[2024-01-24 11:34:42,921] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:42,926] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:42,927] [INFO] DQC Reference Directory: /var/lib/cwl/stge93e0978-7470-4a68-ada2-cc2f145daa43/dqc_reference
[2024-01-24 11:34:44,462] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:44,463] [INFO] Task started: Prodigal
[2024-01-24 11:34:44,463] [INFO] Running command: gunzip -c /var/lib/cwl/stgee52bcb5-7e22-4667-ae98-d6611bc0fc0a/GCF_900639985.1_Leg_rowbothamii_LLAP6.v1_genomic.fna.gz | prodigal -d GCF_900639985.1_Leg_rowbothamii_LLAP6.v1_genomic.fna/cds.fna -a GCF_900639985.1_Leg_rowbothamii_LLAP6.v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:52,922] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:52,922] [INFO] Task started: HMMsearch
[2024-01-24 11:34:52,922] [INFO] Running command: hmmsearch --tblout GCF_900639985.1_Leg_rowbothamii_LLAP6.v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge93e0978-7470-4a68-ada2-cc2f145daa43/dqc_reference/reference_markers.hmm GCF_900639985.1_Leg_rowbothamii_LLAP6.v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:53,243] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:53,244] [INFO] Found 6/6 markers.
[2024-01-24 11:34:53,276] [INFO] Query marker FASTA was written to GCF_900639985.1_Leg_rowbothamii_LLAP6.v1_genomic.fna/markers.fasta
[2024-01-24 11:34:53,276] [INFO] Task started: Blastn
[2024-01-24 11:34:53,276] [INFO] Running command: blastn -query GCF_900639985.1_Leg_rowbothamii_LLAP6.v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge93e0978-7470-4a68-ada2-cc2f145daa43/dqc_reference/reference_markers.fasta -out GCF_900639985.1_Leg_rowbothamii_LLAP6.v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:54,014] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:54,017] [INFO] Selected 16 target genomes.
[2024-01-24 11:34:54,017] [INFO] Target genome list was writen to GCF_900639985.1_Leg_rowbothamii_LLAP6.v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:54,023] [INFO] Task started: fastANI
[2024-01-24 11:34:54,024] [INFO] Running command: fastANI --query /var/lib/cwl/stgee52bcb5-7e22-4667-ae98-d6611bc0fc0a/GCF_900639985.1_Leg_rowbothamii_LLAP6.v1_genomic.fna.gz --refList GCF_900639985.1_Leg_rowbothamii_LLAP6.v1_genomic.fna/target_genomes.txt --output GCF_900639985.1_Leg_rowbothamii_LLAP6.v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:04,875] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:04,876] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge93e0978-7470-4a68-ada2-cc2f145daa43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:04,876] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge93e0978-7470-4a68-ada2-cc2f145daa43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:04,888] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:04,888] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:04,888] [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
Legionella rowbothamii	strain=LLAP6	GCA_900639985.1	96229	96229	type	True	100.0	1303	1307	95	conclusive
Legionella lytica	strain=PCM 2298	GCA_023921225.1	96232	96232	type	True	86.9873	962	1307	95	below_threshold
Legionella saoudiensis	strain=LS-1	GCA_001465875.1	1750561	1750561	type	True	84.249	894	1307	95	below_threshold
Legionella drancourtii	strain=LLAP12	GCA_000162755.2	168933	168933	type	True	79.8437	431	1307	95	below_threshold
Legionella bononiensis	strain=30cs62	GCA_016786415.1	2793102	2793102	type	True	78.7673	164	1307	95	below_threshold
Legionella steelei	strain=IMVS3376	GCA_001468005.1	947033	947033	type	True	78.4588	288	1307	95	below_threshold
Legionella sainthelensi	strain=Mt.St.Helens-4	GCA_001468105.1	28087	28087	type	True	78.3422	227	1307	95	below_threshold
Legionella cherrii	strain=ORW	GCA_001467035.1	28084	28084	type	True	78.2123	247	1307	95	below_threshold
Fluoribacter dumoffii	strain=NY 23	GCA_000236165.1	463	463	type	True	78.199	208	1307	95	below_threshold
Legionella tucsonensis	strain=1087-AZ-H	GCA_900640035.1	40335	40335	type	True	78.0932	222	1307	95	below_threshold
Legionella tucsonensis	strain=ATCC 49180	GCA_001468035.1	40335	40335	type	True	78.0591	227	1307	95	below_threshold
Legionella longbeachae	strain=FDAARGOS_1481	GCA_019930685.1	450	450	type	True	77.9848	235	1307	95	below_threshold
Legionella longbeachae	strain=NCTC11477	GCA_004283175.1	450	450	type	True	77.9481	230	1307	95	below_threshold
Legionella pneumophila subsp. pneumophila	strain=PartS-Lpneumophila-RM8376	GCA_022870105.1	91891	446	type	True	77.8294	148	1307	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:04,890] [INFO] DFAST Taxonomy check result was written to GCF_900639985.1_Leg_rowbothamii_LLAP6.v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:04,891] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:04,891] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:04,891] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge93e0978-7470-4a68-ada2-cc2f145daa43/dqc_reference/checkm_data
[2024-01-24 11:35:04,892] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:04,932] [INFO] Task started: CheckM
[2024-01-24 11:35:04,932] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900639985.1_Leg_rowbothamii_LLAP6.v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900639985.1_Leg_rowbothamii_LLAP6.v1_genomic.fna/checkm_input GCF_900639985.1_Leg_rowbothamii_LLAP6.v1_genomic.fna/checkm_result
[2024-01-24 11:35:34,622] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:34,623] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:34,636] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:34,636] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:34,637] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900639985.1_Leg_rowbothamii_LLAP6.v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:34,637] [INFO] Task started: Blastn
[2024-01-24 11:35:34,637] [INFO] Running command: blastn -query GCF_900639985.1_Leg_rowbothamii_LLAP6.v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge93e0978-7470-4a68-ada2-cc2f145daa43/dqc_reference/reference_markers_gtdb.fasta -out GCF_900639985.1_Leg_rowbothamii_LLAP6.v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:35,692] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:35,696] [INFO] Selected 14 target genomes.
[2024-01-24 11:35:35,697] [INFO] Target genome list was writen to GCF_900639985.1_Leg_rowbothamii_LLAP6.v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:35,707] [INFO] Task started: fastANI
[2024-01-24 11:35:35,708] [INFO] Running command: fastANI --query /var/lib/cwl/stgee52bcb5-7e22-4667-ae98-d6611bc0fc0a/GCF_900639985.1_Leg_rowbothamii_LLAP6.v1_genomic.fna.gz --refList GCF_900639985.1_Leg_rowbothamii_LLAP6.v1_genomic.fna/target_genomes_gtdb.txt --output GCF_900639985.1_Leg_rowbothamii_LLAP6.v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:35:45,043] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:45,057] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:35:45,057] [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_900639985.1	s__Legionella rowbothamii	100.0	1303	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001465875.1	s__Legionella saoudiensis	84.2597	893	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000162755.2	s__Legionella drancourtii	79.8682	429	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423305.1	s__Legionella moravica	79.8378	178	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.09	96.46	0.96	0.86	5	-
GCF_016786215.1	s__Legionella sp016786215	78.8329	170	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.95	99.94	0.97	0.97	3	-
GCF_001467525.1	s__Legionella anisa	78.565	256	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.76	99.61	0.95	0.93	6	-
GCF_001468005.1	s__Legionella steelei	78.4588	288	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	98.95	98.94	0.93	0.93	3	-
GCF_000236165.1	s__Legionella dumoffii	78.199	208	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.81	99.55	0.97	0.94	4	-
GCF_001468065.1	s__Legionella steigerwaltii	78.0617	260	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.99	99.99	0.99	0.99	3	-
GCF_001468035.1	s__Legionella tucsonensis	78.0591	227	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900635815.1	s__Legionella cherrii	77.9558	236	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.87	99.61	0.99	0.97	4	-
GCA_004283175.1	s__Legionella longbeachae	77.9473	230	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.77	99.22	0.96	0.94	9	-
GCA_016191305.1	s__Legionella longbeachae_A	77.9345	163	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001467695.1	s__Legionella gratiana	77.8889	272	1307	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.98	99.98	0.99	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:35:45,059] [INFO] GTDB search result was written to GCF_900639985.1_Leg_rowbothamii_LLAP6.v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:35:45,059] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:35:45,077] [INFO] DFAST_QC result json was written to GCF_900639985.1_Leg_rowbothamii_LLAP6.v1_genomic.fna/dqc_result.json
[2024-01-24 11:35:45,077] [INFO] DFAST_QC completed!
[2024-01-24 11:35:45,077] [INFO] Total running time: 0h1m2s