[2024-01-24 13:49:41,818] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:41,820] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:41,820] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e869320-7a61-4ac8-bfb4-3dfefd83ebde/dqc_reference
[2024-01-24 13:49:43,144] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:43,145] [INFO] Task started: Prodigal
[2024-01-24 13:49:43,145] [INFO] Running command: gunzip -c /var/lib/cwl/stg866f4d7f-3e2a-4a24-bc97-5df42bddd51b/GCF_001038485.1_ASM103848v1_genomic.fna.gz | prodigal -d GCF_001038485.1_ASM103848v1_genomic.fna/cds.fna -a GCF_001038485.1_ASM103848v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:50,891] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:50,891] [INFO] Task started: HMMsearch
[2024-01-24 13:49:50,891] [INFO] Running command: hmmsearch --tblout GCF_001038485.1_ASM103848v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e869320-7a61-4ac8-bfb4-3dfefd83ebde/dqc_reference/reference_markers.hmm GCF_001038485.1_ASM103848v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:51,141] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:51,142] [INFO] Found 6/6 markers.
[2024-01-24 13:49:51,180] [INFO] Query marker FASTA was written to GCF_001038485.1_ASM103848v1_genomic.fna/markers.fasta
[2024-01-24 13:49:51,181] [INFO] Task started: Blastn
[2024-01-24 13:49:51,181] [INFO] Running command: blastn -query GCF_001038485.1_ASM103848v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e869320-7a61-4ac8-bfb4-3dfefd83ebde/dqc_reference/reference_markers.fasta -out GCF_001038485.1_ASM103848v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:51,793] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:51,796] [INFO] Selected 26 target genomes.
[2024-01-24 13:49:51,797] [INFO] Target genome list was writen to GCF_001038485.1_ASM103848v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:51,811] [INFO] Task started: fastANI
[2024-01-24 13:49:51,811] [INFO] Running command: fastANI --query /var/lib/cwl/stg866f4d7f-3e2a-4a24-bc97-5df42bddd51b/GCF_001038485.1_ASM103848v1_genomic.fna.gz --refList GCF_001038485.1_ASM103848v1_genomic.fna/target_genomes.txt --output GCF_001038485.1_ASM103848v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:07,078] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:07,078] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e869320-7a61-4ac8-bfb4-3dfefd83ebde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:07,079] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e869320-7a61-4ac8-bfb4-3dfefd83ebde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:07,095] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:50:07,095] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:50:07,095] [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
Ornithinibacillus contaminans	strain=DSM 22953	GCA_001038425.2	694055	694055	type	True	79.6997	353	1296	95	below_threshold
Ornithinibacillus massiliensis	strain=Marseille-P3601	GCA_018310345.1	1944633	1944633	type	True	79.6062	494	1296	95	below_threshold
Ornithinibacillus scapharcae	strain=TW25	GCA_000190475.2	1147159	1147159	type	True	78.9306	409	1296	95	below_threshold
Ornithinibacillus halotolerans	strain=CGMCC 1.12408	GCA_014637405.1	1274357	1274357	type	True	78.7791	447	1296	95	below_threshold
Oceanobacillus jordanicus	strain=GSFE11	GCA_022095695.1	2867266	2867266	type	True	77.5344	110	1296	95	below_threshold
Ornithinibacillus halophilus	strain=IBRC-M 10683	GCA_900129485.1	930117	930117	type	True	77.4975	236	1296	95	below_threshold
Virgibacillus ndiopensis	strain=Marseille-P3835	GCA_900187325.1	2004408	2004408	type	True	77.4358	133	1296	95	below_threshold
Paraliobacillus quinghaiensis	strain=CGMCC 1.6333	GCA_014645115.1	470815	470815	type	True	77.292	68	1296	95	below_threshold
Oceanobacillus halophilus	strain=DSM 23996	GCA_003628505.1	930130	930130	type	True	77.166	129	1296	95	below_threshold
Oceanobacillus profundus	strain=CL-MP28	GCA_008087205.1	372463	372463	type	True	77.0865	117	1296	95	below_threshold
Oceanobacillus profundus	strain=DSM 18246	GCA_003515705.1	372463	372463	type	True	77.0315	115	1296	95	below_threshold
Aquibacillus koreensis	strain=JCM 12387	GCA_025154055.1	279446	279446	type	True	76.976	83	1296	95	below_threshold
Saliterribacillus persicus	strain=DSM 27696	GCA_003337485.1	930114	930114	type	True	76.8845	66	1296	95	below_threshold
Virgibacillus subterraneus	strain=CGMCC 1.7734	GCA_900110695.1	621109	621109	type	True	76.7548	118	1296	95	below_threshold
Cerasibacillus quisquiliarum	strain=NBRC 102429	GCA_007991195.1	227865	227865	type	True	76.4133	86	1296	95	below_threshold
Cerasibacillus quisquiliarum	strain=DSM 15825	GCA_014202495.1	227865	227865	type	True	76.3671	90	1296	95	below_threshold
Gottfriedia solisilvae	strain=NEAU-cbsb5	GCA_002128405.1	1516104	1516104	type	True	76.2864	56	1296	95	below_threshold
Gottfriedia solisilvae	strain=CGMCC 1.14993	GCA_014640495.1	1516104	1516104	type	True	76.2863	56	1296	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	76.1702	72	1296	95	below_threshold
Psychrobacillus insolitus	strain=DSM 5	GCA_003254155.1	1461	1461	type	True	75.8859	53	1296	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:07,097] [INFO] DFAST Taxonomy check result was written to GCF_001038485.1_ASM103848v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:07,098] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:07,098] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:07,098] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e869320-7a61-4ac8-bfb4-3dfefd83ebde/dqc_reference/checkm_data
[2024-01-24 13:50:07,099] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:07,140] [INFO] Task started: CheckM
[2024-01-24 13:50:07,140] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001038485.1_ASM103848v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001038485.1_ASM103848v1_genomic.fna/checkm_input GCF_001038485.1_ASM103848v1_genomic.fna/checkm_result
[2024-01-24 13:50:36,553] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:36,555] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:36,575] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:36,575] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:36,576] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001038485.1_ASM103848v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:36,576] [INFO] Task started: Blastn
[2024-01-24 13:50:36,576] [INFO] Running command: blastn -query GCF_001038485.1_ASM103848v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e869320-7a61-4ac8-bfb4-3dfefd83ebde/dqc_reference/reference_markers_gtdb.fasta -out GCF_001038485.1_ASM103848v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:37,392] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:37,396] [INFO] Selected 13 target genomes.
[2024-01-24 13:50:37,396] [INFO] Target genome list was writen to GCF_001038485.1_ASM103848v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:37,405] [INFO] Task started: fastANI
[2024-01-24 13:50:37,405] [INFO] Running command: fastANI --query /var/lib/cwl/stg866f4d7f-3e2a-4a24-bc97-5df42bddd51b/GCF_001038485.1_ASM103848v1_genomic.fna.gz --refList GCF_001038485.1_ASM103848v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001038485.1_ASM103848v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:46,501] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:46,511] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:46,512] [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_001038485.1	s__Ornithinibacillus californiensis	100.0	1294	1296	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001038425.2	s__Ornithinibacillus contaminans	79.7141	354	1296	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_000577245.1	s__Ornithinibacillus sp000577245	79.6239	521	1296	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_018310345.1	s__Ornithinibacillus massiliensis	79.5791	498	1296	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Ornithinibacillus	95.0	99.20	99.20	0.97	0.97	2	-
GCF_900184735.1	s__Ornithinibacillus globulus_B	79.3493	524	1296	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_000482485.1	s__Ornithinibacillus globulus	79.1056	516	1296	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_000190475.1	s__Ornithinibacillus scapharcae	78.9248	410	1296	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_000011245.1	s__Oceanobacillus iheyensis	77.2217	106	1296	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_003628505.1	s__Oceanobacillus halophilus	77.1328	127	1296	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_003515705.1	s__Oceanobacillus profundus	77.0696	116	1296	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.49	99.20	0.93	0.85	4	-
GCF_003337485.1	s__Saliterribacillus persicus	76.8845	66	1296	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Saliterribacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202495.1	s__Cerasibacillus quisquiliarum	76.3671	90	1296	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Cerasibacillus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:46,516] [INFO] GTDB search result was written to GCF_001038485.1_ASM103848v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:46,517] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:46,521] [INFO] DFAST_QC result json was written to GCF_001038485.1_ASM103848v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:46,521] [INFO] DFAST_QC completed!
[2024-01-24 13:50:46,521] [INFO] Total running time: 0h1m5s