[2024-01-24 13:01:49,709] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:49,711] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:49,711] [INFO] DQC Reference Directory: /var/lib/cwl/stga8c63a64-6f51-489e-b8a7-5207d7e83419/dqc_reference
[2024-01-24 13:01:51,033] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:51,038] [INFO] Task started: Prodigal
[2024-01-24 13:01:51,038] [INFO] Running command: gunzip -c /var/lib/cwl/stgd79397bb-1382-437c-8882-09be2d301a65/GCF_900112985.1_IMG-taxon_2597490344_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900112985.1_IMG-taxon_2597490344_annotated_assembly_genomic.fna/cds.fna -a GCF_900112985.1_IMG-taxon_2597490344_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:09,102] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:09,102] [INFO] Task started: HMMsearch
[2024-01-24 13:02:09,102] [INFO] Running command: hmmsearch --tblout GCF_900112985.1_IMG-taxon_2597490344_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga8c63a64-6f51-489e-b8a7-5207d7e83419/dqc_reference/reference_markers.hmm GCF_900112985.1_IMG-taxon_2597490344_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:09,521] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:09,522] [INFO] Found 6/6 markers.
[2024-01-24 13:02:09,578] [INFO] Query marker FASTA was written to GCF_900112985.1_IMG-taxon_2597490344_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:02:09,578] [INFO] Task started: Blastn
[2024-01-24 13:02:09,578] [INFO] Running command: blastn -query GCF_900112985.1_IMG-taxon_2597490344_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga8c63a64-6f51-489e-b8a7-5207d7e83419/dqc_reference/reference_markers.fasta -out GCF_900112985.1_IMG-taxon_2597490344_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:10,241] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:10,244] [INFO] Selected 17 target genomes.
[2024-01-24 13:02:10,244] [INFO] Target genome list was writen to GCF_900112985.1_IMG-taxon_2597490344_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:02:10,253] [INFO] Task started: fastANI
[2024-01-24 13:02:10,253] [INFO] Running command: fastANI --query /var/lib/cwl/stgd79397bb-1382-437c-8882-09be2d301a65/GCF_900112985.1_IMG-taxon_2597490344_annotated_assembly_genomic.fna.gz --refList GCF_900112985.1_IMG-taxon_2597490344_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900112985.1_IMG-taxon_2597490344_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:27,965] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:27,966] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga8c63a64-6f51-489e-b8a7-5207d7e83419/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:27,967] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga8c63a64-6f51-489e-b8a7-5207d7e83419/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:27,982] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:02:27,982] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:27,982] [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 antarcticus	strain=ATCC 51969	GCA_900112985.1	34086	34086	type	True	100.0	1511	1512	95	conclusive
Pedobacter antarcticus	strain=4BY	GCA_000722885.1	34086	34086	type	True	99.9402	1446	1512	95	conclusive
Pedobacter hartonius	strain=DSM 19033	GCA_900107535.1	425514	425514	type	True	79.3776	276	1512	95	below_threshold
Pedobacter lusitanus	strain=NL19	GCA_000832545.1	1503925	1503925	type	True	79.1538	354	1512	95	below_threshold
Pedobacter cryoconitis	strain=DSM 14825	GCA_003259615.1	188932	188932	suspected-type	True	79.0734	363	1512	95	below_threshold
Pedobacter westerhofensis	strain=DSM 19036	GCA_900182595.1	425512	425512	type	True	78.8898	319	1512	95	below_threshold
Pedobacter foliorum	strain=LMG 31463	GCA_013266735.1	2739058	2739058	type	True	78.1597	202	1512	95	below_threshold
Pedobacter nutrimenti	strain=DSM 27372	GCA_003208655.1	1241337	1241337	type	True	78.0858	214	1512	95	below_threshold
Pedobacter panaciterrae	strain=LMG 23400	GCA_013204795.1	363849	363849	type	True	78.0504	202	1512	95	below_threshold
Pedobacter endophyticus	strain=JBR3-12	GCA_015679185.1	2789740	2789740	type	True	77.9466	86	1512	95	below_threshold
Pedobacter psychroterrae	strain=RP-1-14	GCA_004331695.1	2530453	2530453	type	True	77.8597	171	1512	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:27,985] [INFO] DFAST Taxonomy check result was written to GCF_900112985.1_IMG-taxon_2597490344_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:02:27,985] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:27,985] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:27,985] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga8c63a64-6f51-489e-b8a7-5207d7e83419/dqc_reference/checkm_data
[2024-01-24 13:02:27,986] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:28,043] [INFO] Task started: CheckM
[2024-01-24 13:02:28,043] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900112985.1_IMG-taxon_2597490344_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900112985.1_IMG-taxon_2597490344_annotated_assembly_genomic.fna/checkm_input GCF_900112985.1_IMG-taxon_2597490344_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:03:20,124] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:20,126] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:20,146] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:20,147] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:20,147] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900112985.1_IMG-taxon_2597490344_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:03:20,147] [INFO] Task started: Blastn
[2024-01-24 13:03:20,148] [INFO] Running command: blastn -query GCF_900112985.1_IMG-taxon_2597490344_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga8c63a64-6f51-489e-b8a7-5207d7e83419/dqc_reference/reference_markers_gtdb.fasta -out GCF_900112985.1_IMG-taxon_2597490344_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:20,968] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:20,973] [INFO] Selected 19 target genomes.
[2024-01-24 13:03:20,973] [INFO] Target genome list was writen to GCF_900112985.1_IMG-taxon_2597490344_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:20,996] [INFO] Task started: fastANI
[2024-01-24 13:03:20,996] [INFO] Running command: fastANI --query /var/lib/cwl/stgd79397bb-1382-437c-8882-09be2d301a65/GCF_900112985.1_IMG-taxon_2597490344_annotated_assembly_genomic.fna.gz --refList GCF_900112985.1_IMG-taxon_2597490344_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900112985.1_IMG-taxon_2597490344_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:03:38,055] [INFO] Task succeeded: fastANI
[2024-01-24 13:03:38,071] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:03:38,071] [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_900112985.1	s__Pedobacter antarcticus	100.0	1511	1512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	99.39	98.80	0.96	0.91	3	conclusive
GCF_900107535.1	s__Pedobacter hartonius	79.3788	274	1512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200595.1	s__Pedobacter cryoconitis_C	79.3409	367	1512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.76	98.76	0.93	0.93	2	-
GCA_014302835.1	s__Pedobacter sp014302835	79.339	276	1512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000832545.1	s__Pedobacter lusitanus	79.1673	353	1512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207135.1	s__Pedobacter cryoconitis_D	79.1497	368	1512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259615.1	s__Pedobacter cryoconitis	79.0926	361	1512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200605.1	s__Pedobacter cryoconitis_B	79.0871	376	1512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.88	98.88	0.94	0.94	2	-
GCF_001590605.1	s__Pedobacter cryoconitis_A	79.0853	390	1512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000170795.1	s__Pedobacter sp000170795	79.0332	181	1512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765875.1	s__Pedobacter sp009765875	78.9079	333	1512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182595.1	s__Pedobacter westerhofensis	78.9042	317	1512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223055.1	s__Pedobacter sp015223055	78.5593	205	1512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002333205.1	s__Pedobacter sp002333205	78.3203	131	1512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331685.1	s__Pedobacter sp004331685	78.2989	207	1512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	97.88	97.88	0.86	0.86	2	-
GCF_013266735.1	s__Pedobacter foliorum	78.1577	201	1512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003208655.1	s__Pedobacter nutrimenti	78.053	212	1512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331695.1	s__Pedobacter sp004331695	77.8298	170	1512	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:03:38,073] [INFO] GTDB search result was written to GCF_900112985.1_IMG-taxon_2597490344_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:03:38,074] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:03:38,077] [INFO] DFAST_QC result json was written to GCF_900112985.1_IMG-taxon_2597490344_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:03:38,077] [INFO] DFAST_QC completed!
[2024-01-24 13:03:38,077] [INFO] Total running time: 0h1m48s