/dqc_reference/reference_markers.hmm GCF_007754155.1_ASM775415v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:48,874] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:48,875] [INFO] Found 6/6 markers.
[2024-01-24 14:23:48,959] [INFO] Query marker FASTA was written to GCF_007754155.1_ASM775415v1_genomic.fna/markers.fasta
[2024-01-24 14:23:48,959] [INFO] Task started: Blastn
[2024-01-24 14:23:48,959] [INFO] Running command: blastn -query GCF_007754155.1_ASM775415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ab486b3-4a30-4d6c-9a97-a5753785238a/dqc_reference/reference_markers.fasta -out GCF_007754155.1_ASM775415v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:49,619] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:49,624] [INFO] Selected 22 target genomes.
[2024-01-24 14:23:49,625] [INFO] Target genome list was writen to GCF_007754155.1_ASM775415v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:49,643] [INFO] Task started: fastANI
[2024-01-24 14:23:49,644] [INFO] Running command: fastANI --query /var/lib/cwl/stg16319168-2c5d-4ddd-bd59-5916021e7883/GCF_007754155.1_ASM775415v1_genomic.fna.gz --refList GCF_007754155.1_ASM775415v1_genomic.fna/target_genomes.txt --output GCF_007754155.1_ASM775415v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:24:26,888] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:26,889] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ab486b3-4a30-4d6c-9a97-a5753785238a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:24:26,889] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ab486b3-4a30-4d6c-9a97-a5753785238a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:24:26,906] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:24:26,906] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:24:26,907] [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
Stieleria neptunia	strain=Enr13	GCA_007754155.1	2527979	2527979	type	True	100.0	3657	3658	95	conclusive
Stieleria maiorica	strain=Mal15	GCA_008035925.1	2795974	2795974	type	True	81.3589	1949	3658	95	below_threshold
Roseiconus nitratireducens	strain=JC645	GCA_008629675.1	2605748	2605748	type	True	77.6934	541	3658	95	below_threshold
Roseiconus lacunae	strain=JC635	GCA_008312935.1	2605694	2605694	type	True	77.1033	400	3658	95	below_threshold
Crateriforma spongiae	strain=JC647	GCA_012290005.1	2724528	2724528	type	True	76.8847	293	3658	95	below_threshold
Stieleria varia	strain=Pla52n	GCA_007860045.1	2528005	2528005	type	True	76.8749	395	3658	95	below_threshold
Crateriforma conspicua	strain=Mal65	GCA_007752935.1	2527996	2527996	type	True	76.8688	315	3658	95	below_threshold
Rhodopirellula maiorica	strain=SM1	GCA_000346295.1	1265734	1265734	type	True	76.6447	264	3658	95	below_threshold
Rubripirellula reticaptiva	strain=Poly59	GCA_007860175.1	2528013	2528013	type	True	76.4195	265	3658	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	74.9841	62	3658	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	74.8747	70	3658	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	74.8704	52	3658	95	below_threshold
Actinoplanes deccanensis	strain=NBRC 13994	GCA_016862115.1	113561	113561	type	True	74.7131	90	3658	95	below_threshold
Actinoplanes ferrugineus	strain=NBRC 15555	GCA_016862195.1	113564	113564	type	True	74.6016	68	3658	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:24:26,909] [INFO] DFAST Taxonomy check result was written to GCF_007754155.1_ASM775415v1_genomic.fna/tc_result.tsv
[2024-01-24 14:24:26,910] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:24:26,910] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:24:26,910] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ab486b3-4a30-4d6c-9a97-a5753785238a/dqc_reference/checkm_data
[2024-01-24 14:24:26,912] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:24:27,011] [INFO] Task started: CheckM
[2024-01-24 14:24:27,012] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007754155.1_ASM775415v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007754155.1_ASM775415v1_genomic.fna/checkm_input GCF_007754155.1_ASM775415v1_genomic.fna/checkm_result
[2024-01-24 14:29:03,665] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:03,666] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:03,698] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:03,698] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:03,699] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007754155.1_ASM775415v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:03,699] [INFO] Task started: Blastn
[2024-01-24 14:29:03,699] [INFO] Running command: blastn -query GCF_007754155.1_ASM775415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ab486b3-4a30-4d6c-9a97-a5753785238a/dqc_reference/reference_markers_gtdb.fasta -out GCF_007754155.1_ASM775415v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:04,598] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:04,603] [INFO] Selected 10 target genomes.
[2024-01-24 14:29:04,603] [INFO] Target genome list was writen to GCF_007754155.1_ASM775415v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:04,615] [INFO] Task started: fastANI
[2024-01-24 14:29:04,616] [INFO] Running command: fastANI --query /var/lib/cwl/stg16319168-2c5d-4ddd-bd59-5916021e7883/GCF_007754155.1_ASM775415v1_genomic.fna.gz --refList GCF_007754155.1_ASM775415v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007754155.1_ASM775415v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:36,854] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:36,869] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:36,870] [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_007754155.1	s__Stieleria neptunia	100.0	3655	3658	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002289565.1	s__Stieleria sp002289565	89.2614	2524	3658	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007753675.1	s__Stieleria sp007753675	87.7125	2606	3658	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	81.5798	1982	3658	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	81.3576	1948	3658	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008629675.1	s__Stieleria nitratireducens	77.6769	544	3658	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002901265.1	s__Stieleria baltica_A	76.9809	421	3658	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	99.97	99.97	0.98	0.98	2	-
GCF_007860175.1	s__Rubripirellula reticaptiva	76.4263	265	3658	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 14:29:36,871] [INFO] GTDB search result was written to GCF_007754155.1_ASM775415v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:36,872] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:36,875] [INFO] DFAST_QC result json was written to GCF_007754155.1_ASM775415v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:36,875] [INFO] DFAST_QC completed!
[2024-01-24 14:29:36,875] [INFO] Total running time: 0h7m19s