[2024-01-25 20:01:21,005] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:01:21,007] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:01:21,007] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa65c18b-5cfc-4165-9822-f922fc31bb8c/dqc_reference
[2024-01-25 20:01:22,125] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:01:22,126] [INFO] Task started: Prodigal
[2024-01-25 20:01:22,127] [INFO] Running command: gunzip -c /var/lib/cwl/stgc9dbcbcf-2f8c-4859-a530-c9c2980c8f75/GCF_003664035.1_ASM366403v1_genomic.fna.gz | prodigal -d GCF_003664035.1_ASM366403v1_genomic.fna/cds.fna -a GCF_003664035.1_ASM366403v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:01:40,781] [INFO] Task succeeded: Prodigal
[2024-01-25 20:01:40,781] [INFO] Task started: HMMsearch
[2024-01-25 20:01:40,781] [INFO] Running command: hmmsearch --tblout GCF_003664035.1_ASM366403v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa65c18b-5cfc-4165-9822-f922fc31bb8c/dqc_reference/reference_markers.hmm GCF_003664035.1_ASM366403v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:01:41,065] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:01:41,066] [INFO] Found 6/6 markers.
[2024-01-25 20:01:41,111] [INFO] Query marker FASTA was written to GCF_003664035.1_ASM366403v1_genomic.fna/markers.fasta
[2024-01-25 20:01:41,111] [INFO] Task started: Blastn
[2024-01-25 20:01:41,111] [INFO] Running command: blastn -query GCF_003664035.1_ASM366403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa65c18b-5cfc-4165-9822-f922fc31bb8c/dqc_reference/reference_markers.fasta -out GCF_003664035.1_ASM366403v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:01:41,695] [INFO] Task succeeded: Blastn
[2024-01-25 20:01:41,698] [INFO] Selected 14 target genomes.
[2024-01-25 20:01:41,698] [INFO] Target genome list was writen to GCF_003664035.1_ASM366403v1_genomic.fna/target_genomes.txt
[2024-01-25 20:01:41,707] [INFO] Task started: fastANI
[2024-01-25 20:01:41,707] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9dbcbcf-2f8c-4859-a530-c9c2980c8f75/GCF_003664035.1_ASM366403v1_genomic.fna.gz --refList GCF_003664035.1_ASM366403v1_genomic.fna/target_genomes.txt --output GCF_003664035.1_ASM366403v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:02:01,611] [INFO] Task succeeded: fastANI
[2024-01-25 20:02:01,611] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa65c18b-5cfc-4165-9822-f922fc31bb8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:02:01,612] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa65c18b-5cfc-4165-9822-f922fc31bb8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:02:01,621] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:02:01,621] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:02:01,621] [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 alluvionis	strain=DSM 19624	GCA_003664035.1	475253	475253	type	True	100.0	2003	2003	95	conclusive
Pedobacter alluvionis	strain=DSM 19624	GCA_004402005.1	475253	475253	type	True	99.9927	2001	2003	95	conclusive
Pedobacter borealis	strain=DSM 19626	GCA_000708285.2	475254	475254	type	True	86.5442	1116	2003	95	below_threshold
Pedobacter ginsenosidimutans	strain=KACC 14530	GCA_001442625.1	687842	687842	type	True	86.4602	1301	2003	95	below_threshold
Pedobacter kyonggii	strain=K-4-11-1	GCA_004310665.1	1926871	1926871	type	True	86.4044	1296	2003	95	below_threshold
Pedobacter psychrodurus	strain=RP-3-21	GCA_004331735.1	2530456	2530456	type	True	85.961	1264	2003	95	below_threshold
Pedobacter terrae	strain=DSM 17933	GCA_900100705.1	405671	405671	type	True	85.9142	1316	2003	95	below_threshold
Pedobacter suwonensis	strain=DSM 18130	GCA_900111825.1	332999	332999	type	True	83.86	1213	2003	95	below_threshold
Pedobacter miscanthi	strain=RS10	GCA_003315595.1	2259170	2259170	type	True	83.116	1152	2003	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	81.6003	989	2003	95	below_threshold
Mucilaginibacter robiniae	strain=F39-2	GCA_012849215.1	2728022	2728022	type	True	76.9112	82	2003	95	below_threshold
Mucilaginibacter conchicola	strain=MYSH2	GCA_003432115.1	2303333	2303333	type	True	76.4594	94	2003	95	below_threshold
Sphingobacterium faecale	strain=C459-1	GCA_016746095.1	2803775	2803775	type	True	76.3312	55	2003	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	76.2152	91	2003	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:02:01,622] [INFO] DFAST Taxonomy check result was written to GCF_003664035.1_ASM366403v1_genomic.fna/tc_result.tsv
[2024-01-25 20:02:01,623] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:02:01,623] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:02:01,623] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa65c18b-5cfc-4165-9822-f922fc31bb8c/dqc_reference/checkm_data
[2024-01-25 20:02:01,624] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:02:01,682] [INFO] Task started: CheckM
[2024-01-25 20:02:01,682] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003664035.1_ASM366403v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003664035.1_ASM366403v1_genomic.fna/checkm_input GCF_003664035.1_ASM366403v1_genomic.fna/checkm_result
[2024-01-25 20:02:55,282] [INFO] Task succeeded: CheckM
[2024-01-25 20:02:55,283] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:02:55,298] [INFO] ===== Completeness check finished =====
[2024-01-25 20:02:55,299] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:02:55,300] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003664035.1_ASM366403v1_genomic.fna/markers.fasta)
[2024-01-25 20:02:55,300] [INFO] Task started: Blastn
[2024-01-25 20:02:55,300] [INFO] Running command: blastn -query GCF_003664035.1_ASM366403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa65c18b-5cfc-4165-9822-f922fc31bb8c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003664035.1_ASM366403v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:02:56,143] [INFO] Task succeeded: Blastn
[2024-01-25 20:02:56,146] [INFO] Selected 12 target genomes.
[2024-01-25 20:02:56,146] [INFO] Target genome list was writen to GCF_003664035.1_ASM366403v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:02:56,159] [INFO] Task started: fastANI
[2024-01-25 20:02:56,160] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9dbcbcf-2f8c-4859-a530-c9c2980c8f75/GCF_003664035.1_ASM366403v1_genomic.fna.gz --refList GCF_003664035.1_ASM366403v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003664035.1_ASM366403v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:03:15,228] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:15,235] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:03:15,236] [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_003664035.1	s__Pedobacter alluvionis	100.0	2003	2003	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_004342125.1	s__Pedobacter sp004342125	94.3703	1591	2003	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	95.29	95.29	0.84	0.84	2	-
GCF_005938645.2	s__Pedobacter sp005938645	90.2076	1445	2003	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994015.1	s__Pedobacter terrae_A	88.9176	1357	2003	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708285.2	s__Pedobacter borealis	86.53	1118	2003	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442625.1	s__Pedobacter ginsenosidimutans	86.4617	1301	2003	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014692875.1	s__Pedobacter sp011759615	86.3864	1292	2003	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.16	98.15	0.91	0.91	3	-
GCF_004310665.1	s__Pedobacter kyonggii	86.3853	1298	2003	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054145.1	s__Pedobacter sp003054145	85.841	1229	2003	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002151545.1	s__Pedobacter sp002151545	85.6086	1220	2003	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014395225.1	s__Pedobacter roseus	85.3911	1234	2003	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315595.1	s__Pedobacter miscanthi	83.1297	1150	2003	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 20:03:15,237] [INFO] GTDB search result was written to GCF_003664035.1_ASM366403v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:03:15,237] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:03:15,240] [INFO] DFAST_QC result json was written to GCF_003664035.1_ASM366403v1_genomic.fna/dqc_result.json
[2024-01-25 20:03:15,240] [INFO] DFAST_QC completed!
[2024-01-25 20:03:15,240] [INFO] Total running time: 0h1m54s