[2024-01-24 10:47:10,567] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:10,575] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:10,575] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc043ce4-4f72-437a-8f28-ebef0439d4c8/dqc_reference
[2024-01-24 10:47:12,301] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,302] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,302] [INFO] Running command: gunzip -c /var/lib/cwl/stg14faa1e5-c04b-4401-9de2-8bbb5663c8ac/GCF_023522835.1_ASM2352283v1_genomic.fna.gz | prodigal -d GCF_023522835.1_ASM2352283v1_genomic.fna/cds.fna -a GCF_023522835.1_ASM2352283v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:21,706] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:21,706] [INFO] Task started: HMMsearch
[2024-01-24 10:47:21,706] [INFO] Running command: hmmsearch --tblout GCF_023522835.1_ASM2352283v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc043ce4-4f72-437a-8f28-ebef0439d4c8/dqc_reference/reference_markers.hmm GCF_023522835.1_ASM2352283v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:21,987] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:21,988] [INFO] Found 6/6 markers.
[2024-01-24 10:47:22,023] [INFO] Query marker FASTA was written to GCF_023522835.1_ASM2352283v1_genomic.fna/markers.fasta
[2024-01-24 10:47:22,023] [INFO] Task started: Blastn
[2024-01-24 10:47:22,023] [INFO] Running command: blastn -query GCF_023522835.1_ASM2352283v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc043ce4-4f72-437a-8f28-ebef0439d4c8/dqc_reference/reference_markers.fasta -out GCF_023522835.1_ASM2352283v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:22,654] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:22,658] [INFO] Selected 23 target genomes.
[2024-01-24 10:47:22,659] [INFO] Target genome list was writen to GCF_023522835.1_ASM2352283v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:23,584] [INFO] Task started: fastANI
[2024-01-24 10:47:23,584] [INFO] Running command: fastANI --query /var/lib/cwl/stg14faa1e5-c04b-4401-9de2-8bbb5663c8ac/GCF_023522835.1_ASM2352283v1_genomic.fna.gz --refList GCF_023522835.1_ASM2352283v1_genomic.fna/target_genomes.txt --output GCF_023522835.1_ASM2352283v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:39,238] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:39,238] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc043ce4-4f72-437a-8f28-ebef0439d4c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:39,238] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc043ce4-4f72-437a-8f28-ebef0439d4c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:39,251] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:47:39,251] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:47:39,252] [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 damuensis	strain=PT-20	GCA_001618145.1	937928	937928	type	True	82.7804	779	1371	95	below_threshold
Oceanobacillus rekensis	strain=PT-11	GCA_002153375.1	937927	937927	type	True	79.8357	529	1371	95	below_threshold
Oceanobacillus massiliensis	strain=Ndiop	GCA_000285495.1	1465765	1465765	type	True	79.0589	404	1371	95	below_threshold
Oceanobacillus polygoni	strain=SA9	GCA_008304605.1	1235259	1235259	type	True	78.7622	326	1371	95	below_threshold
Oceanobacillus profundus	strain=DSM 18246	GCA_003515705.1	372463	372463	type	True	78.4377	337	1371	95	below_threshold
Oceanobacillus profundus	strain=CL-MP28	GCA_008087205.1	372463	372463	type	True	78.393	341	1371	95	below_threshold
Oceanobacillus zhaokaii	strain=160	GCA_003352005.1	2052660	2052660	type	True	77.6508	231	1371	95	below_threshold
Oceanobacillus arenosus	strain=CAU 1183	GCA_003369575.1	1229153	1229153	type	True	77.6351	218	1371	95	below_threshold
Virgibacillus indicus	strain=P2-C2	GCA_002266285.1	2024554	2024554	type	True	77.5836	192	1371	95	below_threshold
Virgibacillus profundi	strain=P3-H5	GCA_002287375.1	2024555	2024555	type	True	77.3858	219	1371	95	below_threshold
Oceanobacillus bengalensis	strain=MCCC 1K00260	GCA_003628445.1	1435466	1435466	type	True	77.2981	189	1371	95	below_threshold
Oceanobacillus salinisoli	strain=YIM B00359	GCA_009733865.1	2678611	2678611	type	True	77.2133	196	1371	95	below_threshold
Ornithinibacillus gellani	strain=LJ137	GCA_003730295.1	2293253	2293253	type	True	77.0486	87	1371	95	below_threshold
Virgibacillus dakarensis	strain=Marseille-P3469	GCA_900155625.1	1917889	1917889	type	True	76.9434	134	1371	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:39,254] [INFO] DFAST Taxonomy check result was written to GCF_023522835.1_ASM2352283v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:39,254] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:39,255] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:39,255] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc043ce4-4f72-437a-8f28-ebef0439d4c8/dqc_reference/checkm_data
[2024-01-24 10:47:39,256] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:39,301] [INFO] Task started: CheckM
[2024-01-24 10:47:39,301] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023522835.1_ASM2352283v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023522835.1_ASM2352283v1_genomic.fna/checkm_input GCF_023522835.1_ASM2352283v1_genomic.fna/checkm_result
[2024-01-24 10:48:12,504] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:12,505] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:12,526] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:12,526] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:12,527] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023522835.1_ASM2352283v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:12,527] [INFO] Task started: Blastn
[2024-01-24 10:48:12,527] [INFO] Running command: blastn -query GCF_023522835.1_ASM2352283v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc043ce4-4f72-437a-8f28-ebef0439d4c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_023522835.1_ASM2352283v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:13,318] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:13,323] [INFO] Selected 19 target genomes.
[2024-01-24 10:48:13,324] [INFO] Target genome list was writen to GCF_023522835.1_ASM2352283v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:13,334] [INFO] Task started: fastANI
[2024-01-24 10:48:13,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg14faa1e5-c04b-4401-9de2-8bbb5663c8ac/GCF_023522835.1_ASM2352283v1_genomic.fna.gz --refList GCF_023522835.1_ASM2352283v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023522835.1_ASM2352283v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:26,972] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:26,994] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:48:26,995] [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_001618145.1	s__Oceanobacillus damuensis	82.7584	783	1371	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_002153375.1	s__Oceanobacillus rekensis	79.8092	533	1371	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_000285495.1	s__Oceanobacillus massiliensis	79.0589	404	1371	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_008304605.1	s__Oceanobacillus polygoni	78.7692	329	1371	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_003515705.1	s__Oceanobacillus profundus	78.4357	336	1371	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_003352005.1	s__Oceanobacillus zhaokaii	77.6609	226	1371	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_003369575.1	s__Oceanobacillus arenosus	77.6225	217	1371	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_002266285.1	s__Virgibacillus_G indicus	77.5408	197	1371	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	-
GCF_003628445.1	s__Oceanobacillus bengalensis	77.2959	191	1371	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_000577245.1	s__Ornithinibacillus sp000577245	77.2673	110	1371	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_016908155.1	s__Oceanobacillus caeni	77.2607	141	1371	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_009733865.1	s__Oceanobacillus salinisoli	77.2054	197	1371	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	77.2022	126	1371	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_003730295.1	s__LJ137 sp003730295	77.0486	87	1371	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__LJ137	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991515.1	s__Oceanobacillus sojae	77.0242	130	1371	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_900112045.1	s__Lentibacillus halodurans	76.627	84	1371	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:26,998] [INFO] GTDB search result was written to GCF_023522835.1_ASM2352283v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:26,999] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:27,003] [INFO] DFAST_QC result json was written to GCF_023522835.1_ASM2352283v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:27,004] [INFO] DFAST_QC completed!
[2024-01-24 10:48:27,004] [INFO] Total running time: 0h1m16s