[2024-01-24 14:38:48,378] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:48,385] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:48,385] [INFO] DQC Reference Directory: /var/lib/cwl/stgbfa27389-c981-458f-9948-007a0af52b45/dqc_reference
[2024-01-24 14:38:50,448] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:50,450] [INFO] Task started: Prodigal
[2024-01-24 14:38:50,451] [INFO] Running command: gunzip -c /var/lib/cwl/stg6941c29f-79fa-4a71-b6b8-0d1f2182ea9e/GCF_014652815.1_ASM1465281v1_genomic.fna.gz | prodigal -d GCF_014652815.1_ASM1465281v1_genomic.fna/cds.fna -a GCF_014652815.1_ASM1465281v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:04,546] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:04,546] [INFO] Task started: HMMsearch
[2024-01-24 14:39:04,547] [INFO] Running command: hmmsearch --tblout GCF_014652815.1_ASM1465281v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbfa27389-c981-458f-9948-007a0af52b45/dqc_reference/reference_markers.hmm GCF_014652815.1_ASM1465281v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:04,912] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:04,916] [INFO] Found 6/6 markers.
[2024-01-24 14:39:04,959] [INFO] Query marker FASTA was written to GCF_014652815.1_ASM1465281v1_genomic.fna/markers.fasta
[2024-01-24 14:39:04,959] [INFO] Task started: Blastn
[2024-01-24 14:39:04,959] [INFO] Running command: blastn -query GCF_014652815.1_ASM1465281v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbfa27389-c981-458f-9948-007a0af52b45/dqc_reference/reference_markers.fasta -out GCF_014652815.1_ASM1465281v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:05,717] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:05,720] [INFO] Selected 10 target genomes.
[2024-01-24 14:39:05,721] [INFO] Target genome list was writen to GCF_014652815.1_ASM1465281v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:05,730] [INFO] Task started: fastANI
[2024-01-24 14:39:05,731] [INFO] Running command: fastANI --query /var/lib/cwl/stg6941c29f-79fa-4a71-b6b8-0d1f2182ea9e/GCF_014652815.1_ASM1465281v1_genomic.fna.gz --refList GCF_014652815.1_ASM1465281v1_genomic.fna/target_genomes.txt --output GCF_014652815.1_ASM1465281v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:13,514] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:13,514] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbfa27389-c981-458f-9948-007a0af52b45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:13,515] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbfa27389-c981-458f-9948-007a0af52b45/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:13,521] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:13,521] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:13,521] [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
Alcaligenes pakistanensis	strain=KCTC 42083	GCA_014652815.1	1482717	1482717	type	True	100.0	1331	1331	95	conclusive
Alcaligenes faecalis subsp. faecalis	strain=NBRC 13111	GCA_000739855.1	32001	511	type	True	86.8069	1133	1331	95	below_threshold
Alcaligenes faecalis subsp. faecalis	strain=NBRC 13111	GCA_001748345.1	32001	511	type	True	86.7709	1135	1331	95	below_threshold
Alcaligenes faecalis	strain=DSM 30030	GCA_002443155.1	511	511	type	True	86.7553	1145	1331	95	below_threshold
Alcaligenes faecalis	strain=ATCC 8750	GCA_001298815.1	511	511	type	True	86.7461	1139	1331	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:13,523] [INFO] DFAST Taxonomy check result was written to GCF_014652815.1_ASM1465281v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:13,524] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:13,524] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:13,524] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbfa27389-c981-458f-9948-007a0af52b45/dqc_reference/checkm_data
[2024-01-24 14:39:13,526] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:13,567] [INFO] Task started: CheckM
[2024-01-24 14:39:13,568] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652815.1_ASM1465281v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652815.1_ASM1465281v1_genomic.fna/checkm_input GCF_014652815.1_ASM1465281v1_genomic.fna/checkm_result
[2024-01-24 14:39:58,972] [INFO] Task succeeded: CheckM
[2024-01-24 14:39:58,973] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:39:58,999] [INFO] ===== Completeness check finished =====
[2024-01-24 14:39:58,999] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:39:59,000] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652815.1_ASM1465281v1_genomic.fna/markers.fasta)
[2024-01-24 14:39:59,000] [INFO] Task started: Blastn
[2024-01-24 14:39:59,000] [INFO] Running command: blastn -query GCF_014652815.1_ASM1465281v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbfa27389-c981-458f-9948-007a0af52b45/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652815.1_ASM1465281v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:00,392] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:00,395] [INFO] Selected 6 target genomes.
[2024-01-24 14:40:00,395] [INFO] Target genome list was writen to GCF_014652815.1_ASM1465281v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:00,406] [INFO] Task started: fastANI
[2024-01-24 14:40:00,406] [INFO] Running command: fastANI --query /var/lib/cwl/stg6941c29f-79fa-4a71-b6b8-0d1f2182ea9e/GCF_014652815.1_ASM1465281v1_genomic.fna.gz --refList GCF_014652815.1_ASM1465281v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652815.1_ASM1465281v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:07,202] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:07,209] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:07,209] [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_014652815.1	s__Alcaligenes pakistanensis	100.0	1331	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	99.29	99.08	0.97	0.96	3	conclusive
GCF_017377875.1	s__Alcaligenes sp017377875	87.9966	1162	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009497775.1	s__Alcaligenes faecalis_D	87.2946	1166	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005311025.1	s__Alcaligenes phenolicus	86.7558	1162	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	97.79	96.15	0.91	0.86	11	-
GCF_002443155.1	s__Alcaligenes faecalis	86.7553	1145	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	98.39	97.71	0.93	0.90	22	-
GCF_003076515.1	s__Alcaligenes aquatilis	85.9011	1055	1331	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	98.23	96.52	0.93	0.89	8	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:07,214] [INFO] GTDB search result was written to GCF_014652815.1_ASM1465281v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:07,214] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:07,217] [INFO] DFAST_QC result json was written to GCF_014652815.1_ASM1465281v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:07,217] [INFO] DFAST_QC completed!
[2024-01-24 14:40:07,217] [INFO] Total running time: 0h1m19s