[2024-01-24 11:02:48,557] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:02:48,560] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:02:48,560] [INFO] DQC Reference Directory: /var/lib/cwl/stgd47f663a-99b4-4c46-bb92-df8164933d27/dqc_reference
[2024-01-24 11:02:49,802] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:02:49,803] [INFO] Task started: Prodigal
[2024-01-24 11:02:49,803] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8b0144a-dba9-47ef-8643-b0ad9eec8ceb/GCF_002812045.1_ASM281204v1_genomic.fna.gz | prodigal -d GCF_002812045.1_ASM281204v1_genomic.fna/cds.fna -a GCF_002812045.1_ASM281204v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:02:58,267] [INFO] Task succeeded: Prodigal
[2024-01-24 11:02:58,268] [INFO] Task started: HMMsearch
[2024-01-24 11:02:58,268] [INFO] Running command: hmmsearch --tblout GCF_002812045.1_ASM281204v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd47f663a-99b4-4c46-bb92-df8164933d27/dqc_reference/reference_markers.hmm GCF_002812045.1_ASM281204v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:02:58,543] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:02:58,545] [INFO] Found 6/6 markers.
[2024-01-24 11:02:58,589] [INFO] Query marker FASTA was written to GCF_002812045.1_ASM281204v1_genomic.fna/markers.fasta
[2024-01-24 11:02:58,590] [INFO] Task started: Blastn
[2024-01-24 11:02:58,590] [INFO] Running command: blastn -query GCF_002812045.1_ASM281204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd47f663a-99b4-4c46-bb92-df8164933d27/dqc_reference/reference_markers.fasta -out GCF_002812045.1_ASM281204v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:02:59,167] [INFO] Task succeeded: Blastn
[2024-01-24 11:02:59,172] [INFO] Selected 9 target genomes.
[2024-01-24 11:02:59,172] [INFO] Target genome list was writen to GCF_002812045.1_ASM281204v1_genomic.fna/target_genomes.txt
[2024-01-24 11:02:59,204] [INFO] Task started: fastANI
[2024-01-24 11:02:59,204] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8b0144a-dba9-47ef-8643-b0ad9eec8ceb/GCF_002812045.1_ASM281204v1_genomic.fna.gz --refList GCF_002812045.1_ASM281204v1_genomic.fna/target_genomes.txt --output GCF_002812045.1_ASM281204v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:03:08,791] [INFO] Task succeeded: fastANI
[2024-01-24 11:03:08,792] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd47f663a-99b4-4c46-bb92-df8164933d27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:03:08,793] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd47f663a-99b4-4c46-bb92-df8164933d27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:03:08,808] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:03:08,809] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:03:08,809] [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
Leptospira haakeii	strain=ATI7-C-A4	GCA_002812045.1	2023198	2023198	type	True	100.0	1378	1379	95	conclusive
Leptospira selangorensis	strain=SSW17	GCA_004769405.1	2484982	2484982	type	True	91.8969	1312	1379	95	below_threshold
Leptospira saintgironsiae	strain=FH4-C-A2	GCA_002811765.1	2023183	2023183	type	True	89.5222	1229	1379	95	below_threshold
Leptospira hartskeerlii	strain=MCA2-B-A3	GCA_002811475.1	2023177	2023177	type	True	88.0845	1209	1379	95	below_threshold
Leptospira venezuelensis	strain=CLM-U50	GCA_002150035.1	1958811	1958811	type	True	87.8334	1217	1379	95	below_threshold
Leptospira neocaledonica	strain=ES4-C-A1	GCA_002812205.1	2023192	2023192	type	True	87.6554	1219	1379	95	below_threshold
Leptospira johnsonii	strain=E8	GCA_003112675.1	1917820	1917820	type	True	87.3978	1205	1379	95	below_threshold
Leptospira licerasiae	strain=VAR 010	GCA_000244755.3	447106	447106	type	True	87.0705	1190	1379	95	below_threshold
Leptospira licerasiae	strain=ATCC BAA-1110	GCA_000526875.1	447106	447106	type	True	87.0509	1212	1379	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:03:08,811] [INFO] DFAST Taxonomy check result was written to GCF_002812045.1_ASM281204v1_genomic.fna/tc_result.tsv
[2024-01-24 11:03:08,812] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:03:08,812] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:03:08,813] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd47f663a-99b4-4c46-bb92-df8164933d27/dqc_reference/checkm_data
[2024-01-24 11:03:08,814] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:03:08,858] [INFO] Task started: CheckM
[2024-01-24 11:03:08,859] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002812045.1_ASM281204v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002812045.1_ASM281204v1_genomic.fna/checkm_input GCF_002812045.1_ASM281204v1_genomic.fna/checkm_result
[2024-01-24 11:03:38,872] [INFO] Task succeeded: CheckM
[2024-01-24 11:03:38,874] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:03:38,899] [INFO] ===== Completeness check finished =====
[2024-01-24 11:03:38,899] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:03:38,900] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002812045.1_ASM281204v1_genomic.fna/markers.fasta)
[2024-01-24 11:03:38,900] [INFO] Task started: Blastn
[2024-01-24 11:03:38,900] [INFO] Running command: blastn -query GCF_002812045.1_ASM281204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd47f663a-99b4-4c46-bb92-df8164933d27/dqc_reference/reference_markers_gtdb.fasta -out GCF_002812045.1_ASM281204v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:03:39,736] [INFO] Task succeeded: Blastn
[2024-01-24 11:03:39,741] [INFO] Selected 10 target genomes.
[2024-01-24 11:03:39,741] [INFO] Target genome list was writen to GCF_002812045.1_ASM281204v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:03:39,825] [INFO] Task started: fastANI
[2024-01-24 11:03:39,825] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8b0144a-dba9-47ef-8643-b0ad9eec8ceb/GCF_002812045.1_ASM281204v1_genomic.fna.gz --refList GCF_002812045.1_ASM281204v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002812045.1_ASM281204v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:03:50,644] [INFO] Task succeeded: fastANI
[2024-01-24 11:03:50,657] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:03:50,658] [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_002812045.1	s__Leptospira_B haakeii	100.0	1378	1379	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_004769405.1	s__Leptospira_B selangorensis	91.8968	1312	1379	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	97.97	97.97	0.98	0.97	3	-
GCF_002811765.1	s__Leptospira_B saintgironsiae	89.5123	1230	1379	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004770105.1	s__Leptospira_B andrefontaineae	89.4237	1236	1379	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004770895.1	s__Leptospira_B dzoumogneensis	89.2145	1257	1379	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004769555.1	s__Leptospira_B koniambonensis	88.9742	1263	1379	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002811475.1	s__Leptospira_B hartskeerlii	88.0956	1208	1379	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002150035.1	s__Leptospira_B venezuelensis	87.8359	1216	1379	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	100.00	100.00	1.00	1.00	3	-
GCF_002812205.1	s__Leptospira_B neocaledonica	87.6515	1220	1379	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000347035.1	s__Leptospira_B sp000347035	85.8159	1197	1379	d__Bacteria;p__Spirochaetota;c__Leptospirae;o__Leptospirales;f__Leptospiraceae;g__Leptospira_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:03:50,660] [INFO] GTDB search result was written to GCF_002812045.1_ASM281204v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:03:50,661] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:03:50,666] [INFO] DFAST_QC result json was written to GCF_002812045.1_ASM281204v1_genomic.fna/dqc_result.json
[2024-01-24 11:03:50,666] [INFO] DFAST_QC completed!
[2024-01-24 11:03:50,666] [INFO] Total running time: 0h1m2s