[2024-01-24 13:36:30,990] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:30,992] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:30,992] [INFO] DQC Reference Directory: /var/lib/cwl/stg9fadbd25-bdbf-4835-8266-1274cfb43426/dqc_reference
[2024-01-24 13:36:32,289] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:32,290] [INFO] Task started: Prodigal
[2024-01-24 13:36:32,290] [INFO] Running command: gunzip -c /var/lib/cwl/stg25318329-cb44-4983-adb6-f21f90da41ab/GCF_013177675.1_ASM1317767v1_genomic.fna.gz | prodigal -d GCF_013177675.1_ASM1317767v1_genomic.fna/cds.fna -a GCF_013177675.1_ASM1317767v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:37,078] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:37,079] [INFO] Task started: HMMsearch
[2024-01-24 13:36:37,079] [INFO] Running command: hmmsearch --tblout GCF_013177675.1_ASM1317767v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9fadbd25-bdbf-4835-8266-1274cfb43426/dqc_reference/reference_markers.hmm GCF_013177675.1_ASM1317767v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:37,354] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:37,356] [INFO] Found 6/6 markers.
[2024-01-24 13:36:37,396] [INFO] Query marker FASTA was written to GCF_013177675.1_ASM1317767v1_genomic.fna/markers.fasta
[2024-01-24 13:36:37,397] [INFO] Task started: Blastn
[2024-01-24 13:36:37,397] [INFO] Running command: blastn -query GCF_013177675.1_ASM1317767v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fadbd25-bdbf-4835-8266-1274cfb43426/dqc_reference/reference_markers.fasta -out GCF_013177675.1_ASM1317767v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:38,033] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:38,037] [INFO] Selected 9 target genomes.
[2024-01-24 13:36:38,038] [INFO] Target genome list was writen to GCF_013177675.1_ASM1317767v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:38,054] [INFO] Task started: fastANI
[2024-01-24 13:36:38,054] [INFO] Running command: fastANI --query /var/lib/cwl/stg25318329-cb44-4983-adb6-f21f90da41ab/GCF_013177675.1_ASM1317767v1_genomic.fna.gz --refList GCF_013177675.1_ASM1317767v1_genomic.fna/target_genomes.txt --output GCF_013177675.1_ASM1317767v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:36:44,664] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:44,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9fadbd25-bdbf-4835-8266-1274cfb43426/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:36:44,666] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9fadbd25-bdbf-4835-8266-1274cfb43426/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:36:44,676] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:36:44,676] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:36:44,677] [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
Arcobacter acticola	strain=KCTC 52212	GCA_013177675.1	1849015	1849015	type	True	100.0	1005	1006	95	conclusive
Arcobacter venerupis	strain=LMG 26156	GCA_013201665.1	1054033	1054033	type	True	83.8988	651	1006	95	below_threshold
Arcobacter caeni	strain=RW17-10	GCA_003063245.1	1912877	1912877	type	True	83.8157	574	1006	95	below_threshold
Arcobacter suis	strain=CECT 7833	GCA_003544815.1	1278212	1278212	type	True	83.6805	608	1006	95	below_threshold
Arcobacter venerupis	strain=CECT7836	GCA_004023405.1	1054033	1054033	type	True	83.6393	638	1006	95	below_threshold
Arcobacter suis	strain=CECT7833	GCA_004023465.1	1278212	1278212	type	True	83.6151	594	1006	95	below_threshold
Arcobacter ellisii	strain=LMG 26155	GCA_003544915.1	913109	913109	type	True	83.3275	647	1006	95	below_threshold
Arcobacter ellisii	strain=CECT 7837	GCA_004115815.1	913109	913109	type	True	83.1761	615	1006	95	below_threshold
Arcobacter cloacae	strain=CECT 7834	GCA_004115805.1	1054034	1054034	type	True	82.6735	588	1006	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:36:44,681] [INFO] DFAST Taxonomy check result was written to GCF_013177675.1_ASM1317767v1_genomic.fna/tc_result.tsv
[2024-01-24 13:36:44,681] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:36:44,681] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:36:44,682] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9fadbd25-bdbf-4835-8266-1274cfb43426/dqc_reference/checkm_data
[2024-01-24 13:36:44,682] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:36:44,719] [INFO] Task started: CheckM
[2024-01-24 13:36:44,720] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013177675.1_ASM1317767v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013177675.1_ASM1317767v1_genomic.fna/checkm_input GCF_013177675.1_ASM1317767v1_genomic.fna/checkm_result
[2024-01-24 13:37:06,041] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:06,044] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:06,066] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:06,067] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:06,067] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013177675.1_ASM1317767v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:06,068] [INFO] Task started: Blastn
[2024-01-24 13:37:06,068] [INFO] Running command: blastn -query GCF_013177675.1_ASM1317767v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9fadbd25-bdbf-4835-8266-1274cfb43426/dqc_reference/reference_markers_gtdb.fasta -out GCF_013177675.1_ASM1317767v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:06,907] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:06,912] [INFO] Selected 10 target genomes.
[2024-01-24 13:37:06,912] [INFO] Target genome list was writen to GCF_013177675.1_ASM1317767v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:06,935] [INFO] Task started: fastANI
[2024-01-24 13:37:06,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg25318329-cb44-4983-adb6-f21f90da41ab/GCF_013177675.1_ASM1317767v1_genomic.fna.gz --refList GCF_013177675.1_ASM1317767v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013177675.1_ASM1317767v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:37:13,526] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:13,535] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:37:13,535] [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_013177675.1	s__Aliarcobacter acticola	100.0	1006	1006	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018816105.1	s__Aliarcobacter sp018816105	87.2889	621	1006	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017995775.1	s__Aliarcobacter sp017995775	84.1246	527	1006	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.13	99.13	0.84	0.84	2	-
GCF_013201665.1	s__Aliarcobacter venerupis	83.9037	652	1006	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003063245.1	s__Aliarcobacter caeni	83.7923	575	1006	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003544815.1	s__Aliarcobacter suis	83.6014	610	1006	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003544915.1	s__Aliarcobacter ellisii	83.34	650	1006	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.73	97.46	0.92	0.84	3	-
GCF_003667345.1	s__Poseidonibacter antarcticus	80.8799	504	1006	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861145.1	s__Poseidonibacter lekithochrous_A	80.653	512	1006	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:37:13,537] [INFO] GTDB search result was written to GCF_013177675.1_ASM1317767v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:37:13,537] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:37:13,541] [INFO] DFAST_QC result json was written to GCF_013177675.1_ASM1317767v1_genomic.fna/dqc_result.json
[2024-01-24 13:37:13,541] [INFO] DFAST_QC completed!
[2024-01-24 13:37:13,541] [INFO] Total running time: 0h0m43s