[2024-01-24 11:05:03,929] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,931] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,931] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a9b9a9c-a9e4-4152-b82c-6542595e789f/dqc_reference
[2024-01-24 11:05:05,762] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,763] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,763] [INFO] Running command: gunzip -c /var/lib/cwl/stg73cd17e3-14d1-4b97-84df-f1ba16a75bf8/GCF_014642755.1_ASM1464275v1_genomic.fna.gz | prodigal -d GCF_014642755.1_ASM1464275v1_genomic.fna/cds.fna -a GCF_014642755.1_ASM1464275v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:17,640] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:17,640] [INFO] Task started: HMMsearch
[2024-01-24 11:05:17,640] [INFO] Running command: hmmsearch --tblout GCF_014642755.1_ASM1464275v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a9b9a9c-a9e4-4152-b82c-6542595e789f/dqc_reference/reference_markers.hmm GCF_014642755.1_ASM1464275v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:17,988] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:17,989] [INFO] Found 6/6 markers.
[2024-01-24 11:05:18,031] [INFO] Query marker FASTA was written to GCF_014642755.1_ASM1464275v1_genomic.fna/markers.fasta
[2024-01-24 11:05:18,031] [INFO] Task started: Blastn
[2024-01-24 11:05:18,031] [INFO] Running command: blastn -query GCF_014642755.1_ASM1464275v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a9b9a9c-a9e4-4152-b82c-6542595e789f/dqc_reference/reference_markers.fasta -out GCF_014642755.1_ASM1464275v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:18,619] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:18,624] [INFO] Selected 23 target genomes.
[2024-01-24 11:05:18,624] [INFO] Target genome list was writen to GCF_014642755.1_ASM1464275v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:18,654] [INFO] Task started: fastANI
[2024-01-24 11:05:18,654] [INFO] Running command: fastANI --query /var/lib/cwl/stg73cd17e3-14d1-4b97-84df-f1ba16a75bf8/GCF_014642755.1_ASM1464275v1_genomic.fna.gz --refList GCF_014642755.1_ASM1464275v1_genomic.fna/target_genomes.txt --output GCF_014642755.1_ASM1464275v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:40,407] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:40,407] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a9b9a9c-a9e4-4152-b82c-6542595e789f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:40,408] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a9b9a9c-a9e4-4152-b82c-6542595e789f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:40,420] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:05:40,420] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:40,420] [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
Paenibacillus aceti	strain=CGMCC 1.15420	GCA_014642755.1	1820010	1820010	type	True	100.0	1740	1748	95	conclusive
Paenibacillus aceti	strain=L14	GCA_003614185.1	1820010	1820010	type	True	99.9913	1748	1748	95	conclusive
Paenibacillus lutimineralis	strain=MBLB1234	GCA_003991425.1	2707005	2707005	type	True	83.2674	1167	1748	95	below_threshold
Paenibacillus ihumii	strain=AT5	GCA_001403875.1	687436	687436	type	True	78.2104	288	1748	95	below_threshold
Paenibacillus bouchesdurhonensis	strain=Marseille-P3071	GCA_900155685.1	1870990	1870990	type	True	78.199	272	1748	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	78.1412	305	1748	95	below_threshold
Paenibacillus uliginis	strain=N3/975	GCA_900177425.1	683737	683737	type	True	78.0934	180	1748	95	below_threshold
Paenibacillus antibioticophila	strain=GD11	GCA_000455265.1	1274374	1274374	type	True	78.0047	260	1748	95	below_threshold
Paenibacillus segetis	strain=CGMCC 1.12769	GCA_014639155.1	1325360	1325360	type	True	77.9625	252	1748	95	below_threshold
Paenibacillus fonticola	strain=DSM 21315	GCA_000381905.1	379896	379896	type	True	77.9273	264	1748	95	below_threshold
Paenibacillus brevis	strain=MSJ-6	GCA_018919145.1	2841508	2841508	type	True	77.8054	271	1748	95	below_threshold
Paenibacillus caui	strain=81-11	GCA_019904135.1	2873927	2873927	type	True	77.7769	149	1748	95	below_threshold
Paenibacillus rubinfantis	strain=MT18	GCA_001486505.1	1720296	1720296	type	True	77.759	280	1748	95	below_threshold
Paenibacillus dakarensis	strain=FF9	GCA_001373415.1	1527293	1527293	type	True	77.4859	130	1748	95	below_threshold
Paenibacillus pinistramenti	strain=ASL46	GCA_005869875.1	1768003	1768003	type	True	77.3677	149	1748	95	below_threshold
Paenibacillus sinensis	strain=HN-1	GCA_019904155.1	2834413	2834413	type	True	77.0865	134	1748	95	below_threshold
Paenibacillus algicola	strain=HB172198	GCA_005577435.1	2565926	2565926	type	True	76.9195	147	1748	95	below_threshold
Paenibacillus silagei	strain=DSM 101953	GCA_017874735.1	1670801	1670801	type	True	76.8373	141	1748	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	76.5691	142	1748	95	below_threshold
Paenibacillus darwinianus	strain=Br	GCA_000598065.1	1380763	1380763	type	True	76.352	54	1748	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:40,425] [INFO] DFAST Taxonomy check result was written to GCF_014642755.1_ASM1464275v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:40,426] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:40,426] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:40,426] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a9b9a9c-a9e4-4152-b82c-6542595e789f/dqc_reference/checkm_data
[2024-01-24 11:05:40,427] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:40,481] [INFO] Task started: CheckM
[2024-01-24 11:05:40,481] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014642755.1_ASM1464275v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014642755.1_ASM1464275v1_genomic.fna/checkm_input GCF_014642755.1_ASM1464275v1_genomic.fna/checkm_result
[2024-01-24 11:06:16,217] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:16,218] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:16,235] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:16,235] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:16,235] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014642755.1_ASM1464275v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:16,236] [INFO] Task started: Blastn
[2024-01-24 11:06:16,236] [INFO] Running command: blastn -query GCF_014642755.1_ASM1464275v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a9b9a9c-a9e4-4152-b82c-6542595e789f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014642755.1_ASM1464275v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:17,050] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:17,053] [INFO] Selected 19 target genomes.
[2024-01-24 11:06:17,054] [INFO] Target genome list was writen to GCF_014642755.1_ASM1464275v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:17,062] [INFO] Task started: fastANI
[2024-01-24 11:06:17,062] [INFO] Running command: fastANI --query /var/lib/cwl/stg73cd17e3-14d1-4b97-84df-f1ba16a75bf8/GCF_014642755.1_ASM1464275v1_genomic.fna.gz --refList GCF_014642755.1_ASM1464275v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014642755.1_ASM1464275v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:35,470] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:35,482] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:35,482] [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_003614185.1	s__Paenibacillus_A aceti	99.9913	1748	1748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_003991425.1	s__Paenibacillus_A lutimineralis	83.2542	1169	1748	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_900069005.2	s__Paenibacillus_A sp900069005	83.11	1092	1748	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_000159955.1	s__Paenibacillus_A sp000159955	78.7843	308	1748	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_900021165.1	s__Paenibacillus_A phocaensis	78.4378	336	1748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002439285.1	s__Paenibacillus_A sp002439285	78.2636	256	1748	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_001403875.1	s__Paenibacillus_A ihumii	78.2193	286	1748	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_018403325.1	s__Paenibacillus_A vini	78.2036	326	1748	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_900155685.1	s__Paenibacillus_A bouchesdurhonensis	78.199	272	1748	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	78.1656	311	1748	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_000455265.1	s__Paenibacillus_A antibioticophila	78.0082	259	1748	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	77.9625	252	1748	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_000381905.1	s__Paenibacillus_A fonticola	77.9229	263	1748	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_018919145.1	s__Paenibacillus_A sp018919145	77.8145	272	1748	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	77.7958	223	1748	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_009725205.1	s__Paenibacillus_A timonensis	77.5806	271	1748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	98.34	98.12	0.92	0.92	3	-
GCF_001373415.1	s__Paenibacillus dakarensis	77.4635	131	1748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005869875.1	s__Paenibacillus_A pinistramenti	77.3716	148	1748	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_017874735.1	s__Paenibacillus silagei	76.8373	141	1748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.84	96.20	0.88	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:35,484] [INFO] GTDB search result was written to GCF_014642755.1_ASM1464275v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:35,484] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:35,487] [INFO] DFAST_QC result json was written to GCF_014642755.1_ASM1464275v1_genomic.fna/dqc_result.json
[2024-01-24 11:06:35,488] [INFO] DFAST_QC completed!
[2024-01-24 11:06:35,488] [INFO] Total running time: 0h1m32s