[2024-01-24 13:40:34,792] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,796] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,796] [INFO] DQC Reference Directory: /var/lib/cwl/stgf02504ce-7918-4527-b040-0a02423b8261/dqc_reference
[2024-01-24 13:40:36,303] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,304] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,305] [INFO] Running command: gunzip -c /var/lib/cwl/stg6447ee1a-5919-4384-929b-49bad5d835b7/GCF_000455265.1_Pa_GD11_genomic.fna.gz | prodigal -d GCF_000455265.1_Pa_GD11_genomic.fna/cds.fna -a GCF_000455265.1_Pa_GD11_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:51,498] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:51,498] [INFO] Task started: HMMsearch
[2024-01-24 13:40:51,499] [INFO] Running command: hmmsearch --tblout GCF_000455265.1_Pa_GD11_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf02504ce-7918-4527-b040-0a02423b8261/dqc_reference/reference_markers.hmm GCF_000455265.1_Pa_GD11_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:51,856] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:51,858] [INFO] Found 6/6 markers.
[2024-01-24 13:40:51,904] [INFO] Query marker FASTA was written to GCF_000455265.1_Pa_GD11_genomic.fna/markers.fasta
[2024-01-24 13:40:51,904] [INFO] Task started: Blastn
[2024-01-24 13:40:51,904] [INFO] Running command: blastn -query GCF_000455265.1_Pa_GD11_genomic.fna/markers.fasta -db /var/lib/cwl/stgf02504ce-7918-4527-b040-0a02423b8261/dqc_reference/reference_markers.fasta -out GCF_000455265.1_Pa_GD11_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:52,540] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:52,543] [INFO] Selected 20 target genomes.
[2024-01-24 13:40:52,544] [INFO] Target genome list was writen to GCF_000455265.1_Pa_GD11_genomic.fna/target_genomes.txt
[2024-01-24 13:40:52,551] [INFO] Task started: fastANI
[2024-01-24 13:40:52,551] [INFO] Running command: fastANI --query /var/lib/cwl/stg6447ee1a-5919-4384-929b-49bad5d835b7/GCF_000455265.1_Pa_GD11_genomic.fna.gz --refList GCF_000455265.1_Pa_GD11_genomic.fna/target_genomes.txt --output GCF_000455265.1_Pa_GD11_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:15,401] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:15,402] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf02504ce-7918-4527-b040-0a02423b8261/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:15,402] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf02504ce-7918-4527-b040-0a02423b8261/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:15,417] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:15,417] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:15,417] [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 antibioticophila	strain=GD11	GCA_000455265.1	1274374	1274374	type	True	100.0	1855	1856	95	conclusive
Paenibacillus brevis	strain=MSJ-6	GCA_018919145.1	2841508	2841508	type	True	92.3003	1402	1856	95	below_threshold
Paenibacillus phocaensis	strain=mt24	GCA_900021165.1	1776378	1776378	type	True	79.392	423	1856	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	78.9057	379	1856	95	below_threshold
Paenibacillus macerans	strain=NCTC6355	GCA_900454495.1	44252	44252	type	True	78.841	382	1856	95	below_threshold
Paenibacillus macerans	strain=NBRC 15307	GCA_004000965.1	44252	44252	type	True	78.8394	361	1856	95	below_threshold
Paenibacillus timonensis	strain=DSM 16943	GCA_022427145.1	225915	225915	type	True	78.0289	337	1856	95	below_threshold
Paenibacillus ihumii	strain=AT5	GCA_001403875.1	687436	687436	type	True	77.8427	288	1856	95	below_threshold
Paenibacillus rubinfantis	strain=MT18	GCA_001486505.1	1720296	1720296	type	True	77.8206	340	1856	95	below_threshold
Paenibacillus lutimineralis	strain=MBLB1234	GCA_003991425.1	2707005	2707005	type	True	77.7235	276	1856	95	below_threshold
Paenibacillus fonticola	strain=DSM 21315	GCA_000381905.1	379896	379896	type	True	77.6635	258	1856	95	below_threshold
Paenibacillus albidus	strain=CGMCC 1.16134	GCA_014644435.1	2041023	2041023	type	True	77.0176	181	1856	95	below_threshold
Paenibacillus algicola	strain=HB172198	GCA_005577435.1	2565926	2565926	type	True	76.9315	149	1856	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	76.8789	202	1856	95	below_threshold
Paenibacillus dakarensis	strain=FF9	GCA_001373415.1	1527293	1527293	type	True	76.8443	118	1856	95	below_threshold
Gorillibacterium timonense	strain=SN4	GCA_001457415.1	1689269	1689269	type	True	76.53	77	1856	95	below_threshold
Paenibacillus tarimensis	strain=DSM 19409	GCA_021532315.1	416012	416012	type	True	76.1713	81	1856	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:15,419] [INFO] DFAST Taxonomy check result was written to GCF_000455265.1_Pa_GD11_genomic.fna/tc_result.tsv
[2024-01-24 13:41:15,420] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:15,420] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:15,420] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf02504ce-7918-4527-b040-0a02423b8261/dqc_reference/checkm_data
[2024-01-24 13:41:15,422] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:15,489] [INFO] Task started: CheckM
[2024-01-24 13:41:15,490] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000455265.1_Pa_GD11_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000455265.1_Pa_GD11_genomic.fna/checkm_input GCF_000455265.1_Pa_GD11_genomic.fna/checkm_result
[2024-01-24 13:42:04,228] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:04,232] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:04,253] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:04,254] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:04,254] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000455265.1_Pa_GD11_genomic.fna/markers.fasta)
[2024-01-24 13:42:04,255] [INFO] Task started: Blastn
[2024-01-24 13:42:04,255] [INFO] Running command: blastn -query GCF_000455265.1_Pa_GD11_genomic.fna/markers.fasta -db /var/lib/cwl/stgf02504ce-7918-4527-b040-0a02423b8261/dqc_reference/reference_markers_gtdb.fasta -out GCF_000455265.1_Pa_GD11_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:05,071] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:05,074] [INFO] Selected 18 target genomes.
[2024-01-24 13:42:05,075] [INFO] Target genome list was writen to GCF_000455265.1_Pa_GD11_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:05,088] [INFO] Task started: fastANI
[2024-01-24 13:42:05,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg6447ee1a-5919-4384-929b-49bad5d835b7/GCF_000455265.1_Pa_GD11_genomic.fna.gz --refList GCF_000455265.1_Pa_GD11_genomic.fna/target_genomes_gtdb.txt --output GCF_000455265.1_Pa_GD11_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:24,668] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:24,690] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:24,690] [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_000455265.1	s__Paenibacillus_A antibioticophila	100.0	1855	1856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	97.82	95.80	0.91	0.82	4	conclusive
GCF_018919145.1	s__Paenibacillus_A sp018919145	92.3003	1402	1856	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	79.5691	379	1856	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_900021165.1	s__Paenibacillus_A phocaensis	79.4088	421	1856	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_003337355.1	s__Paenibacillus_A phaseoli	79.1743	481	1856	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_003863965.1	s__Paenibacillus_A oralis	78.9904	407	1856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002439285.1	s__Paenibacillus_A sp002439285	78.9754	336	1856	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	78.8987	444	1856	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_900454495.1	s__Paenibacillus_A macerans	78.8467	381	1856	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_008084145.1	s__Paenibacillus_A faecis	78.7207	404	1856	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_001403875.1	s__Paenibacillus_A ihumii	77.8456	290	1856	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_001486505.1	s__Paenibacillus_A rubinfantis	77.8234	339	1856	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_900069005.2	s__Paenibacillus_A sp900069005	77.7343	270	1856	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_002272015.1	s__Paenibacillus campinasensis	77.0663	190	1856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	99.23	99.19	0.91	0.90	3	-
GCF_005577435.1	s__Paenibacillus sp005577435	76.9539	150	1856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.84	98.84	0.91	0.91	2	-
GCF_001373415.1	s__Paenibacillus dakarensis	76.8706	119	1856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007679495.1	s__Paenibacillus_L sp007679495	76.3191	51	1856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_L	95.0	99.12	99.12	0.91	0.91	2	-
GCF_017874275.1	s__Paenibacillus_Z sepulcri	75.8789	93	1856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:24,692] [INFO] GTDB search result was written to GCF_000455265.1_Pa_GD11_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:24,693] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:24,699] [INFO] DFAST_QC result json was written to GCF_000455265.1_Pa_GD11_genomic.fna/dqc_result.json
[2024-01-24 13:42:24,700] [INFO] DFAST_QC completed!
[2024-01-24 13:42:24,700] [INFO] Total running time: 0h1m50s