[2024-01-24 13:17:48,010] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:48,015] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:48,015] [INFO] DQC Reference Directory: /var/lib/cwl/stg906f8e8f-2594-4e80-b645-6d1b6fd8652e/dqc_reference
[2024-01-24 13:17:49,288] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:49,289] [INFO] Task started: Prodigal
[2024-01-24 13:17:49,289] [INFO] Running command: gunzip -c /var/lib/cwl/stga11a64d7-0d75-4059-af48-7247b7ca2efc/GCF_003369575.1_ASM336957v1_genomic.fna.gz | prodigal -d GCF_003369575.1_ASM336957v1_genomic.fna/cds.fna -a GCF_003369575.1_ASM336957v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:58,143] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:58,143] [INFO] Task started: HMMsearch
[2024-01-24 13:17:58,143] [INFO] Running command: hmmsearch --tblout GCF_003369575.1_ASM336957v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg906f8e8f-2594-4e80-b645-6d1b6fd8652e/dqc_reference/reference_markers.hmm GCF_003369575.1_ASM336957v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:58,491] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:58,492] [INFO] Found 6/6 markers.
[2024-01-24 13:17:58,528] [INFO] Query marker FASTA was written to GCF_003369575.1_ASM336957v1_genomic.fna/markers.fasta
[2024-01-24 13:17:58,528] [INFO] Task started: Blastn
[2024-01-24 13:17:58,528] [INFO] Running command: blastn -query GCF_003369575.1_ASM336957v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg906f8e8f-2594-4e80-b645-6d1b6fd8652e/dqc_reference/reference_markers.fasta -out GCF_003369575.1_ASM336957v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:59,178] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:59,181] [INFO] Selected 13 target genomes.
[2024-01-24 13:17:59,182] [INFO] Target genome list was writen to GCF_003369575.1_ASM336957v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:59,188] [INFO] Task started: fastANI
[2024-01-24 13:17:59,188] [INFO] Running command: fastANI --query /var/lib/cwl/stga11a64d7-0d75-4059-af48-7247b7ca2efc/GCF_003369575.1_ASM336957v1_genomic.fna.gz --refList GCF_003369575.1_ASM336957v1_genomic.fna/target_genomes.txt --output GCF_003369575.1_ASM336957v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:09,637] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:09,638] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg906f8e8f-2594-4e80-b645-6d1b6fd8652e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:09,638] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg906f8e8f-2594-4e80-b645-6d1b6fd8652e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:09,655] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:09,656] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:09,656] [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 arenosus	strain=CAU 1183	GCA_003369575.1	1229153	1229153	type	True	100.0	1327	1331	95	conclusive
Oceanobacillus zhaokaii	strain=160	GCA_003352005.1	2052660	2052660	type	True	84.2874	906	1331	95	below_threshold
Oceanobacillus chungangensis	strain=CAU 1051	GCA_003369565.1	1229152	1229152	type	True	83.6463	888	1331	95	below_threshold
Oceanobacillus polygoni	strain=SA9	GCA_008304605.1	1235259	1235259	type	True	78.2444	233	1331	95	below_threshold
Virgibacillus profundi	strain=P3-H5	GCA_002287375.1	2024555	2024555	type	True	77.491	227	1331	95	below_threshold
Ornithinibacillus massiliensis	strain=Marseille-P3601	GCA_018310345.1	1944633	1944633	type	True	77.3121	109	1331	95	below_threshold
Ornithinibacillus contaminans	strain=DSM 22953	GCA_001038425.2	694055	694055	type	True	77.2219	126	1331	95	below_threshold
Oceanobacillus halophilus	strain=DSM 23996	GCA_003628505.1	930130	930130	type	True	77.1605	156	1331	95	below_threshold
Virgibacillus ndiopensis	strain=Marseille-P3835	GCA_900187325.1	2004408	2004408	type	True	77.1301	136	1331	95	below_threshold
Oceanobacillus salinisoli	strain=YIM B00359	GCA_009733865.1	2678611	2678611	type	True	77.0518	187	1331	95	below_threshold
Virgibacillus subterraneus	strain=CGMCC 1.7734	GCA_900110695.1	621109	621109	type	True	76.9369	115	1331	95	below_threshold
Oceanobacillus sojae	strain=NBRC 105379	GCA_007991515.1	582851	582851	type	True	76.8739	101	1331	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:09,667] [INFO] DFAST Taxonomy check result was written to GCF_003369575.1_ASM336957v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:09,667] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:09,668] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:09,668] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg906f8e8f-2594-4e80-b645-6d1b6fd8652e/dqc_reference/checkm_data
[2024-01-24 13:18:09,669] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:09,709] [INFO] Task started: CheckM
[2024-01-24 13:18:09,709] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003369575.1_ASM336957v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003369575.1_ASM336957v1_genomic.fna/checkm_input GCF_003369575.1_ASM336957v1_genomic.fna/checkm_result
[2024-01-24 13:18:42,676] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:42,677] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:42,701] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:42,701] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:42,702] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003369575.1_ASM336957v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:42,702] [INFO] Task started: Blastn
[2024-01-24 13:18:42,702] [INFO] Running command: blastn -query GCF_003369575.1_ASM336957v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg906f8e8f-2594-4e80-b645-6d1b6fd8652e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003369575.1_ASM336957v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:43,534] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:43,538] [INFO] Selected 17 target genomes.
[2024-01-24 13:18:43,538] [INFO] Target genome list was writen to GCF_003369575.1_ASM336957v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:43,618] [INFO] Task started: fastANI
[2024-01-24 13:18:43,618] [INFO] Running command: fastANI --query /var/lib/cwl/stga11a64d7-0d75-4059-af48-7247b7ca2efc/GCF_003369575.1_ASM336957v1_genomic.fna.gz --refList GCF_003369575.1_ASM336957v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003369575.1_ASM336957v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:57,017] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:57,036] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:57,037] [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_003369575.1	s__Oceanobacillus arenosus	100.0	1327	1331	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Oceanobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003352005.1	s__Oceanobacillus zhaokaii	84.2729	908	1331	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_003369565.1	s__Oceanobacillus chungangensis	83.6538	887	1331	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_008304605.1	s__Oceanobacillus polygoni	78.2273	234	1331	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	77.7389	238	1331	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	77.5857	153	1331	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_001659985.1	s__Oceanobacillus sp001659985	77.5306	176	1331	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_002287375.1	s__Virgibacillus_G profundi	77.512	226	1331	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_000725285.1	s__Virgibacillus sp000725285	77.4796	127	1331	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_000577245.1	s__Ornithinibacillus sp000577245	77.4577	125	1331	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_002266285.1	s__Virgibacillus_G indicus	77.4432	178	1331	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_018310345.1	s__Ornithinibacillus massiliensis	77.3157	108	1331	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_001038425.2	s__Ornithinibacillus contaminans	77.2219	126	1331	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_900187325.1	s__Virgibacillus_E ndiopensis	77.114	135	1331	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_009733865.1	s__Oceanobacillus salinisoli	77.0307	184	1331	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_016919725.1	s__Virgibacillus sp016919725	77.016	140	1331	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus	95.0	99.34	99.27	0.95	0.91	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:57,038] [INFO] GTDB search result was written to GCF_003369575.1_ASM336957v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:57,039] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:57,042] [INFO] DFAST_QC result json was written to GCF_003369575.1_ASM336957v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:57,043] [INFO] DFAST_QC completed!
[2024-01-24 13:18:57,043] [INFO] Total running time: 0h1m9s