[2024-01-24 14:13:01,576] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:13:01,578] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:13:01,578] [INFO] DQC Reference Directory: /var/lib/cwl/stg099e8f91-5317-4d74-ae99-c9a96884b3bd/dqc_reference
[2024-01-24 14:13:02,819] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:13:02,820] [INFO] Task started: Prodigal
[2024-01-24 14:13:02,820] [INFO] Running command: gunzip -c /var/lib/cwl/stg1c48e0da-d058-4adb-9ba9-9daa7391b7f1/GCF_000302595.1_ASM30259v1_genomic.fna.gz | prodigal -d GCF_000302595.1_ASM30259v1_genomic.fna/cds.fna -a GCF_000302595.1_ASM30259v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:17,998] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:17,998] [INFO] Task started: HMMsearch
[2024-01-24 14:13:17,999] [INFO] Running command: hmmsearch --tblout GCF_000302595.1_ASM30259v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg099e8f91-5317-4d74-ae99-c9a96884b3bd/dqc_reference/reference_markers.hmm GCF_000302595.1_ASM30259v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:18,313] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:18,315] [INFO] Found 6/6 markers.
[2024-01-24 14:13:18,368] [INFO] Query marker FASTA was written to GCF_000302595.1_ASM30259v1_genomic.fna/markers.fasta
[2024-01-24 14:13:18,369] [INFO] Task started: Blastn
[2024-01-24 14:13:18,369] [INFO] Running command: blastn -query GCF_000302595.1_ASM30259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg099e8f91-5317-4d74-ae99-c9a96884b3bd/dqc_reference/reference_markers.fasta -out GCF_000302595.1_ASM30259v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:19,059] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:19,063] [INFO] Selected 15 target genomes.
[2024-01-24 14:13:19,064] [INFO] Target genome list was writen to GCF_000302595.1_ASM30259v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:19,072] [INFO] Task started: fastANI
[2024-01-24 14:13:19,072] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c48e0da-d058-4adb-9ba9-9daa7391b7f1/GCF_000302595.1_ASM30259v1_genomic.fna.gz --refList GCF_000302595.1_ASM30259v1_genomic.fna/target_genomes.txt --output GCF_000302595.1_ASM30259v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:30,506] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:30,507] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg099e8f91-5317-4d74-ae99-c9a96884b3bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:30,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg099e8f91-5317-4d74-ae99-c9a96884b3bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:30,520] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:30,520] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:30,520] [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
Pedobacter arcticus	strain=A12	GCA_000302595.1	752140	752140	type	True	100.0	1400	1401	95	conclusive
Pedobacter cryophilus	strain=AR-3-17	GCA_005116455.1	2571271	2571271	type	True	78.1979	308	1401	95	below_threshold
Pelobium manganitolerans	strain=YS-25	GCA_003609575.1	1842495	1842495	type	True	78.1552	314	1401	95	below_threshold
Pedobacter segetis	strain=SD-b	GCA_016623585.1	2793069	2793069	type	True	77.993	290	1401	95	below_threshold
Pedobacter psychrophilus	strain=CCM 8644	GCA_001652725.1	1826909	1826909	type	True	77.8779	330	1401	95	below_threshold
Pedobacter puniceum	strain=HX-22-1	GCA_009674685.1	2666136	2666136	type	True	77.5679	203	1401	95	below_threshold
Pedobacter glucosidilyticus	strain=DSM 23534	GCA_000425145.1	1122941	1122941	type	True	77.3979	228	1401	95	below_threshold
Pedobacter aquae	strain=CJ43	GCA_008195825.1	2605747	2605747	type	True	77.2876	223	1401	95	below_threshold
Pedobacter chinensis	strain=JDX94	GCA_003339865.1	2282421	2282421	type	True	76.8188	104	1401	95	below_threshold
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	76.8174	113	1401	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:30,522] [INFO] DFAST Taxonomy check result was written to GCF_000302595.1_ASM30259v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:30,523] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:30,523] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:30,524] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg099e8f91-5317-4d74-ae99-c9a96884b3bd/dqc_reference/checkm_data
[2024-01-24 14:13:30,525] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:30,572] [INFO] Task started: CheckM
[2024-01-24 14:13:30,572] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000302595.1_ASM30259v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000302595.1_ASM30259v1_genomic.fna/checkm_input GCF_000302595.1_ASM30259v1_genomic.fna/checkm_result
[2024-01-24 14:14:16,735] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:16,737] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:16,757] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:16,757] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:16,758] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000302595.1_ASM30259v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:16,758] [INFO] Task started: Blastn
[2024-01-24 14:14:16,758] [INFO] Running command: blastn -query GCF_000302595.1_ASM30259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg099e8f91-5317-4d74-ae99-c9a96884b3bd/dqc_reference/reference_markers_gtdb.fasta -out GCF_000302595.1_ASM30259v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:17,623] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:17,629] [INFO] Selected 16 target genomes.
[2024-01-24 14:14:17,629] [INFO] Target genome list was writen to GCF_000302595.1_ASM30259v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:17,650] [INFO] Task started: fastANI
[2024-01-24 14:14:17,650] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c48e0da-d058-4adb-9ba9-9daa7391b7f1/GCF_000302595.1_ASM30259v1_genomic.fna.gz --refList GCF_000302595.1_ASM30259v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000302595.1_ASM30259v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:28,593] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:28,613] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:28,613] [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_000302595.1	s__Pelobium arcticum	100.0	1400	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005116455.1	s__Pelobium sp005116455	78.1965	308	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003609575.1	s__Pelobium manganitolerans	78.1552	314	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018828585.1	s__Pelobium sp018828585	78.1383	235	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	99.93	99.87	0.97	0.95	6	-
GCA_014378105.1	s__Pelobium sp014378105	77.9828	227	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016623585.1	s__Pelobium sp016623585	77.9826	291	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001652725.1	s__Pelobium psychrophilum	77.8679	331	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763615.1	s__Pelobium sp014763615	77.8417	249	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674685.1	s__Pelobium puniceum	77.5679	203	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014378285.1	s__Pelobium sp014378285	77.5355	166	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000799115.1	s__Pelobium glucosidilyticum_A	77.4943	217	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	97.72	97.72	0.84	0.84	2	-
GCA_002483235.1	s__Pelobium glucosidilyticum_B	77.4129	209	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425145.1	s__Pelobium glucosidilyticum	77.3979	228	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834875.1	s__HMF7647 sp009834875	76.8019	50	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__HMF7647	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298995.1	s__Pelobium sp013298995	76.7514	106	1401	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:28,615] [INFO] GTDB search result was written to GCF_000302595.1_ASM30259v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:28,616] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:28,619] [INFO] DFAST_QC result json was written to GCF_000302595.1_ASM30259v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:28,619] [INFO] DFAST_QC completed!
[2024-01-24 14:14:28,619] [INFO] Total running time: 0h1m27s