[2024-01-24 15:10:48,139] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:48,141] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:48,141] [INFO] DQC Reference Directory: /var/lib/cwl/stgca884453-6f8f-497f-b3a5-91930d4cb015/dqc_reference
[2024-01-24 15:10:51,754] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:51,803] [INFO] Task started: Prodigal
[2024-01-24 15:10:51,805] [INFO] Running command: gunzip -c /var/lib/cwl/stg20a4dc82-41b0-4220-b9fc-b82e020b7685/GCF_002993025.1_ASM299302v1_genomic.fna.gz | prodigal -d GCF_002993025.1_ASM299302v1_genomic.fna/cds.fna -a GCF_002993025.1_ASM299302v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:55,081] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:55,081] [INFO] Task started: HMMsearch
[2024-01-24 15:10:55,081] [INFO] Running command: hmmsearch --tblout GCF_002993025.1_ASM299302v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca884453-6f8f-497f-b3a5-91930d4cb015/dqc_reference/reference_markers.hmm GCF_002993025.1_ASM299302v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:55,438] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:55,440] [INFO] Found 6/6 markers.
[2024-01-24 15:10:55,477] [INFO] Query marker FASTA was written to GCF_002993025.1_ASM299302v1_genomic.fna/markers.fasta
[2024-01-24 15:10:55,479] [INFO] Task started: Blastn
[2024-01-24 15:10:55,479] [INFO] Running command: blastn -query GCF_002993025.1_ASM299302v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca884453-6f8f-497f-b3a5-91930d4cb015/dqc_reference/reference_markers.fasta -out GCF_002993025.1_ASM299302v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:59,266] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:59,270] [INFO] Selected 7 target genomes.
[2024-01-24 15:10:59,271] [INFO] Target genome list was writen to GCF_002993025.1_ASM299302v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:59,282] [INFO] Task started: fastANI
[2024-01-24 15:10:59,282] [INFO] Running command: fastANI --query /var/lib/cwl/stg20a4dc82-41b0-4220-b9fc-b82e020b7685/GCF_002993025.1_ASM299302v1_genomic.fna.gz --refList GCF_002993025.1_ASM299302v1_genomic.fna/target_genomes.txt --output GCF_002993025.1_ASM299302v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:02,868] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:02,868] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca884453-6f8f-497f-b3a5-91930d4cb015/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:02,869] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca884453-6f8f-497f-b3a5-91930d4cb015/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:02,882] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:11:02,882] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:11:02,882] [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 cryaerophilus	strain=ATCC 43158	GCA_003660105.1	28198	28198	suspected-type	True	94.1435	554	667	95	below_threshold
Aliarcobacter cryaerophilus	strain=LMG 9904	GCA_006165035.1	28198	28198	suspected-type	True	94.1002	551	667	95	below_threshold
Aliarcobacter cryaerophilus	strain=LMG 24291	GCA_002992955.1	28198	28198	suspected-type	True	94.0892	536	667	95	below_threshold
Aliarcobacter trophiarum	strain=LMG 25534	GCA_024584015.1	708186	708186	type	True	86.4518	483	667	95	below_threshold
Aliarcobacter trophiarum	strain=LMG 25534	GCA_003355515.1	708186	708186	type	True	86.2543	511	667	95	below_threshold
Aliarcobacter skirrowii	strain=LMG 6621	GCA_024584055.1	28200	28200	type	True	85.7531	452	667	95	below_threshold
Aliarcobacter skirrowii	strain=LMG 6621	GCA_004115735.1	28200	28200	type	True	85.7002	454	667	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:02,886] [INFO] DFAST Taxonomy check result was written to GCF_002993025.1_ASM299302v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:02,886] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:02,886] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:02,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca884453-6f8f-497f-b3a5-91930d4cb015/dqc_reference/checkm_data
[2024-01-24 15:11:02,888] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:02,915] [INFO] Task started: CheckM
[2024-01-24 15:11:02,915] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002993025.1_ASM299302v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002993025.1_ASM299302v1_genomic.fna/checkm_input GCF_002993025.1_ASM299302v1_genomic.fna/checkm_result
[2024-01-24 15:11:26,739] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:26,740] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:26,766] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:26,769] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:26,771] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002993025.1_ASM299302v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:26,772] [INFO] Task started: Blastn
[2024-01-24 15:11:26,772] [INFO] Running command: blastn -query GCF_002993025.1_ASM299302v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgca884453-6f8f-497f-b3a5-91930d4cb015/dqc_reference/reference_markers_gtdb.fasta -out GCF_002993025.1_ASM299302v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:28,383] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:28,387] [INFO] Selected 9 target genomes.
[2024-01-24 15:11:28,387] [INFO] Target genome list was writen to GCF_002993025.1_ASM299302v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:28,397] [INFO] Task started: fastANI
[2024-01-24 15:11:28,397] [INFO] Running command: fastANI --query /var/lib/cwl/stg20a4dc82-41b0-4220-b9fc-b82e020b7685/GCF_002993025.1_ASM299302v1_genomic.fna.gz --refList GCF_002993025.1_ASM299302v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002993025.1_ASM299302v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:33,113] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:33,131] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:33,131] [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_002993025.1	s__Aliarcobacter cryaerophilus_B	100.0	665	667	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.88	97.88	0.90	0.90	2	conclusive
GCF_003660105.1	s__Aliarcobacter cryaerophilus	94.1435	554	667	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.99	99.99	1.00	0.99	3	-
GCF_014352935.1	s__Aliarcobacter cryaerophilus_A	92.7297	547	667	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	92.6441	227	667	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.83	97.42	0.84	0.83	6	-
GCF_003355515.1	s__Aliarcobacter trophiarum	86.2543	511	667	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.76	99.53	0.96	0.92	3	-
GCF_003544835.1	s__Aliarcobacter skirrowii	85.741	457	667	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.32	95.07	0.91	0.85	16	-
GCF_013201705.1	s__Aliarcobacter faecis	83.3412	472	667	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.88	99.77	0.97	0.95	3	-
GCF_004214815.1	s__Aliarcobacter thereius	82.1891	433	667	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.14	98.62	0.93	0.89	8	-
GCF_003063295.1	s__Aliarcobacter lacus	81.1598	421	667	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 15:11:33,133] [INFO] GTDB search result was written to GCF_002993025.1_ASM299302v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:33,134] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:33,139] [INFO] DFAST_QC result json was written to GCF_002993025.1_ASM299302v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:33,139] [INFO] DFAST_QC completed!
[2024-01-24 15:11:33,139] [INFO] Total running time: 0h0m45s