[2024-01-24 13:18:40,848] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:40,851] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:40,851] [INFO] DQC Reference Directory: /var/lib/cwl/stg76dd8283-ae7b-4f6b-99cd-9655c7924f1c/dqc_reference
[2024-01-24 13:18:42,083] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:42,084] [INFO] Task started: Prodigal
[2024-01-24 13:18:42,084] [INFO] Running command: gunzip -c /var/lib/cwl/stg8285c2b6-ddb2-4351-8340-992444929cfb/GCF_014202495.1_ASM1420249v1_genomic.fna.gz | prodigal -d GCF_014202495.1_ASM1420249v1_genomic.fna/cds.fna -a GCF_014202495.1_ASM1420249v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:47,393] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:47,393] [INFO] Task started: HMMsearch
[2024-01-24 13:18:47,393] [INFO] Running command: hmmsearch --tblout GCF_014202495.1_ASM1420249v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76dd8283-ae7b-4f6b-99cd-9655c7924f1c/dqc_reference/reference_markers.hmm GCF_014202495.1_ASM1420249v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:47,649] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:47,651] [INFO] Found 6/6 markers.
[2024-01-24 13:18:47,679] [INFO] Query marker FASTA was written to GCF_014202495.1_ASM1420249v1_genomic.fna/markers.fasta
[2024-01-24 13:18:47,679] [INFO] Task started: Blastn
[2024-01-24 13:18:47,679] [INFO] Running command: blastn -query GCF_014202495.1_ASM1420249v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76dd8283-ae7b-4f6b-99cd-9655c7924f1c/dqc_reference/reference_markers.fasta -out GCF_014202495.1_ASM1420249v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:48,372] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:48,376] [INFO] Selected 27 target genomes.
[2024-01-24 13:18:48,376] [INFO] Target genome list was writen to GCF_014202495.1_ASM1420249v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:48,467] [INFO] Task started: fastANI
[2024-01-24 13:18:48,467] [INFO] Running command: fastANI --query /var/lib/cwl/stg8285c2b6-ddb2-4351-8340-992444929cfb/GCF_014202495.1_ASM1420249v1_genomic.fna.gz --refList GCF_014202495.1_ASM1420249v1_genomic.fna/target_genomes.txt --output GCF_014202495.1_ASM1420249v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:02,684] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:02,685] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76dd8283-ae7b-4f6b-99cd-9655c7924f1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:02,685] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76dd8283-ae7b-4f6b-99cd-9655c7924f1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:02,703] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:19:02,703] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:02,703] [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
Cerasibacillus quisquiliarum	strain=DSM 15825	GCA_014202495.1	227865	227865	type	True	100.0	912	912	95	conclusive
Cerasibacillus quisquiliarum	strain=NBRC 102429	GCA_007991195.1	227865	227865	type	True	99.9696	879	912	95	conclusive
Cerasibacillus terrae	strain=CC-CFT480	GCA_008039555.1	2498845	2498845	type	True	78.1758	242	912	95	below_threshold
Ornithinibacillus halophilus	strain=IBRC-M 10683	GCA_900129485.1	930117	930117	type	True	76.7426	81	912	95	below_threshold
Oceanobacillus halotolerans	strain=YIM 98839	GCA_010993955.1	2663380	2663380	type	True	76.6733	75	912	95	below_threshold
Virgibacillus natechei	strain=DSM 25609	GCA_017874115.1	1216297	1216297	type	True	76.6075	63	912	95	below_threshold
Oceanobacillus jordanicus	strain=GSFE11	GCA_022095695.1	2867266	2867266	type	True	76.4833	62	912	95	below_threshold
Ornithinibacillus scapharcae	strain=TW25	GCA_000190475.2	1147159	1147159	type	True	76.2847	77	912	95	below_threshold
Oceanobacillus iheyensis	strain=HTE831	GCA_000011245.1	182710	182710	type	True	76.2785	65	912	95	below_threshold
Virgibacillus halotolerans	strain=DSM 25060	GCA_016908515.1	1071053	1071053	type	True	76.2649	58	912	95	below_threshold
Oceanobacillus kimchii	strain=X50	GCA_000340475.1	746691	746691	type	True	76.2217	65	912	95	below_threshold
Paraliobacillus quinghaiensis	strain=CGMCC 1.6333	GCA_014645115.1	470815	470815	type	True	76.0611	52	912	95	below_threshold
Paraliobacillus quinghaiensis	strain=YIM-C158	GCA_003426025.1	470815	470815	type	True	76.0099	54	912	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:02,705] [INFO] DFAST Taxonomy check result was written to GCF_014202495.1_ASM1420249v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:02,705] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:02,706] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:02,706] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76dd8283-ae7b-4f6b-99cd-9655c7924f1c/dqc_reference/checkm_data
[2024-01-24 13:19:02,707] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:02,740] [INFO] Task started: CheckM
[2024-01-24 13:19:02,740] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014202495.1_ASM1420249v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014202495.1_ASM1420249v1_genomic.fna/checkm_input GCF_014202495.1_ASM1420249v1_genomic.fna/checkm_result
[2024-01-24 13:19:25,874] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:25,875] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:25,897] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:25,897] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:25,898] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014202495.1_ASM1420249v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:25,898] [INFO] Task started: Blastn
[2024-01-24 13:19:25,898] [INFO] Running command: blastn -query GCF_014202495.1_ASM1420249v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76dd8283-ae7b-4f6b-99cd-9655c7924f1c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014202495.1_ASM1420249v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:26,926] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:26,934] [INFO] Selected 28 target genomes.
[2024-01-24 13:19:26,935] [INFO] Target genome list was writen to GCF_014202495.1_ASM1420249v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:27,020] [INFO] Task started: fastANI
[2024-01-24 13:19:27,021] [INFO] Running command: fastANI --query /var/lib/cwl/stg8285c2b6-ddb2-4351-8340-992444929cfb/GCF_014202495.1_ASM1420249v1_genomic.fna.gz --refList GCF_014202495.1_ASM1420249v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014202495.1_ASM1420249v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:42,374] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:42,392] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:42,393] [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_014202495.1	s__Cerasibacillus quisquiliarum	100.0	912	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Cerasibacillus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_008039555.1	s__Cerasibacillus terrae	78.1812	241	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Cerasibacillus	95.0	99.05	99.05	0.92	0.92	2	-
GCF_900129485.1	s__Ornithinibacillus halophilus	76.7426	81	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111445.1	s__Ornithinibacillus limi	76.6782	76	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993955.1	s__YIM-98839 sp010993955	76.6449	76	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__YIM-98839	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874115.1	s__Virgibacillus_H natechei	76.6413	62	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001038485.1	s__Ornithinibacillus californiensis	76.575	79	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900258515.1	s__Virgibacillus_E sp900258515	76.5479	95	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003369565.1	s__Oceanobacillus chungangensis	76.5127	63	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009728145.1	s__Ornithinibacillus caprae	76.5039	84	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016919725.1	s__Virgibacillus sp016919725	76.4138	76	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.34	99.27	0.95	0.91	5	-
GCF_001368815.1	s__Paraliobacillus sp001368815	76.3297	56	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011245.1	s__Oceanobacillus iheyensis	76.3069	64	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190475.1	s__Ornithinibacillus scapharcae	76.2847	77	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352005.1	s__Oceanobacillus zhaokaii	76.2651	70	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.81	99.81	1.00	1.00	2	-
GCF_016908515.1	s__Virgibacillus_I halotolerans	76.2649	58	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000340475.1	s__Oceanobacillus kimchii	76.2217	65	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.20	99.13	0.93	0.91	5	-
GCF_003201975.1	s__Pseudogracilibacillus auburnensis	76.1998	83	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Pseudogracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003426025.1	s__Paraliobacillus_A quinghaiensis	76.0099	54	912	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus_A	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:42,395] [INFO] GTDB search result was written to GCF_014202495.1_ASM1420249v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:42,396] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:42,403] [INFO] DFAST_QC result json was written to GCF_014202495.1_ASM1420249v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:42,404] [INFO] DFAST_QC completed!
[2024-01-24 13:19:42,404] [INFO] Total running time: 0h1m2s