[2024-01-24 14:38:45,556] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:45,558] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:45,558] [INFO] DQC Reference Directory: /var/lib/cwl/stge4f857c7-d754-4108-878f-dd7772af5e15/dqc_reference
[2024-01-24 14:38:48,280] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:48,282] [INFO] Task started: Prodigal
[2024-01-24 14:38:48,282] [INFO] Running command: gunzip -c /var/lib/cwl/stg00308987-7292-4ea6-a981-658d2525c3ee/GCF_014138385.1_ASM1413838v1_genomic.fna.gz | prodigal -d GCF_014138385.1_ASM1413838v1_genomic.fna/cds.fna -a GCF_014138385.1_ASM1413838v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:02,307] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:02,308] [INFO] Task started: HMMsearch
[2024-01-24 14:39:02,308] [INFO] Running command: hmmsearch --tblout GCF_014138385.1_ASM1413838v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4f857c7-d754-4108-878f-dd7772af5e15/dqc_reference/reference_markers.hmm GCF_014138385.1_ASM1413838v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:02,651] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:02,653] [INFO] Found 6/6 markers.
[2024-01-24 14:39:02,715] [INFO] Query marker FASTA was written to GCF_014138385.1_ASM1413838v1_genomic.fna/markers.fasta
[2024-01-24 14:39:02,716] [INFO] Task started: Blastn
[2024-01-24 14:39:02,716] [INFO] Running command: blastn -query GCF_014138385.1_ASM1413838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4f857c7-d754-4108-878f-dd7772af5e15/dqc_reference/reference_markers.fasta -out GCF_014138385.1_ASM1413838v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:03,358] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:03,362] [INFO] Selected 24 target genomes.
[2024-01-24 14:39:03,363] [INFO] Target genome list was writen to GCF_014138385.1_ASM1413838v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:03,408] [INFO] Task started: fastANI
[2024-01-24 14:39:03,408] [INFO] Running command: fastANI --query /var/lib/cwl/stg00308987-7292-4ea6-a981-658d2525c3ee/GCF_014138385.1_ASM1413838v1_genomic.fna.gz --refList GCF_014138385.1_ASM1413838v1_genomic.fna/target_genomes.txt --output GCF_014138385.1_ASM1413838v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:29,515] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:29,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4f857c7-d754-4108-878f-dd7772af5e15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:29,516] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4f857c7-d754-4108-878f-dd7772af5e15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:29,535] [INFO] Found 22 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:39:29,535] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:39:29,535] [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
Fontibacillus solani	strain=CECT 8693	GCA_014138385.1	1572857	1572857	type	True	100.0	1798	1800	95	inconclusive
Fontibacillus panacisegetis	strain=DSM 28129	GCA_900102215.1	670482	670482	type	True	97.1536	1443	1800	95	inconclusive
Paenibacillus antibioticophila	strain=GD11	GCA_000455265.1	1274374	1274374	type	True	78.4426	292	1800	95	below_threshold
Paenibacillus segetis	strain=CGMCC 1.12769	GCA_014639155.1	1325360	1325360	type	True	78.2853	286	1800	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	78.1274	240	1800	95	below_threshold
Paenibacillus bouchesdurhonensis	strain=Marseille-P3071	GCA_900155685.1	1870990	1870990	type	True	78.1027	269	1800	95	below_threshold
Paenibacillus fonticola	strain=DSM 21315	GCA_000381905.1	379896	379896	type	True	78.1001	267	1800	95	below_threshold
Paenibacillus rubinfantis	strain=MT18	GCA_001486505.1	1720296	1720296	type	True	78.082	236	1800	95	below_threshold
Paenibacillus senegalimassiliensis	strain=SIT18	GCA_001486585.1	1737426	1737426	type	True	78.0526	238	1800	95	below_threshold
Paenibacillus lentus	strain=DSM 25539	GCA_003931855.1	1338368	1338368	type	True	77.9792	279	1800	95	below_threshold
Paenibacillus aceti	strain=L14	GCA_003614185.1	1820010	1820010	type	True	77.9122	274	1800	95	below_threshold
Paenibacillus aceti	strain=CGMCC 1.15420	GCA_014642755.1	1820010	1820010	type	True	77.8796	267	1800	95	below_threshold
Paenibacillus brevis	strain=MSJ-6	GCA_018919145.1	2841508	2841508	type	True	77.8121	256	1800	95	below_threshold
Paenibacillus sanguinis	strain=DSM 16941	GCA_000374825.1	225906	225906	type	True	77.7659	230	1800	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	77.6803	281	1800	95	below_threshold
Paenibacillus macerans	strain=NBRC 15307	GCA_004000965.1	44252	44252	type	True	77.5062	272	1800	95	below_threshold
Paenibacillus zeisoli	strain=3-5-3	GCA_003994465.1	2496267	2496267	type	True	77.4132	161	1800	95	below_threshold
Paenibacillus sophorae	strain=CGMCC 1.10238	GCA_900110315.1	1333845	1333845	type	True	77.0571	109	1800	95	below_threshold
Paenibacillus doosanensis	strain=CAU 1055	GCA_025060755.1	1229154	1229154	type	True	76.9864	71	1800	95	below_threshold
Paenibacillus forsythiae	strain=T98	GCA_000520735.1	365616	365616	type	True	76.8439	80	1800	95	below_threshold
Paenibacillus tarimensis	strain=DSM 19409	GCA_021532315.1	416012	416012	type	True	76.781	55	1800	95	below_threshold
Paenibacillus alkaliterrae	strain=DSM 17040	GCA_021532375.1	320909	320909	type	True	76.2853	67	1800	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:29,537] [INFO] DFAST Taxonomy check result was written to GCF_014138385.1_ASM1413838v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:29,538] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:29,538] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:29,538] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4f857c7-d754-4108-878f-dd7772af5e15/dqc_reference/checkm_data
[2024-01-24 14:39:29,539] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:29,595] [INFO] Task started: CheckM
[2024-01-24 14:39:29,595] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014138385.1_ASM1413838v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014138385.1_ASM1413838v1_genomic.fna/checkm_input GCF_014138385.1_ASM1413838v1_genomic.fna/checkm_result
[2024-01-24 14:40:18,248] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:18,249] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:18,274] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:18,275] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:18,275] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014138385.1_ASM1413838v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:18,276] [INFO] Task started: Blastn
[2024-01-24 14:40:18,276] [INFO] Running command: blastn -query GCF_014138385.1_ASM1413838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4f857c7-d754-4108-878f-dd7772af5e15/dqc_reference/reference_markers_gtdb.fasta -out GCF_014138385.1_ASM1413838v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:19,159] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:19,162] [INFO] Selected 29 target genomes.
[2024-01-24 14:40:19,163] [INFO] Target genome list was writen to GCF_014138385.1_ASM1413838v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:19,181] [INFO] Task started: fastANI
[2024-01-24 14:40:19,181] [INFO] Running command: fastANI --query /var/lib/cwl/stg00308987-7292-4ea6-a981-658d2525c3ee/GCF_014138385.1_ASM1413838v1_genomic.fna.gz --refList GCF_014138385.1_ASM1413838v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014138385.1_ASM1413838v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:51,998] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:52,028] [INFO] Found 29 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:52,028] [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_900102215.1	s__Paenibacillus_A panacisegetis	97.1573	1443	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	97.17	97.17	0.85	0.85	2	conclusive
GCF_003337355.1	s__Paenibacillus_A phaseoli	78.9886	399	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018403325.1	s__Paenibacillus_A vini	78.4938	367	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	98.00	98.00	0.91	0.91	2	-
GCF_003991425.1	s__Paenibacillus_A lutimineralis	78.4685	285	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455265.1	s__Paenibacillus_A antibioticophila	78.4571	290	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	97.82	95.80	0.91	0.82	4	-
GCF_014639155.1	s__Paenibacillus_A segetis	78.2853	286	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008084145.1	s__Paenibacillus_A faecis	78.285	283	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	97.85	97.85	0.92	0.92	2	-
GCF_900069005.2	s__Paenibacillus_A sp900069005	78.0872	254	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	99.72	99.44	0.97	0.94	3	-
GCF_900155685.1	s__Paenibacillus_A bouchesdurhonensis	78.0871	272	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001486505.1	s__Paenibacillus_A rubinfantis	78.0831	236	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000381905.1	s__Paenibacillus_A fonticola	78.0747	269	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001486585.1	s__Paenibacillus_A senegalimassiliensis	78.0537	238	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003863965.1	s__Paenibacillus_A oralis	77.9986	280	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003931855.1	s__Paenibacillus_A lentus	77.9853	279	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000758585.1	s__Paenibacillus sp000758585	77.8871	138	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.21	98.21	0.91	0.91	2	-
GCF_003614185.1	s__Paenibacillus_A aceti	77.881	271	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_018919145.1	s__Paenibacillus_A sp018919145	77.793	258	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374825.1	s__Paenibacillus_A sanguinis	77.7398	231	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003060825.1	s__Paenibacillus_A sp003060825	77.7259	164	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000745.1	s__Paenibacillus_A barengoltzii	77.6392	236	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	98.39	97.66	0.91	0.90	5	-
GCA_900766135.1	s__Paenibacillus_A sp900766135	77.6167	204	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900454495.1	s__Paenibacillus_A macerans	77.5956	288	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	99.51	99.09	0.97	0.93	8	-
GCF_003994465.1	s__Paenibacillus_A zeisoli	77.4132	161	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002968835.1	s__Paenibacillus sp002968835	77.3655	98	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000316035.1	s__Paenibacillus sp000316035	77.1515	124	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.8348	N/A	N/A	N/A	N/A	1	-
GCF_018966525.1	s__Paenibacillus sophorae	77.0873	109	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001570725.1	s__Paenibacillus amylolyticus_A	76.8694	130	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.59	97.52	0.92	0.91	3	-
GCF_000520735.1	s__Paenibacillus forsythiae	76.8439	80	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014639235.1	s__Paenibacillus silvae	76.7953	124	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.52	95.24	0.88	0.86	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:52,031] [INFO] GTDB search result was written to GCF_014138385.1_ASM1413838v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:52,032] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:52,041] [INFO] DFAST_QC result json was written to GCF_014138385.1_ASM1413838v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:52,041] [INFO] DFAST_QC completed!
[2024-01-24 14:40:52,041] [INFO] Total running time: 0h2m6s