[2024-01-25 19:53:50,604] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:53:50,607] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:53:50,607] [INFO] DQC Reference Directory: /var/lib/cwl/stgec35446b-ac13-4b26-9b09-2d384351693c/dqc_reference
[2024-01-25 19:53:51,762] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:53:51,763] [INFO] Task started: Prodigal
[2024-01-25 19:53:51,763] [INFO] Running command: gunzip -c /var/lib/cwl/stg44ac0527-a191-49c0-afec-db61879a82de/GCF_026344105.1_ASM2634410v1_genomic.fna.gz | prodigal -d GCF_026344105.1_ASM2634410v1_genomic.fna/cds.fna -a GCF_026344105.1_ASM2634410v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:54:04,733] [INFO] Task succeeded: Prodigal
[2024-01-25 19:54:04,733] [INFO] Task started: HMMsearch
[2024-01-25 19:54:04,733] [INFO] Running command: hmmsearch --tblout GCF_026344105.1_ASM2634410v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec35446b-ac13-4b26-9b09-2d384351693c/dqc_reference/reference_markers.hmm GCF_026344105.1_ASM2634410v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:54:05,078] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:54:05,079] [INFO] Found 6/6 markers.
[2024-01-25 19:54:05,140] [INFO] Query marker FASTA was written to GCF_026344105.1_ASM2634410v1_genomic.fna/markers.fasta
[2024-01-25 19:54:05,140] [INFO] Task started: Blastn
[2024-01-25 19:54:05,140] [INFO] Running command: blastn -query GCF_026344105.1_ASM2634410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec35446b-ac13-4b26-9b09-2d384351693c/dqc_reference/reference_markers.fasta -out GCF_026344105.1_ASM2634410v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:05,862] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:05,864] [INFO] Selected 11 target genomes.
[2024-01-25 19:54:05,865] [INFO] Target genome list was writen to GCF_026344105.1_ASM2634410v1_genomic.fna/target_genomes.txt
[2024-01-25 19:54:05,879] [INFO] Task started: fastANI
[2024-01-25 19:54:05,879] [INFO] Running command: fastANI --query /var/lib/cwl/stg44ac0527-a191-49c0-afec-db61879a82de/GCF_026344105.1_ASM2634410v1_genomic.fna.gz --refList GCF_026344105.1_ASM2634410v1_genomic.fna/target_genomes.txt --output GCF_026344105.1_ASM2634410v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:54:15,357] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:15,357] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec35446b-ac13-4b26-9b09-2d384351693c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:54:15,357] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec35446b-ac13-4b26-9b09-2d384351693c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:54:15,366] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:54:15,366] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:54:15,366] [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 faecalis subsp. faecalis	strain=NBRC 13111	GCA_001748345.1	32001	511	type	True	93.2756	1136	1394	95	below_threshold
Alcaligenes faecalis	strain=DSM 30030	GCA_002443155.1	511	511	type	True	93.2455	1151	1394	95	below_threshold
Alcaligenes faecalis	strain=ATCC 8750	GCA_001298815.1	511	511	type	True	93.2381	1141	1394	95	below_threshold
Alcaligenes faecalis subsp. faecalis	strain=NBRC 13111	GCA_000739855.1	32001	511	type	True	93.2345	1146	1394	95	below_threshold
Alcaligenes ammonioxydans	strain=HO-1	GCA_019343455.1	2582914	2582914	type	True	87.27	1029	1394	95	below_threshold
Alcaligenes pakistanensis	strain=KCTC 42083	GCA_014652815.1	1482717	1482717	type	True	86.766	1090	1394	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	77.7879	195	1394	95	below_threshold
Pusillimonas faecipullorum	strain=CC-YST705	GCA_020539505.1	2755040	2755040	type	True	77.1494	130	1394	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	76.9593	197	1394	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	76.711	187	1394	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	76.1719	67	1394	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:54:15,367] [INFO] DFAST Taxonomy check result was written to GCF_026344105.1_ASM2634410v1_genomic.fna/tc_result.tsv
[2024-01-25 19:54:15,368] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:54:15,368] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:54:15,368] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec35446b-ac13-4b26-9b09-2d384351693c/dqc_reference/checkm_data
[2024-01-25 19:54:15,369] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:54:15,409] [INFO] Task started: CheckM
[2024-01-25 19:54:15,410] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026344105.1_ASM2634410v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026344105.1_ASM2634410v1_genomic.fna/checkm_input GCF_026344105.1_ASM2634410v1_genomic.fna/checkm_result
[2024-01-25 19:54:54,497] [INFO] Task succeeded: CheckM
[2024-01-25 19:54:54,498] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:54:54,516] [INFO] ===== Completeness check finished =====
[2024-01-25 19:54:54,516] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:54:54,516] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026344105.1_ASM2634410v1_genomic.fna/markers.fasta)
[2024-01-25 19:54:54,517] [INFO] Task started: Blastn
[2024-01-25 19:54:54,517] [INFO] Running command: blastn -query GCF_026344105.1_ASM2634410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec35446b-ac13-4b26-9b09-2d384351693c/dqc_reference/reference_markers_gtdb.fasta -out GCF_026344105.1_ASM2634410v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:55,794] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:55,797] [INFO] Selected 5 target genomes.
[2024-01-25 19:54:55,797] [INFO] Target genome list was writen to GCF_026344105.1_ASM2634410v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:54:55,807] [INFO] Task started: fastANI
[2024-01-25 19:54:55,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg44ac0527-a191-49c0-afec-db61879a82de/GCF_026344105.1_ASM2634410v1_genomic.fna.gz --refList GCF_026344105.1_ASM2634410v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026344105.1_ASM2634410v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:55:01,089] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:01,094] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:55:01,094] [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_005311025.1	s__Alcaligenes phenolicus	96.2532	1195	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	97.79	96.15	0.91	0.86	11	conclusive
GCF_002443155.1	s__Alcaligenes faecalis	93.2455	1151	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	98.39	97.71	0.93	0.90	22	-
GCF_009497775.1	s__Alcaligenes faecalis_D	93.1485	1170	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003076515.1	s__Alcaligenes aquatilis	90.1258	1082	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	98.23	96.52	0.93	0.89	8	-
GCF_017377875.1	s__Alcaligenes sp017377875	89.4736	1136	1394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Alcaligenes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:55:01,096] [INFO] GTDB search result was written to GCF_026344105.1_ASM2634410v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:55:01,096] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:55:01,099] [INFO] DFAST_QC result json was written to GCF_026344105.1_ASM2634410v1_genomic.fna/dqc_result.json
[2024-01-25 19:55:01,099] [INFO] DFAST_QC completed!
[2024-01-25 19:55:01,099] [INFO] Total running time: 0h1m10s