[2024-01-24 11:34:55,258] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:55,263] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:55,263] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f2b0049-e86f-4ceb-876f-5fb3f9e7f88c/dqc_reference
[2024-01-24 11:34:56,727] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:56,728] [INFO] Task started: Prodigal
[2024-01-24 11:34:56,728] [INFO] Running command: gunzip -c /var/lib/cwl/stg4472e8e4-46a8-404a-b68b-2f2a846c9756/GCF_001857945.1_ASM185794v1_genomic.fna.gz | prodigal -d GCF_001857945.1_ASM185794v1_genomic.fna/cds.fna -a GCF_001857945.1_ASM185794v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:07,471] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:07,471] [INFO] Task started: HMMsearch
[2024-01-24 11:35:07,471] [INFO] Running command: hmmsearch --tblout GCF_001857945.1_ASM185794v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f2b0049-e86f-4ceb-876f-5fb3f9e7f88c/dqc_reference/reference_markers.hmm GCF_001857945.1_ASM185794v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:07,789] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:07,790] [INFO] Found 6/6 markers.
[2024-01-24 11:35:07,829] [INFO] Query marker FASTA was written to GCF_001857945.1_ASM185794v1_genomic.fna/markers.fasta
[2024-01-24 11:35:07,829] [INFO] Task started: Blastn
[2024-01-24 11:35:07,829] [INFO] Running command: blastn -query GCF_001857945.1_ASM185794v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f2b0049-e86f-4ceb-876f-5fb3f9e7f88c/dqc_reference/reference_markers.fasta -out GCF_001857945.1_ASM185794v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:08,417] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:08,420] [INFO] Selected 16 target genomes.
[2024-01-24 11:35:08,420] [INFO] Target genome list was writen to GCF_001857945.1_ASM185794v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:08,427] [INFO] Task started: fastANI
[2024-01-24 11:35:08,427] [INFO] Running command: fastANI --query /var/lib/cwl/stg4472e8e4-46a8-404a-b68b-2f2a846c9756/GCF_001857945.1_ASM185794v1_genomic.fna.gz --refList GCF_001857945.1_ASM185794v1_genomic.fna/target_genomes.txt --output GCF_001857945.1_ASM185794v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:23,969] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:23,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f2b0049-e86f-4ceb-876f-5fb3f9e7f88c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:23,970] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f2b0049-e86f-4ceb-876f-5fb3f9e7f88c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:23,980] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:23,980] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:23,980] [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 crassostreae	strain=LPB0068	GCA_001857945.1	1763538	1763538	type	True	100.0	1584	1584	95	conclusive
Paenibacillus crassostreae	strain=LPB0068	GCA_001637335.1	1763538	1763538	type	True	99.9822	1529	1584	95	conclusive
Paenibacillus glacialis	strain=DSM 22343	GCA_001637205.1	494026	494026	type	True	79.6386	589	1584	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	79.6255	115	1584	95	below_threshold
Paenibacillus macquariensis	strain=ATCC 23464	GCA_900156375.1	948756	948756	type	True	79.4508	580	1584	95	below_threshold
Paenibacillus macquariensis subsp. macquariensis	strain=DSM 2	GCA_001637165.1	1468	948756	type	True	79.3954	573	1584	95	below_threshold
Paenibacillus antarcticus	strain=CECT 5836	GCA_001637225.1	253703	253703	type	True	79.3163	554	1584	95	below_threshold
Paenibacillus odorifer	strain=DSM 15391	GCA_000758725.1	189426	189426	type	True	79.2518	143	1584	95	below_threshold
Paenibacillus pini	strain=JCM 16418	GCA_001315125.1	669461	669461	type	True	77.6944	175	1584	95	below_threshold
Paenibacillus pini	strain=JCM 16418	GCA_000576305.1	669461	669461	type	True	77.6935	175	1584	95	below_threshold
Paenibacillus uliginis	strain=N3/975	GCA_900177425.1	683737	683737	type	True	77.1291	142	1584	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:23,982] [INFO] DFAST Taxonomy check result was written to GCF_001857945.1_ASM185794v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:23,982] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:23,983] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:23,983] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f2b0049-e86f-4ceb-876f-5fb3f9e7f88c/dqc_reference/checkm_data
[2024-01-24 11:35:23,984] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:24,031] [INFO] Task started: CheckM
[2024-01-24 11:35:24,031] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001857945.1_ASM185794v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001857945.1_ASM185794v1_genomic.fna/checkm_input GCF_001857945.1_ASM185794v1_genomic.fna/checkm_result
[2024-01-24 11:36:00,542] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:00,544] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:00,565] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:00,565] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:00,565] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001857945.1_ASM185794v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:00,566] [INFO] Task started: Blastn
[2024-01-24 11:36:00,566] [INFO] Running command: blastn -query GCF_001857945.1_ASM185794v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f2b0049-e86f-4ceb-876f-5fb3f9e7f88c/dqc_reference/reference_markers_gtdb.fasta -out GCF_001857945.1_ASM185794v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:01,356] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:01,361] [INFO] Selected 13 target genomes.
[2024-01-24 11:36:01,361] [INFO] Target genome list was writen to GCF_001857945.1_ASM185794v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:01,372] [INFO] Task started: fastANI
[2024-01-24 11:36:01,372] [INFO] Running command: fastANI --query /var/lib/cwl/stg4472e8e4-46a8-404a-b68b-2f2a846c9756/GCF_001857945.1_ASM185794v1_genomic.fna.gz --refList GCF_001857945.1_ASM185794v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001857945.1_ASM185794v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:15,532] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:15,550] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:15,551] [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_001857945.1	s__Paenibacillus crassostreae	100.0	1582	1584	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001637205.1	s__Paenibacillus glacialis	79.6221	590	1584	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156375.1	s__Paenibacillus macquariensis	79.4863	577	1584	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.68	95.38	0.90	0.81	3	-
GCF_001637225.1	s__Paenibacillus antarcticus	79.325	553	1584	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000949425.1	s__Paenibacillus sp000949425	79.2275	388	1584	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000758725.1	s__Paenibacillus odorifer	79.183	143	1584	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.05	97.01	0.93	0.91	32	-
GCF_000576305.1	s__Paenibacillus pini	77.6935	175	1584	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900116105.1	s__Paenibacillus sp900116105	77.6172	90	1584	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002264395.1	s__Paenibacillus sp002264395	77.535	127	1584	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.86	98.86	0.89	0.89	2	-
GCF_001373415.1	s__Paenibacillus dakarensis	77.423	99	1584	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102085.1	s__Paenibacillus polysaccharolyticus	77.2576	78	1584	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	97.73	97.72	0.92	0.92	4	-
GCF_900177425.1	s__Paenibacillus uliginis	77.1171	141	1584	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908805.1	s__Paenibacillus_J nicotianae	76.7172	101	1584	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_J	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:15,552] [INFO] GTDB search result was written to GCF_001857945.1_ASM185794v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:15,553] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:15,556] [INFO] DFAST_QC result json was written to GCF_001857945.1_ASM185794v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:15,556] [INFO] DFAST_QC completed!
[2024-01-24 11:36:15,556] [INFO] Total running time: 0h1m20s