[2024-01-24 14:38:48,310] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:48,313] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:48,313] [INFO] DQC Reference Directory: /var/lib/cwl/stgb055bebb-96a2-408a-aaa2-effbbf3e4079/dqc_reference
[2024-01-24 14:38:50,451] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:50,453] [INFO] Task started: Prodigal
[2024-01-24 14:38:50,454] [INFO] Running command: gunzip -c /var/lib/cwl/stg5cacb5e3-716f-47e0-abec-b9b2d59fe64c/GCF_005577435.1_ASM557743v1_genomic.fna.gz | prodigal -d GCF_005577435.1_ASM557743v1_genomic.fna/cds.fna -a GCF_005577435.1_ASM557743v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:03,341] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:03,341] [INFO] Task started: HMMsearch
[2024-01-24 14:39:03,341] [INFO] Running command: hmmsearch --tblout GCF_005577435.1_ASM557743v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb055bebb-96a2-408a-aaa2-effbbf3e4079/dqc_reference/reference_markers.hmm GCF_005577435.1_ASM557743v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:03,728] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:03,730] [INFO] Found 6/6 markers.
[2024-01-24 14:39:03,770] [INFO] Query marker FASTA was written to GCF_005577435.1_ASM557743v1_genomic.fna/markers.fasta
[2024-01-24 14:39:03,770] [INFO] Task started: Blastn
[2024-01-24 14:39:03,770] [INFO] Running command: blastn -query GCF_005577435.1_ASM557743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb055bebb-96a2-408a-aaa2-effbbf3e4079/dqc_reference/reference_markers.fasta -out GCF_005577435.1_ASM557743v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:04,420] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:04,424] [INFO] Selected 18 target genomes.
[2024-01-24 14:39:04,425] [INFO] Target genome list was writen to GCF_005577435.1_ASM557743v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:04,438] [INFO] Task started: fastANI
[2024-01-24 14:39:04,438] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cacb5e3-716f-47e0-abec-b9b2d59fe64c/GCF_005577435.1_ASM557743v1_genomic.fna.gz --refList GCF_005577435.1_ASM557743v1_genomic.fna/target_genomes.txt --output GCF_005577435.1_ASM557743v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:22,654] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:22,654] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb055bebb-96a2-408a-aaa2-effbbf3e4079/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:22,654] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb055bebb-96a2-408a-aaa2-effbbf3e4079/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:22,669] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:22,669] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:22,670] [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 algicola	strain=HB172198	GCA_005577435.1	2565926	2565926	type	True	100.0	1491	1491	95	conclusive
Paenibacillus lemnae	strain=L7-75	GCA_012933385.1	1330551	1330551	type	True	79.6729	519	1491	95	below_threshold
Paenibacillus polymyxa	strain=ATCC 842	GCA_022811565.1	1406	1406	type	True	79.021	115	1491	95	below_threshold
Paenibacillus ihbetae	strain=IHBB 9852	GCA_002741055.1	1870820	1870820	suspected-type	True	78.9272	326	1491	95	below_threshold
Paenibacillus uliginis	strain=N3/975	GCA_900177425.1	683737	683737	type	True	78.6265	275	1491	95	below_threshold
Paenibacillus faecalis	strain=Marseille-P3787	GCA_900289175.1	2079532	2079532	type	True	78.5322	261	1491	95	below_threshold
Paenibacillus lactis	strain=DSM 15596	GCA_017873605.1	228574	228574	type	True	78.5159	324	1491	95	below_threshold
Paenibacillus sabinae	strain=T27	GCA_000612505.1	365617	365617	type	True	78.5148	181	1491	95	below_threshold
Paenibacillus lautus	strain=NBRC 15380	GCA_004000945.1	1401	1401	suspected-type	True	78.3907	292	1491	95	below_threshold
Paenibacillus dakarensis	strain=FF9	GCA_001373415.1	1527293	1527293	type	True	78.3112	256	1491	95	below_threshold
Paenibacillus glucanolyticus	strain=NBRC 15330	GCA_004000885.1	59843	59843	type	True	78.2038	288	1491	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	77.9887	171	1491	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	77.5617	154	1491	95	below_threshold
Paenibacillus brevis	strain=MSJ-6	GCA_018919145.1	2841508	2841508	type	True	77.2504	123	1491	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	77.0858	158	1491	95	below_threshold
Paenibacillus antibioticophila	strain=GD11	GCA_000455265.1	1274374	1274374	type	True	77.0439	149	1491	95	below_threshold
Paenibacillus barcinonensis	strain=CECT 7022	GCA_003217495.1	198119	198119	type	True	76.9476	151	1491	95	below_threshold
Paenibacillus silvae	strain=CGMCC 1.12770	GCA_014639235.1	1325358	1325358	type	True	76.7451	145	1491	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:22,672] [INFO] DFAST Taxonomy check result was written to GCF_005577435.1_ASM557743v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:22,672] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:22,673] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:22,673] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb055bebb-96a2-408a-aaa2-effbbf3e4079/dqc_reference/checkm_data
[2024-01-24 14:39:22,674] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:22,724] [INFO] Task started: CheckM
[2024-01-24 14:39:22,724] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005577435.1_ASM557743v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005577435.1_ASM557743v1_genomic.fna/checkm_input GCF_005577435.1_ASM557743v1_genomic.fna/checkm_result
[2024-01-24 14:40:05,827] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:05,829] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:05,851] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:05,852] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:05,852] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005577435.1_ASM557743v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:05,852] [INFO] Task started: Blastn
[2024-01-24 14:40:05,852] [INFO] Running command: blastn -query GCF_005577435.1_ASM557743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb055bebb-96a2-408a-aaa2-effbbf3e4079/dqc_reference/reference_markers_gtdb.fasta -out GCF_005577435.1_ASM557743v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:06,800] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:06,804] [INFO] Selected 20 target genomes.
[2024-01-24 14:40:06,804] [INFO] Target genome list was writen to GCF_005577435.1_ASM557743v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:06,823] [INFO] Task started: fastANI
[2024-01-24 14:40:06,823] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cacb5e3-716f-47e0-abec-b9b2d59fe64c/GCF_005577435.1_ASM557743v1_genomic.fna.gz --refList GCF_005577435.1_ASM557743v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005577435.1_ASM557743v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:27,472] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:27,493] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:27,494] [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_005577435.1	s__Paenibacillus sp005577435	100.0	1491	1491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.84	98.84	0.91	0.91	2	conclusive
GCF_012933385.1	s__Paenibacillus lemnae	79.6656	520	1491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014863545.1	s__Paenibacillus lautus_A	79.0758	314	1491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.37	95.82	0.93	0.90	10	-
GCF_000987955.1	s__Paenibacillus sp000987955	79.0094	357	1491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741055.1	s__Paenibacillus ihbetae	78.8982	323	1491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.87	98.87	0.95	0.95	2	-
GCF_900177425.1	s__Paenibacillus uliginis	78.6244	277	1491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900289175.1	s__Paenibacillus sp900289175	78.5477	261	1491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017873605.1	s__Paenibacillus lactis	78.5159	324	1491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.99	97.11	0.89	0.86	16	-
GCF_000612505.1	s__Paenibacillus sabinae	78.4671	180	1491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.70	95.69	0.89	0.89	3	-
GCF_018966525.1	s__Paenibacillus sophorae	78.442	160	1491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000993825.1	s__Paenibacillus durus_B	78.3715	167	1491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009363095.1	s__Paenibacillus cellulositrophicus_A	78.3177	219	1491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.73	96.59	0.92	0.91	14	-
GCF_001373415.1	s__Paenibacillus dakarensis	78.3112	256	1491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004000885.1	s__Paenibacillus glucanolyticus	78.1921	287	1491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.37	98.87	0.95	0.92	9	-
GCF_900454495.1	s__Paenibacillus_A macerans	78.0333	165	1491	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_002272015.1	s__Paenibacillus campinasensis	77.8885	325	1491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.23	99.19	0.91	0.90	3	-
GCF_003854965.1	s__Paenibacillus sp003854965	77.5604	154	1491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.02	95.02	0.86	0.86	2	-
GCF_000520735.1	s__Paenibacillus forsythiae	77.0968	150	1491	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455265.1	s__Paenibacillus_A antibioticophila	77.0438	150	1491	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_014639235.1	s__Paenibacillus silvae	76.7313	150	1491	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 14:40:27,496] [INFO] GTDB search result was written to GCF_005577435.1_ASM557743v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:27,497] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:27,502] [INFO] DFAST_QC result json was written to GCF_005577435.1_ASM557743v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:27,502] [INFO] DFAST_QC completed!
[2024-01-24 14:40:27,502] [INFO] Total running time: 0h1m39s