[2024-01-24 15:02:18,886] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:18,892] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:18,892] [INFO] DQC Reference Directory: /var/lib/cwl/stgea2efa35-20cb-447a-9fc2-b9003895e3c9/dqc_reference
[2024-01-24 15:02:20,834] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:20,836] [INFO] Task started: Prodigal
[2024-01-24 15:02:20,836] [INFO] Running command: gunzip -c /var/lib/cwl/stg164a7fc7-36b4-4e8d-8b52-a4179ae84d66/GCF_014642175.1_ASM1464217v1_genomic.fna.gz | prodigal -d GCF_014642175.1_ASM1464217v1_genomic.fna/cds.fna -a GCF_014642175.1_ASM1464217v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:39,332] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:39,333] [INFO] Task started: HMMsearch
[2024-01-24 15:02:39,333] [INFO] Running command: hmmsearch --tblout GCF_014642175.1_ASM1464217v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea2efa35-20cb-447a-9fc2-b9003895e3c9/dqc_reference/reference_markers.hmm GCF_014642175.1_ASM1464217v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:39,622] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:39,623] [INFO] Found 6/6 markers.
[2024-01-24 15:02:39,657] [INFO] Query marker FASTA was written to GCF_014642175.1_ASM1464217v1_genomic.fna/markers.fasta
[2024-01-24 15:02:39,657] [INFO] Task started: Blastn
[2024-01-24 15:02:39,657] [INFO] Running command: blastn -query GCF_014642175.1_ASM1464217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea2efa35-20cb-447a-9fc2-b9003895e3c9/dqc_reference/reference_markers.fasta -out GCF_014642175.1_ASM1464217v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:40,297] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:40,302] [INFO] Selected 25 target genomes.
[2024-01-24 15:02:40,302] [INFO] Target genome list was writen to GCF_014642175.1_ASM1464217v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:40,322] [INFO] Task started: fastANI
[2024-01-24 15:02:40,323] [INFO] Running command: fastANI --query /var/lib/cwl/stg164a7fc7-36b4-4e8d-8b52-a4179ae84d66/GCF_014642175.1_ASM1464217v1_genomic.fna.gz --refList GCF_014642175.1_ASM1464217v1_genomic.fna/target_genomes.txt --output GCF_014642175.1_ASM1464217v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:06,769] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:06,770] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea2efa35-20cb-447a-9fc2-b9003895e3c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:06,770] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea2efa35-20cb-447a-9fc2-b9003895e3c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:06,785] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:03:06,786] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:03:06,786] [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 quisquiliarum	strain=CGMCC 1.15343	GCA_014642175.1	1834438	1834438	type	True	100.0	1241	1242	95	conclusive
Pedobacter duraquae	strain=DSM 19034	GCA_004362245.1	425511	425511	type	True	78.9622	203	1242	95	below_threshold
Pedobacter antarcticus	strain=4BY	GCA_000722885.1	34086	34086	type	True	78.8234	139	1242	95	below_threshold
Pedobacter antarcticus	strain=ATCC 51969	GCA_900112985.1	34086	34086	type	True	78.8184	153	1242	95	below_threshold
Pedobacter westerhofensis	strain=DSM 19036	GCA_900182595.1	425512	425512	type	True	78.5662	184	1242	95	below_threshold
Pedobacter hiemivivus	strain=RP-3-8	GCA_004331685.1	2530454	2530454	type	True	78.3728	159	1242	95	below_threshold
Pedobacter nyackensis	strain=DSM 19625	GCA_900176505.1	475255	475255	type	True	78.3432	162	1242	95	below_threshold
Pedobacter lusitanus	strain=NL19	GCA_000832545.1	1503925	1503925	type	True	78.3107	159	1242	95	below_threshold
Pedobacter foliorum	strain=LMG 31463	GCA_013266735.1	2739058	2739058	type	True	78.2108	155	1242	95	below_threshold
Pedobacter cryoconitis	strain=DSM 14825	GCA_003259615.1	188932	188932	suspected-type	True	78.1762	169	1242	95	below_threshold
Pedobacter gandavensis	strain=LMG 31462	GCA_014172405.1	2679963	2679963	type	True	78.1618	180	1242	95	below_threshold
Pedobacter caeni	strain=DSM 16990	GCA_900129215.1	288992	288992	type	True	78.1144	190	1242	95	below_threshold
Pedobacter panaciterrae	strain=LMG 23400	GCA_013204795.1	363849	363849	type	True	78.1143	160	1242	95	below_threshold
Pedobacter frigoris	strain=RP-3-15	GCA_005116445.1	2571272	2571272	type	True	77.9669	172	1242	95	below_threshold
Pedobacter helvus	strain=P-25	GCA_005925325.1	2563444	2563444	type	True	77.6878	87	1242	95	below_threshold
Pedobacter frigiditerrae	strain=RP-1-13	GCA_004331645.1	2530452	2530452	type	True	77.6341	115	1242	95	below_threshold
Pedobacter psychroterrae	strain=RP-1-14	GCA_004331695.1	2530453	2530453	type	True	77.6245	143	1242	95	below_threshold
Pedobacter soli	strain=DSM 18609	GCA_900101435.1	390242	390242	type	True	77.394	123	1242	95	below_threshold
Pedobacter ureilyticus	strain=THG-T11	GCA_005925345.1	1393051	1393051	type	True	77.2745	93	1242	95	below_threshold
Pedobacter aquae	strain=CJ43	GCA_008195825.1	2605747	2605747	type	True	76.379	60	1242	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:06,795] [INFO] DFAST Taxonomy check result was written to GCF_014642175.1_ASM1464217v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:06,796] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:06,796] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:06,796] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea2efa35-20cb-447a-9fc2-b9003895e3c9/dqc_reference/checkm_data
[2024-01-24 15:03:06,798] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:06,841] [INFO] Task started: CheckM
[2024-01-24 15:03:06,841] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014642175.1_ASM1464217v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014642175.1_ASM1464217v1_genomic.fna/checkm_input GCF_014642175.1_ASM1464217v1_genomic.fna/checkm_result
[2024-01-24 15:04:02,101] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:02,104] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:02,130] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:02,131] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:02,131] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014642175.1_ASM1464217v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:02,131] [INFO] Task started: Blastn
[2024-01-24 15:04:02,131] [INFO] Running command: blastn -query GCF_014642175.1_ASM1464217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea2efa35-20cb-447a-9fc2-b9003895e3c9/dqc_reference/reference_markers_gtdb.fasta -out GCF_014642175.1_ASM1464217v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:03,142] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:03,147] [INFO] Selected 18 target genomes.
[2024-01-24 15:04:03,147] [INFO] Target genome list was writen to GCF_014642175.1_ASM1464217v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:03,161] [INFO] Task started: fastANI
[2024-01-24 15:04:03,162] [INFO] Running command: fastANI --query /var/lib/cwl/stg164a7fc7-36b4-4e8d-8b52-a4179ae84d66/GCF_014642175.1_ASM1464217v1_genomic.fna.gz --refList GCF_014642175.1_ASM1464217v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014642175.1_ASM1464217v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:22,088] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:22,103] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:22,104] [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_014642175.1	s__Pedobacter quisquiliarum	100.0	1241	1242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	96.56	96.56	0.95	0.95	2	conclusive
GCA_002320935.1	s__Pedobacter sp002320935	82.0073	668	1242	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	81.9019	642	1242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362245.1	s__Pedobacter duraquae	78.9622	203	1242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112985.1	s__Pedobacter antarcticus	78.8175	152	1242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	99.39	98.80	0.96	0.91	3	-
GCF_900176505.1	s__Pedobacter nyackensis	78.3432	162	1242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001412655.1	s__Pedobacter sp001412655	78.2034	186	1242	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	78.1828	154	1242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014172405.1	s__Pedobacter gandavensis	78.1404	181	1242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129215.1	s__Pedobacter caeni	78.1325	189	1242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001721645.1	s__Pedobacter steynii_A	78.0971	190	1242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001636695.1	s__Pedobacter panaciterrae_A	78.0936	158	1242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364225.1	s__Pedobacter sp004364225	78.0761	181	1242	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	78.0244	167	1242	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	78.0103	174	1242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000523515.1	s__Pedobacter sp000523515	77.8474	169	1242	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	77.8309	176	1242	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003061025.1	s__Pedobacter sp003061025	77.805	147	1242	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 15:04:22,105] [INFO] GTDB search result was written to GCF_014642175.1_ASM1464217v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:22,106] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:22,110] [INFO] DFAST_QC result json was written to GCF_014642175.1_ASM1464217v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:22,110] [INFO] DFAST_QC completed!
[2024-01-24 15:04:22,110] [INFO] Total running time: 0h2m3s