[2024-01-25 18:08:35,513] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:08:35,514] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:08:35,515] [INFO] DQC Reference Directory: /var/lib/cwl/stg484b9ad0-ea61-4410-b337-7270ae42b949/dqc_reference
[2024-01-25 18:08:36,674] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:08:36,675] [INFO] Task started: Prodigal
[2024-01-25 18:08:36,675] [INFO] Running command: gunzip -c /var/lib/cwl/stg37f00577-4425-465c-945e-d77cf585e713/GCF_009674685.1_ASM967468v1_genomic.fna.gz | prodigal -d GCF_009674685.1_ASM967468v1_genomic.fna/cds.fna -a GCF_009674685.1_ASM967468v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:08:46,617] [INFO] Task succeeded: Prodigal
[2024-01-25 18:08:46,618] [INFO] Task started: HMMsearch
[2024-01-25 18:08:46,618] [INFO] Running command: hmmsearch --tblout GCF_009674685.1_ASM967468v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg484b9ad0-ea61-4410-b337-7270ae42b949/dqc_reference/reference_markers.hmm GCF_009674685.1_ASM967468v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:08:46,864] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:08:46,865] [INFO] Found 6/6 markers.
[2024-01-25 18:08:46,894] [INFO] Query marker FASTA was written to GCF_009674685.1_ASM967468v1_genomic.fna/markers.fasta
[2024-01-25 18:08:46,894] [INFO] Task started: Blastn
[2024-01-25 18:08:46,895] [INFO] Running command: blastn -query GCF_009674685.1_ASM967468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg484b9ad0-ea61-4410-b337-7270ae42b949/dqc_reference/reference_markers.fasta -out GCF_009674685.1_ASM967468v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:47,450] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:47,452] [INFO] Selected 13 target genomes.
[2024-01-25 18:08:47,453] [INFO] Target genome list was writen to GCF_009674685.1_ASM967468v1_genomic.fna/target_genomes.txt
[2024-01-25 18:08:47,462] [INFO] Task started: fastANI
[2024-01-25 18:08:47,462] [INFO] Running command: fastANI --query /var/lib/cwl/stg37f00577-4425-465c-945e-d77cf585e713/GCF_009674685.1_ASM967468v1_genomic.fna.gz --refList GCF_009674685.1_ASM967468v1_genomic.fna/target_genomes.txt --output GCF_009674685.1_ASM967468v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:08:57,542] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:57,542] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg484b9ad0-ea61-4410-b337-7270ae42b949/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:08:57,542] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg484b9ad0-ea61-4410-b337-7270ae42b949/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:08:57,550] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:08:57,550] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:08:57,551] [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 puniceum	strain=HX-22-1	GCA_009674685.1	2666136	2666136	type	True	100.0	1294	1294	95	conclusive
Pedobacter aquae	strain=CJ43	GCA_008195825.1	2605747	2605747	type	True	91.5554	1029	1294	95	below_threshold
Pedobacter glucosidilyticus	strain=DSM 23534	GCA_000425145.1	1122941	1122941	type	True	90.3132	955	1294	95	below_threshold
Pseudopedobacter saltans	strain=DSM 12145	GCA_000190735.2	151895	151895	type	True	78.2376	212	1294	95	below_threshold
Pelobium manganitolerans	strain=YS-25	GCA_003609575.1	1842495	1842495	type	True	78.0438	172	1294	95	below_threshold
Pedobacter arcticus	strain=A12	GCA_000302595.1	752140	752140	type	True	77.5715	214	1294	95	below_threshold
Pedobacter cryophilus	strain=AR-3-17	GCA_005116455.1	2571271	2571271	type	True	77.5633	362	1294	95	below_threshold
Pedobacter psychrophilus	strain=CCM 8644	GCA_001652725.1	1826909	1826909	type	True	77.5452	246	1294	95	below_threshold
Pedobacter segetis	strain=SD-b	GCA_016623585.1	2793069	2793069	type	True	77.3077	196	1294	95	below_threshold
Pedobacter frigidisoli	strain=RP-3-11	GCA_004331675.1	2530455	2530455	type	True	76.7586	102	1294	95	below_threshold
Mucilaginibacter arboris	strain=HMF7410	GCA_009754915.1	2682090	2682090	type	True	76.6668	74	1294	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:08:57,552] [INFO] DFAST Taxonomy check result was written to GCF_009674685.1_ASM967468v1_genomic.fna/tc_result.tsv
[2024-01-25 18:08:57,552] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:08:57,552] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:08:57,553] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg484b9ad0-ea61-4410-b337-7270ae42b949/dqc_reference/checkm_data
[2024-01-25 18:08:57,553] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:08:57,592] [INFO] Task started: CheckM
[2024-01-25 18:08:57,592] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009674685.1_ASM967468v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009674685.1_ASM967468v1_genomic.fna/checkm_input GCF_009674685.1_ASM967468v1_genomic.fna/checkm_result
[2024-01-25 18:09:28,765] [INFO] Task succeeded: CheckM
[2024-01-25 18:09:28,766] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:09:28,784] [INFO] ===== Completeness check finished =====
[2024-01-25 18:09:28,784] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:09:28,784] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009674685.1_ASM967468v1_genomic.fna/markers.fasta)
[2024-01-25 18:09:28,785] [INFO] Task started: Blastn
[2024-01-25 18:09:28,785] [INFO] Running command: blastn -query GCF_009674685.1_ASM967468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg484b9ad0-ea61-4410-b337-7270ae42b949/dqc_reference/reference_markers_gtdb.fasta -out GCF_009674685.1_ASM967468v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:29,628] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:29,631] [INFO] Selected 9 target genomes.
[2024-01-25 18:09:29,631] [INFO] Target genome list was writen to GCF_009674685.1_ASM967468v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:09:29,661] [INFO] Task started: fastANI
[2024-01-25 18:09:29,661] [INFO] Running command: fastANI --query /var/lib/cwl/stg37f00577-4425-465c-945e-d77cf585e713/GCF_009674685.1_ASM967468v1_genomic.fna.gz --refList GCF_009674685.1_ASM967468v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009674685.1_ASM967468v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:09:37,797] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:37,807] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:09:37,807] [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_009674685.1	s__Pelobium puniceum	100.0	1294	1294	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_000799115.1	s__Pelobium glucosidilyticum_A	91.2681	1044	1294	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	97.72	97.72	0.84	0.84	2	-
GCF_000425145.1	s__Pelobium glucosidilyticum	90.3222	954	1294	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483235.1	s__Pelobium glucosidilyticum_B	88.1053	940	1294	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190735.1	s__Pelobium saltans	78.2551	211	1294	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	78.0438	172	1294	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	77.569	239	1294	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116455.1	s__Pelobium sp005116455	77.5471	364	1294	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205835.1	s__Pedobacter sp014205835	76.866	109	1294	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:09:37,809] [INFO] GTDB search result was written to GCF_009674685.1_ASM967468v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:09:37,809] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:09:37,811] [INFO] DFAST_QC result json was written to GCF_009674685.1_ASM967468v1_genomic.fna/dqc_result.json
[2024-01-25 18:09:37,812] [INFO] DFAST_QC completed!
[2024-01-25 18:09:37,812] [INFO] Total running time: 0h1m2s