[2024-01-24 13:18:33,477] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:33,480] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:33,480] [INFO] DQC Reference Directory: /var/lib/cwl/stg8bdd86ab-4882-46a5-ba14-5f9634e0c9d6/dqc_reference
[2024-01-24 13:18:34,905] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:34,906] [INFO] Task started: Prodigal
[2024-01-24 13:18:34,906] [INFO] Running command: gunzip -c /var/lib/cwl/stg321ca2e3-4291-476c-85ce-a4c07f58d282/GCF_014196715.1_ASM1419671v1_genomic.fna.gz | prodigal -d GCF_014196715.1_ASM1419671v1_genomic.fna/cds.fna -a GCF_014196715.1_ASM1419671v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:56,073] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:56,073] [INFO] Task started: HMMsearch
[2024-01-24 13:18:56,073] [INFO] Running command: hmmsearch --tblout GCF_014196715.1_ASM1419671v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8bdd86ab-4882-46a5-ba14-5f9634e0c9d6/dqc_reference/reference_markers.hmm GCF_014196715.1_ASM1419671v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:56,428] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:56,430] [INFO] Found 6/6 markers.
[2024-01-24 13:18:56,476] [INFO] Query marker FASTA was written to GCF_014196715.1_ASM1419671v1_genomic.fna/markers.fasta
[2024-01-24 13:18:56,477] [INFO] Task started: Blastn
[2024-01-24 13:18:56,477] [INFO] Running command: blastn -query GCF_014196715.1_ASM1419671v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bdd86ab-4882-46a5-ba14-5f9634e0c9d6/dqc_reference/reference_markers.fasta -out GCF_014196715.1_ASM1419671v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:57,118] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:57,122] [INFO] Selected 16 target genomes.
[2024-01-24 13:18:57,122] [INFO] Target genome list was writen to GCF_014196715.1_ASM1419671v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:57,142] [INFO] Task started: fastANI
[2024-01-24 13:18:57,142] [INFO] Running command: fastANI --query /var/lib/cwl/stg321ca2e3-4291-476c-85ce-a4c07f58d282/GCF_014196715.1_ASM1419671v1_genomic.fna.gz --refList GCF_014196715.1_ASM1419671v1_genomic.fna/target_genomes.txt --output GCF_014196715.1_ASM1419671v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:16,884] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:16,884] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8bdd86ab-4882-46a5-ba14-5f9634e0c9d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:16,885] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8bdd86ab-4882-46a5-ba14-5f9634e0c9d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:16,898] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:19:16,898] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:16,898] [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 zeae	strain=DSM 100774	GCA_014196715.1	1737356	1737356	type	True	100.0	1808	1808	95	conclusive
Pedobacter zeae	strain=CGMCC 1.15287	GCA_014641575.1	1737356	1737356	type	True	99.9989	1806	1808	95	conclusive
Pedobacter miscanthi	strain=RS10	GCA_003315595.1	2259170	2259170	type	True	83.1291	1154	1808	95	below_threshold
Pedobacter alluvionis	strain=DSM 19624	GCA_003664035.1	475253	475253	type	True	83.1072	1174	1808	95	below_threshold
Pedobacter borealis	strain=DSM 19626	GCA_000708285.2	475254	475254	type	True	83.0705	1056	1808	95	below_threshold
Pedobacter ginsenosidimutans	strain=KACC 14530	GCA_001442625.1	687842	687842	type	True	82.9318	1227	1808	95	below_threshold
Pedobacter psychrodurus	strain=RP-3-21	GCA_004331735.1	2530456	2530456	type	True	82.7804	1152	1808	95	below_threshold
Pedobacter terrae	strain=DSM 17933	GCA_900100705.1	405671	405671	type	True	82.6146	1089	1808	95	below_threshold
Pedobacter soli	strain=DSM 18609	GCA_900101435.1	390242	390242	type	True	82.2596	1032	1808	95	below_threshold
Pedobacter kyungheensis	strain=KACC 16221	GCA_000812965.1	1069985	1069985	type	True	82.2417	1062	1808	95	below_threshold
Pedobacter suwonensis	strain=DSM 18130	GCA_900111825.1	332999	332999	type	True	82.0364	1079	1808	95	below_threshold
Pedobacter ghigonis	strain=Marseille-Q2390	GCA_903166585.1	2730403	2730403	type	True	81.8246	1028	1808	95	below_threshold
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	79.6523	624	1808	95	below_threshold
Pedobacter mucosus	strain=Q8-18	GCA_022200785.1	2895286	2895286	type	True	78.813	460	1808	95	below_threshold
Sphingobacterium prati	strain=arapr2	GCA_013167215.1	2737006	2737006	type	True	76.5863	54	1808	95	below_threshold
Mucilaginibacter gilvus	strain=F01003	GCA_004054195.1	2305909	2305909	type	True	76.5161	83	1808	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:16,900] [INFO] DFAST Taxonomy check result was written to GCF_014196715.1_ASM1419671v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:16,901] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:16,901] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:16,901] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8bdd86ab-4882-46a5-ba14-5f9634e0c9d6/dqc_reference/checkm_data
[2024-01-24 13:19:16,902] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:16,959] [INFO] Task started: CheckM
[2024-01-24 13:19:16,959] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196715.1_ASM1419671v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196715.1_ASM1419671v1_genomic.fna/checkm_input GCF_014196715.1_ASM1419671v1_genomic.fna/checkm_result
[2024-01-24 13:20:17,296] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:17,298] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:17,320] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:17,320] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:17,320] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196715.1_ASM1419671v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:17,321] [INFO] Task started: Blastn
[2024-01-24 13:20:17,321] [INFO] Running command: blastn -query GCF_014196715.1_ASM1419671v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bdd86ab-4882-46a5-ba14-5f9634e0c9d6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196715.1_ASM1419671v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:18,230] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:18,234] [INFO] Selected 12 target genomes.
[2024-01-24 13:20:18,235] [INFO] Target genome list was writen to GCF_014196715.1_ASM1419671v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:18,260] [INFO] Task started: fastANI
[2024-01-24 13:20:18,260] [INFO] Running command: fastANI --query /var/lib/cwl/stg321ca2e3-4291-476c-85ce-a4c07f58d282/GCF_014196715.1_ASM1419671v1_genomic.fna.gz --refList GCF_014196715.1_ASM1419671v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196715.1_ASM1419671v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:34,510] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:34,526] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:34,526] [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_014196715.1	s__Pedobacter zeae	100.0	1808	1808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_017745075.1	s__Pedobacter sp017745075	89.3298	1510	1808	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	83.8146	1306	1808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	98.16	98.15	0.91	0.91	3	-
GCF_014395225.1	s__Pedobacter roseus	83.7535	1207	1808	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	83.7341	1286	1808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000633455.1	s__Pedobacter jeongneungensis	83.6408	1180	1808	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	83.1365	1154	1808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002432345.1	s__Pedobacter sp002432345	83.126	1037	1808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100705.1	s__Pedobacter terrae	82.6175	1090	1808	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	82.2598	1032	1808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000812965.1	s__Pedobacter kyungheensis	82.2353	1061	1808	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903166585.1	s__Pedobacter sp903166585	81.8314	1027	1808	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 13:20:34,528] [INFO] GTDB search result was written to GCF_014196715.1_ASM1419671v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:34,528] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:34,532] [INFO] DFAST_QC result json was written to GCF_014196715.1_ASM1419671v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:34,532] [INFO] DFAST_QC completed!
[2024-01-24 13:20:34,532] [INFO] Total running time: 0h2m1s