[2024-01-24 11:51:24,929] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:24,931] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:24,932] [INFO] DQC Reference Directory: /var/lib/cwl/stg051d6a9b-833d-41ab-9c17-0f45db942d54/dqc_reference
[2024-01-24 11:51:26,279] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:26,280] [INFO] Task started: Prodigal
[2024-01-24 11:51:26,281] [INFO] Running command: gunzip -c /var/lib/cwl/stg8e64c161-6110-4a07-8e30-6d56220e87d3/GCF_900637745.1_52551_F01_genomic.fna.gz | prodigal -d GCF_900637745.1_52551_F01_genomic.fna/cds.fna -a GCF_900637745.1_52551_F01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:32,681] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:32,682] [INFO] Task started: HMMsearch
[2024-01-24 11:51:32,682] [INFO] Running command: hmmsearch --tblout GCF_900637745.1_52551_F01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg051d6a9b-833d-41ab-9c17-0f45db942d54/dqc_reference/reference_markers.hmm GCF_900637745.1_52551_F01_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:32,970] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:32,972] [INFO] Found 6/6 markers.
[2024-01-24 11:51:32,998] [INFO] Query marker FASTA was written to GCF_900637745.1_52551_F01_genomic.fna/markers.fasta
[2024-01-24 11:51:32,998] [INFO] Task started: Blastn
[2024-01-24 11:51:32,998] [INFO] Running command: blastn -query GCF_900637745.1_52551_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stg051d6a9b-833d-41ab-9c17-0f45db942d54/dqc_reference/reference_markers.fasta -out GCF_900637745.1_52551_F01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:33,588] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:33,592] [INFO] Selected 10 target genomes.
[2024-01-24 11:51:33,592] [INFO] Target genome list was writen to GCF_900637745.1_52551_F01_genomic.fna/target_genomes.txt
[2024-01-24 11:51:33,599] [INFO] Task started: fastANI
[2024-01-24 11:51:33,599] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e64c161-6110-4a07-8e30-6d56220e87d3/GCF_900637745.1_52551_F01_genomic.fna.gz --refList GCF_900637745.1_52551_F01_genomic.fna/target_genomes.txt --output GCF_900637745.1_52551_F01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:40,448] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:40,449] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg051d6a9b-833d-41ab-9c17-0f45db942d54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:40,450] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg051d6a9b-833d-41ab-9c17-0f45db942d54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:40,462] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:51:40,462] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:51:40,462] [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
Listeria ivanovii subsp. ivanovii	strain=NCTC11007	GCA_900187195.1	202751	1638	type	True	93.4352	869	1002	95	below_threshold
Listeria ivanovii subsp. ivanovii	strain=NCTC11846	GCA_900187025.1	202751	1638	type	True	93.4346	869	1002	95	below_threshold
Listeria ivanovii subsp. ivanovii	strain=WSLC 3010	GCA_000763515.1	202751	1638	type	True	93.4238	866	1002	95	below_threshold
Listeria ivanovii subsp. ivanovii	strain=PAM 55	GCA_000252975.1	202751	1638	claderef	True	93.4211	861	1002	95	below_threshold
Listeria seeligeri	strain=SLCC3954	GCA_000027145.1	1640	1640	type	True	88.8536	782	1002	95	below_threshold
Listeria immobilis	strain=FSL L7-1519	GCA_014322765.1	2713502	2713502	type	True	88.0752	796	1002	95	below_threshold
Listeria innocua	strain=F4078	GCA_024721565.1	1642	1642	type	True	84.2047	714	1002	95	below_threshold
Listeria monocytogenes	strain=G4599	GCA_001466295.1	1639	1639	claderef	True	84.1131	728	1002	95	below_threshold
Listeria innocua	strain=F4078	GCA_014527425.1	1642	1642	type	True	84.0927	718	1002	95	below_threshold
Listeria monocytogenes	strain=J0099	GCA_013625995.1	1639	1639	claderef	True	84.0344	720	1002	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:40,466] [INFO] DFAST Taxonomy check result was written to GCF_900637745.1_52551_F01_genomic.fna/tc_result.tsv
[2024-01-24 11:51:40,467] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:40,467] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:40,467] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg051d6a9b-833d-41ab-9c17-0f45db942d54/dqc_reference/checkm_data
[2024-01-24 11:51:40,469] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:40,502] [INFO] Task started: CheckM
[2024-01-24 11:51:40,502] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900637745.1_52551_F01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900637745.1_52551_F01_genomic.fna/checkm_input GCF_900637745.1_52551_F01_genomic.fna/checkm_result
[2024-01-24 11:52:05,956] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:05,957] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:05,977] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:05,977] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:05,978] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900637745.1_52551_F01_genomic.fna/markers.fasta)
[2024-01-24 11:52:05,978] [INFO] Task started: Blastn
[2024-01-24 11:52:05,978] [INFO] Running command: blastn -query GCF_900637745.1_52551_F01_genomic.fna/markers.fasta -db /var/lib/cwl/stg051d6a9b-833d-41ab-9c17-0f45db942d54/dqc_reference/reference_markers_gtdb.fasta -out GCF_900637745.1_52551_F01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:06,793] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:06,797] [INFO] Selected 9 target genomes.
[2024-01-24 11:52:06,798] [INFO] Target genome list was writen to GCF_900637745.1_52551_F01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:06,805] [INFO] Task started: fastANI
[2024-01-24 11:52:06,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e64c161-6110-4a07-8e30-6d56220e87d3/GCF_900637745.1_52551_F01_genomic.fna.gz --refList GCF_900637745.1_52551_F01_genomic.fna/target_genomes_gtdb.txt --output GCF_900637745.1_52551_F01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:13,608] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:13,621] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:13,621] [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_000763495.1	s__Listeria londoniensis	99.3571	943	1002	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.36	98.73	0.96	0.94	17	conclusive
GCF_900187025.1	s__Listeria ivanovii	93.4342	869	1002	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.75	99.44	0.99	0.97	26	-
GCF_000027145.1	s__Listeria seeligeri	88.8649	783	1002	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	97.08	96.23	0.92	0.88	167	-
GCF_014322765.1	s__Listeria immobilis	88.0752	796	1002	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.35	97.95	0.95	0.87	9	-
GCF_000307025.1	s__Listeria monocytogenes_B	84.1355	731	1002	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.46	95.21	0.96	0.90	1699	-
GCF_014229645.1	s__Listeria sp014229645	84.0948	694	1002	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187225.1	s__Listeria monocytogenes	84.0105	743	1002	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	99.04	95.98	0.97	0.89	1977	-
GCF_015276835.1	s__Listeria innocua	84.0072	730	1002	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	98.16	96.24	0.95	0.92	107	-
GCF_014229095.1	s__Listeria cayugensis	83.9826	693	1002	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Listeriaceae;g__Listeria	95.0	97.39	97.39	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:13,623] [INFO] GTDB search result was written to GCF_900637745.1_52551_F01_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:13,624] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:13,627] [INFO] DFAST_QC result json was written to GCF_900637745.1_52551_F01_genomic.fna/dqc_result.json
[2024-01-24 11:52:13,627] [INFO] DFAST_QC completed!
[2024-01-24 11:52:13,628] [INFO] Total running time: 0h0m49s