[2024-01-24 11:59:35,708] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:35,709] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:35,710] [INFO] DQC Reference Directory: /var/lib/cwl/stg974c1056-8a46-4777-8943-9936afa85a95/dqc_reference
[2024-01-24 11:59:36,971] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:36,972] [INFO] Task started: Prodigal
[2024-01-24 11:59:36,972] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b8b3984-44cd-4545-bcd0-1607af1e2d1e/GCF_002082905.2_ASM208290v2_genomic.fna.gz | prodigal -d GCF_002082905.2_ASM208290v2_genomic.fna/cds.fna -a GCF_002082905.2_ASM208290v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:46,914] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:46,915] [INFO] Task started: HMMsearch
[2024-01-24 11:59:46,915] [INFO] Running command: hmmsearch --tblout GCF_002082905.2_ASM208290v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg974c1056-8a46-4777-8943-9936afa85a95/dqc_reference/reference_markers.hmm GCF_002082905.2_ASM208290v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:47,262] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:47,263] [INFO] Found 6/6 markers.
[2024-01-24 11:59:47,302] [INFO] Query marker FASTA was written to GCF_002082905.2_ASM208290v2_genomic.fna/markers.fasta
[2024-01-24 11:59:47,303] [INFO] Task started: Blastn
[2024-01-24 11:59:47,303] [INFO] Running command: blastn -query GCF_002082905.2_ASM208290v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg974c1056-8a46-4777-8943-9936afa85a95/dqc_reference/reference_markers.fasta -out GCF_002082905.2_ASM208290v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:47,951] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:47,955] [INFO] Selected 10 target genomes.
[2024-01-24 11:59:47,956] [INFO] Target genome list was writen to GCF_002082905.2_ASM208290v2_genomic.fna/target_genomes.txt
[2024-01-24 11:59:47,975] [INFO] Task started: fastANI
[2024-01-24 11:59:47,975] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b8b3984-44cd-4545-bcd0-1607af1e2d1e/GCF_002082905.2_ASM208290v2_genomic.fna.gz --refList GCF_002082905.2_ASM208290v2_genomic.fna/target_genomes.txt --output GCF_002082905.2_ASM208290v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:59,070] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:59,071] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg974c1056-8a46-4777-8943-9936afa85a95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:59,072] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg974c1056-8a46-4777-8943-9936afa85a95/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:59,083] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:59:59,084] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:59,084] [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 anisa	strain=FDAARGOS_200	GCA_002082905.2	28082	28082	type	True	100.0	1516	1520	95	conclusive
Legionella anisa	strain=FDAARGOS_1480	GCA_019930885.1	28082	28082	type	True	99.9947	1477	1520	95	conclusive
Legionella anisa	strain=WA-316-C3	GCA_001467525.1	28082	28082	type	True	99.9532	1439	1520	95	conclusive
Legionella anisa	strain=WA-316-C3	GCA_900639785.1	28082	28082	type	True	99.667	1316	1520	95	conclusive
Legionella tucsonensis	strain=ATCC 49180	GCA_001468035.1	40335	40335	type	True	89.154	956	1520	95	below_threshold
Legionella bozemanae	strain=WIGA	GCA_001467045.1	447	447	type	True	88.9704	1066	1520	95	below_threshold
Legionella lytica	strain=PCM 2298	GCA_023921225.1	96232	96232	type	True	79.1397	266	1520	95	below_threshold
Legionella rowbothamii	strain=LLAP6	GCA_900639985.1	96229	96229	type	True	78.4158	267	1520	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:59,085] [INFO] DFAST Taxonomy check result was written to GCF_002082905.2_ASM208290v2_genomic.fna/tc_result.tsv
[2024-01-24 11:59:59,086] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:59,086] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:59,086] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg974c1056-8a46-4777-8943-9936afa85a95/dqc_reference/checkm_data
[2024-01-24 11:59:59,087] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:59,136] [INFO] Task started: CheckM
[2024-01-24 11:59:59,136] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002082905.2_ASM208290v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002082905.2_ASM208290v2_genomic.fna/checkm_input GCF_002082905.2_ASM208290v2_genomic.fna/checkm_result
[2024-01-24 12:00:36,070] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:36,071] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:36,094] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:36,095] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:36,095] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002082905.2_ASM208290v2_genomic.fna/markers.fasta)
[2024-01-24 12:00:36,096] [INFO] Task started: Blastn
[2024-01-24 12:00:36,096] [INFO] Running command: blastn -query GCF_002082905.2_ASM208290v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg974c1056-8a46-4777-8943-9936afa85a95/dqc_reference/reference_markers_gtdb.fasta -out GCF_002082905.2_ASM208290v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:37,108] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:37,112] [INFO] Selected 5 target genomes.
[2024-01-24 12:00:37,112] [INFO] Target genome list was writen to GCF_002082905.2_ASM208290v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:37,119] [INFO] Task started: fastANI
[2024-01-24 12:00:37,119] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b8b3984-44cd-4545-bcd0-1607af1e2d1e/GCF_002082905.2_ASM208290v2_genomic.fna.gz --refList GCF_002082905.2_ASM208290v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002082905.2_ASM208290v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:43,115] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:43,122] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:43,122] [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_001467525.1	s__Legionella anisa	99.9532	1439	1520	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.76	99.61	0.95	0.93	6	conclusive
GCF_014109805.1	s__Legionella sp014109805	90.5835	1133	1520	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001468035.1	s__Legionella tucsonensis	89.154	956	1520	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001648595.1	s__Legionella bozemanae	88.9743	1060	1520	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.47	97.91	0.97	0.91	5	-
GCF_001467945.1	s__Legionella parisiensis	88.1613	1139	1520	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Legionellales;f__Legionellaceae;g__Legionella	95.0	99.99	99.98	1.00	1.00	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:43,124] [INFO] GTDB search result was written to GCF_002082905.2_ASM208290v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:43,125] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:43,127] [INFO] DFAST_QC result json was written to GCF_002082905.2_ASM208290v2_genomic.fna/dqc_result.json
[2024-01-24 12:00:43,128] [INFO] DFAST_QC completed!
[2024-01-24 12:00:43,128] [INFO] Total running time: 0h1m7s