[2024-01-24 12:53:55,412] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:55,415] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:55,415] [INFO] DQC Reference Directory: /var/lib/cwl/stgb259c8cd-6063-468c-90e2-3a364d72b290/dqc_reference
[2024-01-24 12:53:56,651] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:56,653] [INFO] Task started: Prodigal
[2024-01-24 12:53:56,654] [INFO] Running command: gunzip -c /var/lib/cwl/stgdfc40227-2cf9-422f-bd07-2aeee6c085b9/GCF_005818875.1_ASM581887v1_genomic.fna.gz | prodigal -d GCF_005818875.1_ASM581887v1_genomic.fna/cds.fna -a GCF_005818875.1_ASM581887v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:59,708] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:59,709] [INFO] Task started: HMMsearch
[2024-01-24 12:53:59,709] [INFO] Running command: hmmsearch --tblout GCF_005818875.1_ASM581887v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb259c8cd-6063-468c-90e2-3a364d72b290/dqc_reference/reference_markers.hmm GCF_005818875.1_ASM581887v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:59,936] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:59,937] [INFO] Found 6/6 markers.
[2024-01-24 12:53:59,960] [INFO] Query marker FASTA was written to GCF_005818875.1_ASM581887v1_genomic.fna/markers.fasta
[2024-01-24 12:53:59,960] [INFO] Task started: Blastn
[2024-01-24 12:53:59,960] [INFO] Running command: blastn -query GCF_005818875.1_ASM581887v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb259c8cd-6063-468c-90e2-3a364d72b290/dqc_reference/reference_markers.fasta -out GCF_005818875.1_ASM581887v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:00,586] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:00,590] [INFO] Selected 14 target genomes.
[2024-01-24 12:54:00,590] [INFO] Target genome list was writen to GCF_005818875.1_ASM581887v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:00,619] [INFO] Task started: fastANI
[2024-01-24 12:54:00,620] [INFO] Running command: fastANI --query /var/lib/cwl/stgdfc40227-2cf9-422f-bd07-2aeee6c085b9/GCF_005818875.1_ASM581887v1_genomic.fna.gz --refList GCF_005818875.1_ASM581887v1_genomic.fna/target_genomes.txt --output GCF_005818875.1_ASM581887v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:06,830] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:06,830] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb259c8cd-6063-468c-90e2-3a364d72b290/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:06,831] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb259c8cd-6063-468c-90e2-3a364d72b290/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:06,844] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:54:06,844] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:06,844] [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
Aliarcobacter cibarius	strain=DSM 17680	GCA_005818875.1	255507	255507	type	True	100.0	681	684	95	conclusive
Aliarcobacter cibarius	strain=LMG 21996	GCA_000522465.1	255507	255507	type	True	99.1457	635	684	95	conclusive
Aliarcobacter cibarius	strain=LMG 21996	GCA_013372265.1	255507	255507	type	True	99.1094	641	684	95	conclusive
Aliarcobacter faecis	strain=CCUG 66484	GCA_013201705.1	1564138	1564138	type	True	85.2097	528	684	95	below_threshold
Aliarcobacter faecis	strain=LMG 28519	GCA_024584135.1	1564138	1564138	type	True	85.1947	525	684	95	below_threshold
Aliarcobacter faecis	strain=AF1078	GCA_000585155.1	1564138	1564138	type	True	85.1755	534	684	95	below_threshold
Arcobacter vandammei	strain=LMG 31429	GCA_024583975.1	2782243	2782243	type	True	83.9696	488	684	95	below_threshold
Arcobacter vandammei	strain=R-73987	GCA_016106035.1	2782243	2782243	type	True	83.9421	487	684	95	below_threshold
Aliarcobacter thereius	strain=LMG 24486	GCA_004214815.1	544718	544718	type	True	81.4478	388	684	95	below_threshold
Aliarcobacter thereius	strain=DSM 23385	GCA_005818985.1	544718	544718	type	True	81.4147	386	684	95	below_threshold
Aliarcobacter thereius	strain=LMG 24486	GCA_024584025.1	544718	544718	type	True	81.3392	402	684	95	below_threshold
Aliarcobacter thereius	strain=LMG 24486	GCA_001695395.1	544718	544718	type	True	81.2828	407	684	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:06,847] [INFO] DFAST Taxonomy check result was written to GCF_005818875.1_ASM581887v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:06,848] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:06,848] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:06,848] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb259c8cd-6063-468c-90e2-3a364d72b290/dqc_reference/checkm_data
[2024-01-24 12:54:06,850] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:06,875] [INFO] Task started: CheckM
[2024-01-24 12:54:06,876] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005818875.1_ASM581887v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005818875.1_ASM581887v1_genomic.fna/checkm_input GCF_005818875.1_ASM581887v1_genomic.fna/checkm_result
[2024-01-24 12:54:24,631] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:24,634] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:24,664] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:24,665] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:24,665] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005818875.1_ASM581887v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:24,665] [INFO] Task started: Blastn
[2024-01-24 12:54:24,665] [INFO] Running command: blastn -query GCF_005818875.1_ASM581887v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb259c8cd-6063-468c-90e2-3a364d72b290/dqc_reference/reference_markers_gtdb.fasta -out GCF_005818875.1_ASM581887v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:25,675] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:25,678] [INFO] Selected 12 target genomes.
[2024-01-24 12:54:25,679] [INFO] Target genome list was writen to GCF_005818875.1_ASM581887v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:25,691] [INFO] Task started: fastANI
[2024-01-24 12:54:25,691] [INFO] Running command: fastANI --query /var/lib/cwl/stgdfc40227-2cf9-422f-bd07-2aeee6c085b9/GCF_005818875.1_ASM581887v1_genomic.fna.gz --refList GCF_005818875.1_ASM581887v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005818875.1_ASM581887v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:32,198] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:32,209] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:32,209] [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_013372265.1	s__Aliarcobacter cibarius	99.1479	640	684	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.17	98.67	0.91	0.84	6	conclusive
GCF_013201705.1	s__Aliarcobacter faecis	85.243	527	684	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.88	99.77	0.97	0.95	3	-
GCF_016106035.1	s__Aliarcobacter sp016106035	83.9229	488	684	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014352935.1	s__Aliarcobacter cryaerophilus_A	83.4566	439	684	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.54	96.41	0.86	0.82	23	-
GCA_017996075.1	s__Aliarcobacter sp017996075	83.0416	204	684	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.83	97.42	0.84	0.83	6	-
GCF_003660105.1	s__Aliarcobacter cryaerophilus	82.8754	439	684	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.99	99.99	1.00	0.99	3	-
GCF_002993025.1	s__Aliarcobacter cryaerophilus_B	82.8122	426	684	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.88	97.88	0.90	0.90	2	-
GCF_003355515.1	s__Aliarcobacter trophiarum	81.5426	411	684	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.76	99.53	0.96	0.92	3	-
GCF_004299785.2	s__Aliarcobacter porcinus	81.4884	394	684	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.76	98.06	0.91	0.88	6	-
GCF_004214815.1	s__Aliarcobacter thereius	81.3627	392	684	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.14	98.62	0.93	0.89	8	-
GCF_013201725.1	s__Aliarcobacter defluvii	80.409	444	684	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.85	98.15	0.93	0.88	4	-
GCF_013177675.1	s__Aliarcobacter acticola	79.6442	373	684	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:32,211] [INFO] GTDB search result was written to GCF_005818875.1_ASM581887v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:32,212] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:32,215] [INFO] DFAST_QC result json was written to GCF_005818875.1_ASM581887v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:32,216] [INFO] DFAST_QC completed!
[2024-01-24 12:54:32,216] [INFO] Total running time: 0h0m37s