[2024-01-24 12:06:14,603] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:14,606] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:14,606] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d76f6fa-430a-4f59-a469-3c9169142843/dqc_reference
[2024-01-24 12:06:15,963] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:15,964] [INFO] Task started: Prodigal
[2024-01-24 12:06:15,964] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a85bab6-c183-4c74-b659-4ffc428f242b/GCF_013204885.1_ASM1320488v1_genomic.fna.gz | prodigal -d GCF_013204885.1_ASM1320488v1_genomic.fna/cds.fna -a GCF_013204885.1_ASM1320488v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:34,792] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:34,792] [INFO] Task started: HMMsearch
[2024-01-24 12:06:34,792] [INFO] Running command: hmmsearch --tblout GCF_013204885.1_ASM1320488v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d76f6fa-430a-4f59-a469-3c9169142843/dqc_reference/reference_markers.hmm GCF_013204885.1_ASM1320488v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:35,234] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:35,236] [INFO] Found 6/6 markers.
[2024-01-24 12:06:35,304] [INFO] Query marker FASTA was written to GCF_013204885.1_ASM1320488v1_genomic.fna/markers.fasta
[2024-01-24 12:06:35,304] [INFO] Task started: Blastn
[2024-01-24 12:06:35,304] [INFO] Running command: blastn -query GCF_013204885.1_ASM1320488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d76f6fa-430a-4f59-a469-3c9169142843/dqc_reference/reference_markers.fasta -out GCF_013204885.1_ASM1320488v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:35,954] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:35,959] [INFO] Selected 9 target genomes.
[2024-01-24 12:06:35,960] [INFO] Target genome list was writen to GCF_013204885.1_ASM1320488v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:35,965] [INFO] Task started: fastANI
[2024-01-24 12:06:35,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a85bab6-c183-4c74-b659-4ffc428f242b/GCF_013204885.1_ASM1320488v1_genomic.fna.gz --refList GCF_013204885.1_ASM1320488v1_genomic.fna/target_genomes.txt --output GCF_013204885.1_ASM1320488v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:52,731] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:52,732] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d76f6fa-430a-4f59-a469-3c9169142843/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:52,732] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d76f6fa-430a-4f59-a469-3c9169142843/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:52,743] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:52,743] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:52,748] [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 tritici	strain=LMG 29502	GCA_013204885.1	1873425	1873425	type	True	100.0	2428	2433	95	conclusive
Paenibacillus silagei	strain=DSM 101953	GCA_017874735.1	1670801	1670801	type	True	86.9085	1935	2433	95	below_threshold
Paenibacillus phytohabitans	strain=LMG 31459	GCA_013141775.1	2654978	2654978	type	True	85.3203	1709	2433	95	below_threshold
Paenibacillus borealis	strain=DSM 13188	GCA_000758665.1	160799	160799	type	True	85.0353	1679	2433	95	below_threshold
Paenibacillus piscarius	strain=P121	GCA_022234545.1	1089681	1089681	type	True	83.9458	1731	2433	95	below_threshold
Paenibacillus sonchi	strain=LMG 24727	GCA_016772475.1	373687	373687	type	True	80.6686	1130	2433	95	below_threshold
Paenibacillus tianjinensis	strain=TB2019	GCA_017086365.1	2810347	2810347	type	True	80.4983	1010	2433	95	below_threshold
Paenibacillus agri	strain=JW14	GCA_013359945.1	2744309	2744309	type	True	79.0643	597	2433	95	below_threshold
Paenibacillus rhizophilus	strain=7197	GCA_003854965.1	1850366	1850366	type	True	78.125	453	2433	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:52,753] [INFO] DFAST Taxonomy check result was written to GCF_013204885.1_ASM1320488v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:52,754] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:52,754] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:52,754] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d76f6fa-430a-4f59-a469-3c9169142843/dqc_reference/checkm_data
[2024-01-24 12:06:52,756] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:52,827] [INFO] Task started: CheckM
[2024-01-24 12:06:52,827] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013204885.1_ASM1320488v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013204885.1_ASM1320488v1_genomic.fna/checkm_input GCF_013204885.1_ASM1320488v1_genomic.fna/checkm_result
[2024-01-24 12:07:50,439] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:50,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:50,470] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:50,470] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:50,471] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013204885.1_ASM1320488v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:50,471] [INFO] Task started: Blastn
[2024-01-24 12:07:50,471] [INFO] Running command: blastn -query GCF_013204885.1_ASM1320488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d76f6fa-430a-4f59-a469-3c9169142843/dqc_reference/reference_markers_gtdb.fasta -out GCF_013204885.1_ASM1320488v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:51,302] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:51,305] [INFO] Selected 7 target genomes.
[2024-01-24 12:07:51,306] [INFO] Target genome list was writen to GCF_013204885.1_ASM1320488v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:51,311] [INFO] Task started: fastANI
[2024-01-24 12:07:51,312] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a85bab6-c183-4c74-b659-4ffc428f242b/GCF_013204885.1_ASM1320488v1_genomic.fna.gz --refList GCF_013204885.1_ASM1320488v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013204885.1_ASM1320488v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:05,233] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:05,244] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:05,244] [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_013204885.1	s__Paenibacillus tritici	100.0	2428	2433	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.22	98.22	0.93	0.93	2	conclusive
GCF_017874765.1	s__Paenibacillus rhizoplanae	88.735	1947	2433	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874735.1	s__Paenibacillus silagei	86.9275	1932	2433	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.84	96.20	0.88	0.87	3	-
GCF_001955925.1	s__Paenibacillus sp001955925	86.3917	1810	2433	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	98.91	98.91	0.92	0.92	2	-
GCF_000758605.1	s__Paenibacillus sp000758605	85.6121	1769	2433	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013141775.1	s__Paenibacillus phytohabitans	85.3033	1713	2433	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	96.61	96.02	0.84	0.83	4	-
GCF_000758665.1	s__Paenibacillus borealis	85.0566	1675	2433	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:05,245] [INFO] GTDB search result was written to GCF_013204885.1_ASM1320488v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:05,246] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:05,249] [INFO] DFAST_QC result json was written to GCF_013204885.1_ASM1320488v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:05,249] [INFO] DFAST_QC completed!
[2024-01-24 12:08:05,249] [INFO] Total running time: 0h1m51s