[2024-01-25 18:11:35,693] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:11:35,695] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:11:35,695] [INFO] DQC Reference Directory: /var/lib/cwl/stg8238c98a-c0c5-4046-8bc5-19a768df40a2/dqc_reference
[2024-01-25 18:11:36,922] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:11:36,923] [INFO] Task started: Prodigal
[2024-01-25 18:11:36,923] [INFO] Running command: gunzip -c /var/lib/cwl/stgd3409aab-978d-4c0a-bdd1-ddcd357f189e/GCF_002266285.1_ASM226628v1_genomic.fna.gz | prodigal -d GCF_002266285.1_ASM226628v1_genomic.fna/cds.fna -a GCF_002266285.1_ASM226628v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:11:44,479] [INFO] Task succeeded: Prodigal
[2024-01-25 18:11:44,480] [INFO] Task started: HMMsearch
[2024-01-25 18:11:44,480] [INFO] Running command: hmmsearch --tblout GCF_002266285.1_ASM226628v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8238c98a-c0c5-4046-8bc5-19a768df40a2/dqc_reference/reference_markers.hmm GCF_002266285.1_ASM226628v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:11:44,713] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:11:44,714] [INFO] Found 6/6 markers.
[2024-01-25 18:11:44,744] [INFO] Query marker FASTA was written to GCF_002266285.1_ASM226628v1_genomic.fna/markers.fasta
[2024-01-25 18:11:44,744] [INFO] Task started: Blastn
[2024-01-25 18:11:44,744] [INFO] Running command: blastn -query GCF_002266285.1_ASM226628v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8238c98a-c0c5-4046-8bc5-19a768df40a2/dqc_reference/reference_markers.fasta -out GCF_002266285.1_ASM226628v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:45,289] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:45,292] [INFO] Selected 26 target genomes.
[2024-01-25 18:11:45,292] [INFO] Target genome list was writen to GCF_002266285.1_ASM226628v1_genomic.fna/target_genomes.txt
[2024-01-25 18:11:45,301] [INFO] Task started: fastANI
[2024-01-25 18:11:45,301] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3409aab-978d-4c0a-bdd1-ddcd357f189e/GCF_002266285.1_ASM226628v1_genomic.fna.gz --refList GCF_002266285.1_ASM226628v1_genomic.fna/target_genomes.txt --output GCF_002266285.1_ASM226628v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:12:03,483] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:03,484] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8238c98a-c0c5-4046-8bc5-19a768df40a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:12:03,484] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8238c98a-c0c5-4046-8bc5-19a768df40a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:12:03,498] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:12:03,499] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:12:03,500] [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
Virgibacillus indicus	strain=P2-C2	GCA_002266285.1	2024554	2024554	type	True	100.0	1284	1284	95	conclusive
Virgibacillus profundi	strain=P3-H5	GCA_002287375.1	2024555	2024555	type	True	80.2105	646	1284	95	below_threshold
Oceanobacillus jordanicus	strain=GSFE11	GCA_022095695.1	2867266	2867266	type	True	77.8891	175	1284	95	below_threshold
Virgibacillus pantothenticus	strain=DSM 26	GCA_001189575.1	1473	1473	type	True	77.6388	121	1284	95	below_threshold
Oceanobacillus polygoni	strain=SA9	GCA_008304605.1	1235259	1235259	type	True	77.588	196	1284	95	below_threshold
Virgibacillus ndiopensis	strain=Marseille-P3835	GCA_900187325.1	2004408	2004408	type	True	77.5855	222	1284	95	below_threshold
Virgibacillus natechei	strain=DSM 25609	GCA_017874115.1	1216297	1216297	type	True	77.5796	206	1284	95	below_threshold
Virgibacillus doumboii	strain=Marseille-Q1616	GCA_902806455.1	2697503	2697503	type	True	77.5005	233	1284	95	below_threshold
Virgibacillus halotolerans	strain=DSM 25060	GCA_016908515.1	1071053	1071053	type	True	77.4498	228	1284	95	below_threshold
Virgibacillus phasianinus	strain=LM2416	GCA_002216775.1	2017483	2017483	type	True	77.3754	176	1284	95	below_threshold
Lentibacillus jeotgali	strain=Grbi	GCA_000224785.2	558169	558169	type	True	77.3392	110	1284	95	below_threshold
Oceanobacillus senegalensis	strain=Marseille-P3587	GCA_900176885.1	1936063	1936063	type	True	77.3274	154	1284	95	below_threshold
Oceanobacillus bengalensis	strain=MCCC 1K00260	GCA_003628445.1	1435466	1435466	type	True	77.2038	176	1284	95	below_threshold
Virgibacillus litoralis	strain=DSM 21085	GCA_017873675.1	578221	578221	type	True	77.1618	202	1284	95	below_threshold
Virgibacillus subterraneus	strain=CGMCC 1.7734	GCA_900110695.1	621109	621109	type	True	77.1123	199	1284	95	below_threshold
Virgibacillus alimentarius	strain=J18	GCA_000709085.1	698769	698769	type	True	77.0816	133	1284	95	below_threshold
Oceanobacillus salinisoli	strain=YIM B00359	GCA_009733865.1	2678611	2678611	type	True	76.9047	193	1284	95	below_threshold
Oceanobacillus alkalisoli	strain=APA_J-2 (6-2)	GCA_021556485.1	2925113	2925113	type	True	76.8434	109	1284	95	below_threshold
Gracilibacillus thailandensis	strain=TP2-8	GCA_010994055.1	563735	563735	type	True	76.7551	78	1284	95	below_threshold
Gracilibacillus salitolerans	strain=SCU50	GCA_009650095.1	2663022	2663022	type	True	76.6758	81	1284	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:12:03,501] [INFO] DFAST Taxonomy check result was written to GCF_002266285.1_ASM226628v1_genomic.fna/tc_result.tsv
[2024-01-25 18:12:03,502] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:12:03,502] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:12:03,502] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8238c98a-c0c5-4046-8bc5-19a768df40a2/dqc_reference/checkm_data
[2024-01-25 18:12:03,503] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:12:03,543] [INFO] Task started: CheckM
[2024-01-25 18:12:03,543] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002266285.1_ASM226628v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002266285.1_ASM226628v1_genomic.fna/checkm_input GCF_002266285.1_ASM226628v1_genomic.fna/checkm_result
[2024-01-25 18:12:30,666] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:30,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:30,704] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:30,704] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:30,704] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002266285.1_ASM226628v1_genomic.fna/markers.fasta)
[2024-01-25 18:12:30,705] [INFO] Task started: Blastn
[2024-01-25 18:12:30,705] [INFO] Running command: blastn -query GCF_002266285.1_ASM226628v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8238c98a-c0c5-4046-8bc5-19a768df40a2/dqc_reference/reference_markers_gtdb.fasta -out GCF_002266285.1_ASM226628v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:31,464] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:31,470] [INFO] Selected 31 target genomes.
[2024-01-25 18:12:31,470] [INFO] Target genome list was writen to GCF_002266285.1_ASM226628v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:31,500] [INFO] Task started: fastANI
[2024-01-25 18:12:31,500] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3409aab-978d-4c0a-bdd1-ddcd357f189e/GCF_002266285.1_ASM226628v1_genomic.fna.gz --refList GCF_002266285.1_ASM226628v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002266285.1_ASM226628v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:12:52,293] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:52,309] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:12:52,310] [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_002266285.1	s__Virgibacillus_G indicus	100.0	1284	1284	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_G	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002287375.1	s__Virgibacillus_G profundi	80.2057	647	1284	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_G	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000612865.1	s__Virgibacillus picturae	77.656	165	1284	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	97.99	95.34	0.93	0.90	5	-
GCF_017874115.1	s__Virgibacillus_H natechei	77.5987	204	1284	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_000285495.1	s__Oceanobacillus massiliensis	77.5717	178	1284	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900187325.1	s__Virgibacillus_E ndiopensis	77.5612	223	1284	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_003369575.1	s__Oceanobacillus arenosus	77.535	172	1284	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_902806455.1	s__Lentibacillus doumboii	77.4907	233	1284	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908515.1	s__Virgibacillus_I halotolerans	77.4642	226	1284	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_014638995.1	s__Virgibacillus_E oceani	77.4029	207	1284	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_002153375.1	s__Oceanobacillus rekensis	77.3861	220	1284	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_002216775.1	s__Virgibacillus_F phasianinus	77.3765	176	1284	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000224785.1	s__Lentibacillus jeotgali	77.3673	108	1284	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002224365.1	s__Virgibacillus_F necropolis	77.3405	188	1284	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_F	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176885.1	s__Oceanobacillus senegalensis	77.3224	155	1284	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_009649745.1	s__Aquibacillus_A halophilus	77.2517	67	1284	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Aquibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003628445.1	s__Oceanobacillus bengalensis	77.23	176	1284	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_003369565.1	s__Oceanobacillus chungangensis	77.2101	175	1284	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_017873675.1	s__Lentibacillus litoralis	77.1606	202	1284	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110695.1	s__Lentibacillus subterraneus	77.153	195	1284	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	98.85	98.85	0.91	0.91	2	-
GCA_004145795.1	s__Lentibacillus lipolyticus	77.1053	89	1284	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000709085.1	s__Virgibacillus_B alimentarius	77.0816	133	1284	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_B	95.0	99.59	99.59	0.92	0.92	2	-
GCF_010994035.1	s__Virgibacillus sp010994035	77.0339	167	1284	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458115.1	s__Gracilibacillus massiliensis	77.0086	61	1284	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009733865.1	s__Oceanobacillus salinisoli	76.8854	194	1284	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_009650095.1	s__Gracilibacillus sp002797295	76.6758	81	1284	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	98.80	98.80	0.91	0.91	2	-
GCF_900143085.1	s__Gracilibacillus kekensis	76.635	60	1284	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:12:52,311] [INFO] GTDB search result was written to GCF_002266285.1_ASM226628v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:12:52,311] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:12:52,315] [INFO] DFAST_QC result json was written to GCF_002266285.1_ASM226628v1_genomic.fna/dqc_result.json
[2024-01-25 18:12:52,315] [INFO] DFAST_QC completed!
[2024-01-25 18:12:52,315] [INFO] Total running time: 0h1m17s