[2024-01-24 13:28:00,040] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:00,044] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:00,044] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d43d424-3b06-47b7-8318-ac450e8386ab/dqc_reference
[2024-01-24 13:28:01,323] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:01,324] [INFO] Task started: Prodigal
[2024-01-24 13:28:01,324] [INFO] Running command: gunzip -c /var/lib/cwl/stg6275dd16-e0ce-4539-880f-b636716aa3b2/GCF_903166585.1_Q2390_genomic.fna.gz | prodigal -d GCF_903166585.1_Q2390_genomic.fna/cds.fna -a GCF_903166585.1_Q2390_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:23,708] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:23,709] [INFO] Task started: HMMsearch
[2024-01-24 13:28:23,709] [INFO] Running command: hmmsearch --tblout GCF_903166585.1_Q2390_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d43d424-3b06-47b7-8318-ac450e8386ab/dqc_reference/reference_markers.hmm GCF_903166585.1_Q2390_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:24,020] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:24,021] [INFO] Found 6/6 markers.
[2024-01-24 13:28:24,065] [INFO] Query marker FASTA was written to GCF_903166585.1_Q2390_genomic.fna/markers.fasta
[2024-01-24 13:28:24,065] [INFO] Task started: Blastn
[2024-01-24 13:28:24,065] [INFO] Running command: blastn -query GCF_903166585.1_Q2390_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d43d424-3b06-47b7-8318-ac450e8386ab/dqc_reference/reference_markers.fasta -out GCF_903166585.1_Q2390_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:24,683] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:24,687] [INFO] Selected 13 target genomes.
[2024-01-24 13:28:24,687] [INFO] Target genome list was writen to GCF_903166585.1_Q2390_genomic.fna/target_genomes.txt
[2024-01-24 13:28:24,694] [INFO] Task started: fastANI
[2024-01-24 13:28:24,695] [INFO] Running command: fastANI --query /var/lib/cwl/stg6275dd16-e0ce-4539-880f-b636716aa3b2/GCF_903166585.1_Q2390_genomic.fna.gz --refList GCF_903166585.1_Q2390_genomic.fna/target_genomes.txt --output GCF_903166585.1_Q2390_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:42,297] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:42,298] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d43d424-3b06-47b7-8318-ac450e8386ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:42,298] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d43d424-3b06-47b7-8318-ac450e8386ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:42,309] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:42,309] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:42,310] [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 ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	100.0	1953	1955	95	conclusive
Pedobacter kyungheensis	strain=KACC 16221	GCA_000812965.1	1069985	1069985	type	True	86.4643	1506	1955	95	below_threshold
Pedobacter soli	strain=DSM 18609	GCA_900101435.1	390242	390242	type	True	86.4112	1540	1955	95	below_threshold
Pedobacter kyonggii	strain=K-4-11-1	GCA_004310665.1	1926871	1926871	type	True	81.7584	1050	1955	95	below_threshold
Pedobacter ginsenosidimutans	strain=KACC 14530	GCA_001442625.1	687842	687842	type	True	81.7405	1078	1955	95	below_threshold
Pedobacter miscanthi	strain=RS10	GCA_003315595.1	2259170	2259170	type	True	81.6354	1089	1955	95	below_threshold
Pedobacter terrae	strain=DSM 17933	GCA_900100705.1	405671	405671	type	True	81.5757	919	1955	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_004402005.1	475253	475253	type	True	81.571	994	1955	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_003664035.1	475253	475253	type	True	81.5615	983	1955	95	below_threshold
Pedobacter psychrodurus	strain=RP-3-21	GCA_004331735.1	2530456	2530456	type	True	81.4215	1103	1955	95	below_threshold
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	79.9454	675	1955	95	below_threshold
Pedobacter xinjiangensis	strain=CCTCC AB 208092	GCA_024436435.1	539206	539206	type	True	76.8258	59	1955	95	below_threshold
Mucilaginibacter agri	strain=R11	GCA_009928685.1	2695265	2695265	type	True	76.7738	132	1955	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:42,311] [INFO] DFAST Taxonomy check result was written to GCF_903166585.1_Q2390_genomic.fna/tc_result.tsv
[2024-01-24 13:28:42,312] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:42,312] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:42,312] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d43d424-3b06-47b7-8318-ac450e8386ab/dqc_reference/checkm_data
[2024-01-24 13:28:42,314] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:42,375] [INFO] Task started: CheckM
[2024-01-24 13:28:42,375] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_903166585.1_Q2390_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_903166585.1_Q2390_genomic.fna/checkm_input GCF_903166585.1_Q2390_genomic.fna/checkm_result
[2024-01-24 13:29:43,869] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:43,870] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:43,889] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:43,889] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:43,889] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_903166585.1_Q2390_genomic.fna/markers.fasta)
[2024-01-24 13:29:43,890] [INFO] Task started: Blastn
[2024-01-24 13:29:43,890] [INFO] Running command: blastn -query GCF_903166585.1_Q2390_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d43d424-3b06-47b7-8318-ac450e8386ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_903166585.1_Q2390_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:44,664] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:44,667] [INFO] Selected 11 target genomes.
[2024-01-24 13:29:44,667] [INFO] Target genome list was writen to GCF_903166585.1_Q2390_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:44,679] [INFO] Task started: fastANI
[2024-01-24 13:29:44,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg6275dd16-e0ce-4539-880f-b636716aa3b2/GCF_903166585.1_Q2390_genomic.fna.gz --refList GCF_903166585.1_Q2390_genomic.fna/target_genomes_gtdb.txt --output GCF_903166585.1_Q2390_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:59,011] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:59,021] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:59,021] [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_903166585.1	s__Pedobacter sp903166585	100.0	1953	1955	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011303555.1	s__Pedobacter sp003852395	91.4614	1624	1955	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	99.47	99.47	0.90	0.90	2	-
GCF_000812965.1	s__Pedobacter kyungheensis	86.4465	1509	1955	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101435.1	s__Pedobacter soli	86.4182	1538	1955	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	82.0356	1055	1955	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.16	98.15	0.91	0.91	3	-
GCA_017745075.1	s__Pedobacter sp017745075	82.0054	1036	1955	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205835.1	s__Pedobacter sp014205835	81.8263	1042	1955	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310665.1	s__Pedobacter kyonggii	81.7649	1049	1955	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	81.6665	1148	1955	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	81.6518	1087	1955	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664035.1	s__Pedobacter alluvionis	81.5676	982	1955	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:59,023] [INFO] GTDB search result was written to GCF_903166585.1_Q2390_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:59,023] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:59,026] [INFO] DFAST_QC result json was written to GCF_903166585.1_Q2390_genomic.fna/dqc_result.json
[2024-01-24 13:29:59,027] [INFO] DFAST_QC completed!
[2024-01-24 13:29:59,027] [INFO] Total running time: 0h1m59s