[2024-01-24 13:18:45,408] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:45,410] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:45,410] [INFO] DQC Reference Directory: /var/lib/cwl/stg360b3215-5417-4595-9be1-ce9b380f5f65/dqc_reference
[2024-01-24 13:18:46,828] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:46,829] [INFO] Task started: Prodigal
[2024-01-24 13:18:46,829] [INFO] Running command: gunzip -c /var/lib/cwl/stgb33c86b0-c3da-4eb9-bd29-c31f0368b6f8/GCF_900289175.1_PRJEB24604_genomic.fna.gz | prodigal -d GCF_900289175.1_PRJEB24604_genomic.fna/cds.fna -a GCF_900289175.1_PRJEB24604_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:59,922] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:59,922] [INFO] Task started: HMMsearch
[2024-01-24 13:18:59,922] [INFO] Running command: hmmsearch --tblout GCF_900289175.1_PRJEB24604_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg360b3215-5417-4595-9be1-ce9b380f5f65/dqc_reference/reference_markers.hmm GCF_900289175.1_PRJEB24604_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:00,246] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:00,247] [INFO] Found 6/6 markers.
[2024-01-24 13:19:00,290] [INFO] Query marker FASTA was written to GCF_900289175.1_PRJEB24604_genomic.fna/markers.fasta
[2024-01-24 13:19:00,290] [INFO] Task started: Blastn
[2024-01-24 13:19:00,290] [INFO] Running command: blastn -query GCF_900289175.1_PRJEB24604_genomic.fna/markers.fasta -db /var/lib/cwl/stg360b3215-5417-4595-9be1-ce9b380f5f65/dqc_reference/reference_markers.fasta -out GCF_900289175.1_PRJEB24604_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:00,874] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:00,877] [INFO] Selected 17 target genomes.
[2024-01-24 13:19:00,878] [INFO] Target genome list was writen to GCF_900289175.1_PRJEB24604_genomic.fna/target_genomes.txt
[2024-01-24 13:19:00,888] [INFO] Task started: fastANI
[2024-01-24 13:19:00,888] [INFO] Running command: fastANI --query /var/lib/cwl/stgb33c86b0-c3da-4eb9-bd29-c31f0368b6f8/GCF_900289175.1_PRJEB24604_genomic.fna.gz --refList GCF_900289175.1_PRJEB24604_genomic.fna/target_genomes.txt --output GCF_900289175.1_PRJEB24604_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:19,301] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:19,301] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg360b3215-5417-4595-9be1-ce9b380f5f65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:19,302] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg360b3215-5417-4595-9be1-ce9b380f5f65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:19,315] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:19:19,316] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:19:19,316] [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 faecalis	strain=Marseille-P3787	GCA_900289175.1	2079532	2079532	type	True	100.0	1610	1610	95	conclusive
Paenibacillus uliginis	strain=N3/975	GCA_900177425.1	683737	683737	type	True	81.6436	979	1610	95	below_threshold
Paenibacillus dakarensis	strain=FF9	GCA_001373415.1	1527293	1527293	type	True	79.3765	479	1610	95	below_threshold
Paenibacillus ihbetae	strain=IHBB 9852	GCA_002741055.1	1870820	1870820	suspected-type	True	78.9505	353	1610	95	below_threshold
Paenibacillus glucanolyticus	strain=NBRC 15330	GCA_004000885.1	59843	59843	type	True	78.7352	352	1610	95	below_threshold
Paenibacillus lactis	strain=DSM 15596	GCA_017873605.1	228574	228574	type	True	78.7296	344	1610	95	below_threshold
Paenibacillus lautus	strain=NBRC 15380	GCA_004000945.1	1401	1401	suspected-type	True	78.5974	382	1610	95	below_threshold
Paenibacillus solani	strain=FJAT-22460	GCA_001277345.1	1705565	1705565	type	True	78.5454	362	1610	95	below_threshold
Paenibacillus lemnae	strain=L7-75	GCA_012933385.1	1330551	1330551	type	True	78.4059	296	1610	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	78.0766	134	1610	95	below_threshold
Paenibacillus albus	strain=18JY67-1	GCA_003952225.1	2495582	2495582	type	True	78.0655	79	1610	95	below_threshold
Paenibacillus glacialis	strain=DSM 22343	GCA_001637205.1	494026	494026	type	True	77.9078	112	1610	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	77.7781	115	1610	95	below_threshold
Paenibacillus xylanilyticus	strain=LMG 21957	GCA_013359935.1	248903	248903	type	True	77.7234	133	1610	95	below_threshold
Paenibacillus illinoisensis	strain=NBRC 15959	GCA_004000925.1	59845	59845	type	True	77.1269	132	1610	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	77.0452	115	1610	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	76.8345	113	1610	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:19,318] [INFO] DFAST Taxonomy check result was written to GCF_900289175.1_PRJEB24604_genomic.fna/tc_result.tsv
[2024-01-24 13:19:19,319] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:19,319] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:19,319] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg360b3215-5417-4595-9be1-ce9b380f5f65/dqc_reference/checkm_data
[2024-01-24 13:19:19,320] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:19,368] [INFO] Task started: CheckM
[2024-01-24 13:19:19,368] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900289175.1_PRJEB24604_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900289175.1_PRJEB24604_genomic.fna/checkm_input GCF_900289175.1_PRJEB24604_genomic.fna/checkm_result
[2024-01-24 13:20:01,236] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:01,237] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:01,255] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:01,255] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:01,256] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900289175.1_PRJEB24604_genomic.fna/markers.fasta)
[2024-01-24 13:20:01,256] [INFO] Task started: Blastn
[2024-01-24 13:20:01,256] [INFO] Running command: blastn -query GCF_900289175.1_PRJEB24604_genomic.fna/markers.fasta -db /var/lib/cwl/stg360b3215-5417-4595-9be1-ce9b380f5f65/dqc_reference/reference_markers_gtdb.fasta -out GCF_900289175.1_PRJEB24604_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:02,105] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:02,108] [INFO] Selected 15 target genomes.
[2024-01-24 13:20:02,108] [INFO] Target genome list was writen to GCF_900289175.1_PRJEB24604_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:02,161] [INFO] Task started: fastANI
[2024-01-24 13:20:02,161] [INFO] Running command: fastANI --query /var/lib/cwl/stgb33c86b0-c3da-4eb9-bd29-c31f0368b6f8/GCF_900289175.1_PRJEB24604_genomic.fna.gz --refList GCF_900289175.1_PRJEB24604_genomic.fna/target_genomes_gtdb.txt --output GCF_900289175.1_PRJEB24604_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:18,101] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:18,113] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:18,114] [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_900289175.1	s__Paenibacillus sp900289175	100.0	1610	1610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900177425.1	s__Paenibacillus uliginis	81.666	975	1610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000987955.1	s__Paenibacillus sp000987955	79.4504	499	1610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001373415.1	s__Paenibacillus dakarensis	79.3747	478	1610	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	78.9856	353	1610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.87	98.87	0.95	0.95	2	-
GCF_014863545.1	s__Paenibacillus lautus_A	78.9218	384	1610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.37	95.82	0.93	0.90	10	-
GCF_004000885.1	s__Paenibacillus glucanolyticus	78.7543	352	1610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.37	98.87	0.95	0.92	9	-
GCF_017873605.1	s__Paenibacillus lactis	78.7416	343	1610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.99	97.11	0.89	0.86	16	-
GCF_001315105.1	s__Paenibacillus sp001315105	78.5547	290	1610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012933385.1	s__Paenibacillus lemnae	78.3796	297	1610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952225.1	s__Paenibacillus_Z albus	77.9433	81	1610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001637205.1	s__Paenibacillus glacialis	77.8784	115	1610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013359935.1	s__Paenibacillus xylanilyticus	77.7225	131	1610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018333315.1	s__Paenibacillus azoreducens	77.4879	197	1610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.74	97.74	0.88	0.88	2	-
GCF_004000925.1	s__Paenibacillus illinoisensis	77.0949	132	1610	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	95.55	95.10	0.89	0.77	9	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:18,116] [INFO] GTDB search result was written to GCF_900289175.1_PRJEB24604_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:18,116] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:18,120] [INFO] DFAST_QC result json was written to GCF_900289175.1_PRJEB24604_genomic.fna/dqc_result.json
[2024-01-24 13:20:18,120] [INFO] DFAST_QC completed!
[2024-01-24 13:20:18,120] [INFO] Total running time: 0h1m33s