[2024-01-24 14:07:31,153] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:07:31,155] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:07:31,155] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e19a330-b105-4970-8ffb-e6daf2ed169f/dqc_reference
[2024-01-24 14:07:32,376] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:32,377] [INFO] Task started: Prodigal
[2024-01-24 14:07:32,378] [INFO] Running command: gunzip -c /var/lib/cwl/stg921c21c3-39e5-41fe-b9da-6aedb3ea0b53/GCF_902806455.1_Q1616_genomic.fna.gz | prodigal -d GCF_902806455.1_Q1616_genomic.fna/cds.fna -a GCF_902806455.1_Q1616_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:41,700] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:41,700] [INFO] Task started: HMMsearch
[2024-01-24 14:07:41,700] [INFO] Running command: hmmsearch --tblout GCF_902806455.1_Q1616_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e19a330-b105-4970-8ffb-e6daf2ed169f/dqc_reference/reference_markers.hmm GCF_902806455.1_Q1616_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:42,010] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:42,011] [INFO] Found 6/6 markers.
[2024-01-24 14:07:42,053] [INFO] Query marker FASTA was written to GCF_902806455.1_Q1616_genomic.fna/markers.fasta
[2024-01-24 14:07:42,053] [INFO] Task started: Blastn
[2024-01-24 14:07:42,054] [INFO] Running command: blastn -query GCF_902806455.1_Q1616_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e19a330-b105-4970-8ffb-e6daf2ed169f/dqc_reference/reference_markers.fasta -out GCF_902806455.1_Q1616_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:42,699] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:42,704] [INFO] Selected 23 target genomes.
[2024-01-24 14:07:42,705] [INFO] Target genome list was writen to GCF_902806455.1_Q1616_genomic.fna/target_genomes.txt
[2024-01-24 14:07:42,716] [INFO] Task started: fastANI
[2024-01-24 14:07:42,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg921c21c3-39e5-41fe-b9da-6aedb3ea0b53/GCF_902806455.1_Q1616_genomic.fna.gz --refList GCF_902806455.1_Q1616_genomic.fna/target_genomes.txt --output GCF_902806455.1_Q1616_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:59,237] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:59,237] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e19a330-b105-4970-8ffb-e6daf2ed169f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:59,238] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e19a330-b105-4970-8ffb-e6daf2ed169f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:59,252] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:07:59,253] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:59,253] [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 doumboii	strain=Marseille-Q1616	GCA_902806455.1	2697503	2697503	type	True	100.0	1302	1302	95	conclusive
Heyndrickxia oleronia	strain=DSM 9356	GCA_025263665.1	38875	38875	type	True	79.3214	51	1302	95	below_threshold
Virgibacillus ihumii	strain=Marseille-Q1233	GCA_902726655.1	2686091	2686091	type	True	78.7694	304	1302	95	below_threshold
Virgibacillus litoralis	strain=DSM 21085	GCA_017873675.1	578221	578221	type	True	78.4079	414	1302	95	below_threshold
Oceanobacillus senegalensis	strain=Marseille-P3587	GCA_900176885.1	1936063	1936063	type	True	78.298	107	1302	95	below_threshold
Virgibacillus necropolis	strain=LMG 19488	GCA_002224365.1	163877	163877	type	True	78.1952	172	1302	95	below_threshold
Virgibacillus ndiopensis	strain=Marseille-P3835	GCA_900187325.1	2004408	2004408	type	True	77.8722	232	1302	95	below_threshold
Lentibacillus cibarius	strain=NKC220-2	GCA_005887555.1	2583219	2583219	type	True	77.7493	174	1302	95	below_threshold
Lentibacillus halodurans	strain=CGMCC 1.3702	GCA_900112045.1	237679	237679	type	True	77.696	267	1302	95	below_threshold
Virgibacillus oceani	strain=CGMCC 1.12754	GCA_014638995.1	1479511	1479511	type	True	77.6124	210	1302	95	below_threshold
Virgibacillus profundi	strain=P3-H5	GCA_002287375.1	2024555	2024555	type	True	77.5728	216	1302	95	below_threshold
Virgibacillus indicus	strain=P2-C2	GCA_002266285.1	2024554	2024554	type	True	77.5525	234	1302	95	below_threshold
Ornithinibacillus scapharcae	strain=TW25	GCA_000190475.2	1147159	1147159	type	True	77.4934	86	1302	95	below_threshold
Ornithinibacillus halophilus	strain=IBRC-M 10683	GCA_900129485.1	930117	930117	type	True	77.1439	125	1302	95	below_threshold
Oceanobacillus polygoni	strain=SA9	GCA_008304605.1	1235259	1235259	type	True	77.1186	121	1302	95	below_threshold
Virgibacillus halotolerans	strain=DSM 25060	GCA_016908515.1	1071053	1071053	type	True	77.0247	140	1302	95	below_threshold
Oceanobacillus salinisoli	strain=YIM B00359	GCA_009733865.1	2678611	2678611	type	True	76.7553	127	1302	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:59,254] [INFO] DFAST Taxonomy check result was written to GCF_902806455.1_Q1616_genomic.fna/tc_result.tsv
[2024-01-24 14:07:59,255] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:59,255] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:59,255] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e19a330-b105-4970-8ffb-e6daf2ed169f/dqc_reference/checkm_data
[2024-01-24 14:07:59,257] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:59,297] [INFO] Task started: CheckM
[2024-01-24 14:07:59,297] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902806455.1_Q1616_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902806455.1_Q1616_genomic.fna/checkm_input GCF_902806455.1_Q1616_genomic.fna/checkm_result
[2024-01-24 14:08:33,615] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:33,616] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:33,634] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:33,635] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:33,635] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902806455.1_Q1616_genomic.fna/markers.fasta)
[2024-01-24 14:08:33,636] [INFO] Task started: Blastn
[2024-01-24 14:08:33,636] [INFO] Running command: blastn -query GCF_902806455.1_Q1616_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e19a330-b105-4970-8ffb-e6daf2ed169f/dqc_reference/reference_markers_gtdb.fasta -out GCF_902806455.1_Q1616_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:34,424] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:34,428] [INFO] Selected 22 target genomes.
[2024-01-24 14:08:34,428] [INFO] Target genome list was writen to GCF_902806455.1_Q1616_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:34,444] [INFO] Task started: fastANI
[2024-01-24 14:08:34,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg921c21c3-39e5-41fe-b9da-6aedb3ea0b53/GCF_902806455.1_Q1616_genomic.fna.gz --refList GCF_902806455.1_Q1616_genomic.fna/target_genomes_gtdb.txt --output GCF_902806455.1_Q1616_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:52,106] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:52,123] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:52,124] [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_902806455.1	s__Lentibacillus doumboii	100.0	1302	1302	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900162695.1	s__Lentibacillus siamensis	78.589	298	1302	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	78.3807	402	1302	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	98.85	98.85	0.91	0.91	2	-
GCF_017873675.1	s__Lentibacillus litoralis	78.3628	418	1302	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	78.2063	172	1302	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_013373365.1	s__Lentibacillus sp013373365	78.1782	262	1302	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_900258515.1	s__Virgibacillus_E sp900258515	78.1203	228	1302	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_900187325.1	s__Virgibacillus_E ndiopensis	77.8774	231	1302	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_005887555.1	s__Lentibacillus cibarius	77.7577	173	1302	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Lentibacillus	95.0	98.44	97.49	0.90	0.85	3	-
GCF_900112045.1	s__Lentibacillus halodurans	77.6838	268	1302	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_014638995.1	s__Virgibacillus_E oceani	77.645	207	1302	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_002287375.1	s__Virgibacillus_G profundi	77.5843	214	1302	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_002266285.1	s__Virgibacillus_G indicus	77.57	231	1302	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_004565465.1	s__Lentibacillus salicampi	77.5415	251	1302	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_000190475.1	s__Ornithinibacillus scapharcae	77.4558	85	1302	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_900129485.1	s__Ornithinibacillus halophilus	77.1675	124	1302	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_009733865.1	s__Oceanobacillus salinisoli	76.7719	126	1302	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 14:08:52,126] [INFO] GTDB search result was written to GCF_902806455.1_Q1616_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:52,127] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:52,131] [INFO] DFAST_QC result json was written to GCF_902806455.1_Q1616_genomic.fna/dqc_result.json
[2024-01-24 14:08:52,132] [INFO] DFAST_QC completed!
[2024-01-24 14:08:52,132] [INFO] Total running time: 0h1m21s