[2024-01-24 11:43:42,132] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:42,140] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:42,140] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6574d62-e375-4c69-9e98-100271177e51/dqc_reference
[2024-01-24 11:43:43,505] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:43,506] [INFO] Task started: Prodigal
[2024-01-24 11:43:43,506] [INFO] Running command: gunzip -c /var/lib/cwl/stg758acb42-38c1-47ed-9eb5-0c5d48400286/GCF_003515705.1_ASM351570v1_genomic.fna.gz | prodigal -d GCF_003515705.1_ASM351570v1_genomic.fna/cds.fna -a GCF_003515705.1_ASM351570v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:53,727] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:53,727] [INFO] Task started: HMMsearch
[2024-01-24 11:43:53,727] [INFO] Running command: hmmsearch --tblout GCF_003515705.1_ASM351570v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6574d62-e375-4c69-9e98-100271177e51/dqc_reference/reference_markers.hmm GCF_003515705.1_ASM351570v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:54,180] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:54,182] [INFO] Found 6/6 markers.
[2024-01-24 11:43:54,222] [INFO] Query marker FASTA was written to GCF_003515705.1_ASM351570v1_genomic.fna/markers.fasta
[2024-01-24 11:43:54,223] [INFO] Task started: Blastn
[2024-01-24 11:43:54,223] [INFO] Running command: blastn -query GCF_003515705.1_ASM351570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6574d62-e375-4c69-9e98-100271177e51/dqc_reference/reference_markers.fasta -out GCF_003515705.1_ASM351570v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:54,818] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:54,821] [INFO] Selected 17 target genomes.
[2024-01-24 11:43:54,821] [INFO] Target genome list was writen to GCF_003515705.1_ASM351570v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:54,827] [INFO] Task started: fastANI
[2024-01-24 11:43:54,828] [INFO] Running command: fastANI --query /var/lib/cwl/stg758acb42-38c1-47ed-9eb5-0c5d48400286/GCF_003515705.1_ASM351570v1_genomic.fna.gz --refList GCF_003515705.1_ASM351570v1_genomic.fna/target_genomes.txt --output GCF_003515705.1_ASM351570v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:09,140] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:09,140] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6574d62-e375-4c69-9e98-100271177e51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:09,141] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6574d62-e375-4c69-9e98-100271177e51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:09,153] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:44:09,154] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:09,154] [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
Oceanobacillus profundus	strain=DSM 18246	GCA_003515705.1	372463	372463	type	True	100.0	1555	1558	95	conclusive
Oceanobacillus profundus	strain=CL-MP28	GCA_008087205.1	372463	372463	type	True	99.9995	1540	1558	95	conclusive
Oceanobacillus polygoni	strain=SA9	GCA_008304605.1	1235259	1235259	type	True	87.9098	1159	1558	95	below_threshold
Oceanobacillus rekensis	strain=PT-11	GCA_002153375.1	937927	937927	type	True	78.5807	335	1558	95	below_threshold
Oceanobacillus damuensis	strain=PT-20	GCA_001618145.1	937928	937928	type	True	78.4165	315	1558	95	below_threshold
Oceanobacillus zhaokaii	strain=160	GCA_003352005.1	2052660	2052660	type	True	78.301	235	1558	95	below_threshold
Oceanobacillus jordanicus	strain=GSFE11	GCA_022095695.1	2867266	2867266	type	True	77.9598	167	1558	95	below_threshold
Oceanobacillus iheyensis	strain=HTE831	GCA_000011245.1	182710	182710	type	True	77.7967	191	1558	95	below_threshold
Oceanobacillus bengalensis	strain=MCCC 1K00260	GCA_003628445.1	1435466	1435466	type	True	77.6977	211	1558	95	below_threshold
Oceanobacillus neutriphilus	strain=CGMCC 1.7693	GCA_014645515.1	531815	531815	type	True	77.496	173	1558	95	below_threshold
Oceanobacillus salinisoli	strain=YIM B00359	GCA_009733865.1	2678611	2678611	type	True	77.3772	215	1558	95	below_threshold
Oceanobacillus halophilus	strain=DSM 23996	GCA_003628505.1	930130	930130	type	True	77.208	181	1558	95	below_threshold
Oceanobacillus sojae	strain=NBRC 105379	GCA_007991515.1	582851	582851	type	True	77.0193	180	1558	95	below_threshold
Lentibacillus amyloliquefaciens	strain=LAM0015	GCA_001307805.2	1472767	1472767	type	True	76.7756	84	1558	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:09,160] [INFO] DFAST Taxonomy check result was written to GCF_003515705.1_ASM351570v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:09,161] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:09,161] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:09,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6574d62-e375-4c69-9e98-100271177e51/dqc_reference/checkm_data
[2024-01-24 11:44:09,164] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:09,242] [INFO] Task started: CheckM
[2024-01-24 11:44:09,242] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003515705.1_ASM351570v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003515705.1_ASM351570v1_genomic.fna/checkm_input GCF_003515705.1_ASM351570v1_genomic.fna/checkm_result
[2024-01-24 11:44:44,846] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:44,848] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:44,871] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:44,871] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:44,872] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003515705.1_ASM351570v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:44,872] [INFO] Task started: Blastn
[2024-01-24 11:44:44,872] [INFO] Running command: blastn -query GCF_003515705.1_ASM351570v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6574d62-e375-4c69-9e98-100271177e51/dqc_reference/reference_markers_gtdb.fasta -out GCF_003515705.1_ASM351570v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:45,696] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:45,699] [INFO] Selected 20 target genomes.
[2024-01-24 11:44:45,700] [INFO] Target genome list was writen to GCF_003515705.1_ASM351570v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:45,713] [INFO] Task started: fastANI
[2024-01-24 11:44:45,713] [INFO] Running command: fastANI --query /var/lib/cwl/stg758acb42-38c1-47ed-9eb5-0c5d48400286/GCF_003515705.1_ASM351570v1_genomic.fna.gz --refList GCF_003515705.1_ASM351570v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003515705.1_ASM351570v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:59,897] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:59,911] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:59,911] [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_003515705.1	s__Oceanobacillus profundus	100.0	1555	1558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.49	99.20	0.93	0.85	4	conclusive
GCF_008304605.1	s__Oceanobacillus polygoni	87.9214	1158	1558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002153375.1	s__Oceanobacillus rekensis	78.6005	334	1558	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_001618145.1	s__Oceanobacillus damuensis	78.4343	313	1558	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_016908155.1	s__Oceanobacillus caeni	78.3653	180	1558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	98.65	98.42	0.88	0.86	14	-
GCF_018333215.1	s__Oceanobacillus sp018333215	78.1051	193	1558	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_000011245.1	s__Oceanobacillus iheyensis	77.8121	190	1558	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_003628445.1	s__Oceanobacillus bengalensis	77.7112	210	1558	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	77.7012	238	1558	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_014645515.1	s__Oceanobacillus neutriphilus	77.4804	174	1558	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_009733865.1	s__Oceanobacillus salinisoli	77.3583	211	1558	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_001659985.1	s__Oceanobacillus sp001659985	77.3352	181	1558	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	77.208	181	1558	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_900129485.1	s__Ornithinibacillus halophilus	77.1416	148	1558	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_007991515.1	s__Oceanobacillus sojae	76.9976	179	1558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	98.95	98.95	0.93	0.93	2	-
GCF_001038485.1	s__Ornithinibacillus californiensis	76.8502	130	1558	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_009389585.1	s__Oceanobacillus sp009389585	76.7212	164	1558	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:59,913] [INFO] GTDB search result was written to GCF_003515705.1_ASM351570v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:59,914] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:59,918] [INFO] DFAST_QC result json was written to GCF_003515705.1_ASM351570v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:59,918] [INFO] DFAST_QC completed!
[2024-01-24 11:44:59,918] [INFO] Total running time: 0h1m18s