[2024-01-24 13:02:06,342] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:02:06,344] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:02:06,345] [INFO] DQC Reference Directory: /var/lib/cwl/stg7cbbc2b0-87ff-4ddf-a0ab-43176e12f585/dqc_reference
[2024-01-24 13:02:07,843] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:02:07,844] [INFO] Task started: Prodigal
[2024-01-24 13:02:07,844] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf444bfe-82bb-4a6d-8963-369cb9f43de5/GCF_024584095.1_ASM2458409v1_genomic.fna.gz | prodigal -d GCF_024584095.1_ASM2458409v1_genomic.fna/cds.fna -a GCF_024584095.1_ASM2458409v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:11,396] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:11,397] [INFO] Task started: HMMsearch
[2024-01-24 13:02:11,397] [INFO] Running command: hmmsearch --tblout GCF_024584095.1_ASM2458409v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7cbbc2b0-87ff-4ddf-a0ab-43176e12f585/dqc_reference/reference_markers.hmm GCF_024584095.1_ASM2458409v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:11,655] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:11,658] [INFO] Found 6/6 markers.
[2024-01-24 13:02:11,685] [INFO] Query marker FASTA was written to GCF_024584095.1_ASM2458409v1_genomic.fna/markers.fasta
[2024-01-24 13:02:11,686] [INFO] Task started: Blastn
[2024-01-24 13:02:11,686] [INFO] Running command: blastn -query GCF_024584095.1_ASM2458409v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cbbc2b0-87ff-4ddf-a0ab-43176e12f585/dqc_reference/reference_markers.fasta -out GCF_024584095.1_ASM2458409v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:12,378] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:12,381] [INFO] Selected 7 target genomes.
[2024-01-24 13:02:12,382] [INFO] Target genome list was writen to GCF_024584095.1_ASM2458409v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:12,385] [INFO] Task started: fastANI
[2024-01-24 13:02:12,385] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf444bfe-82bb-4a6d-8963-369cb9f43de5/GCF_024584095.1_ASM2458409v1_genomic.fna.gz --refList GCF_024584095.1_ASM2458409v1_genomic.fna/target_genomes.txt --output GCF_024584095.1_ASM2458409v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:16,945] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:16,945] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7cbbc2b0-87ff-4ddf-a0ab-43176e12f585/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:16,946] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7cbbc2b0-87ff-4ddf-a0ab-43176e12f585/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:16,960] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:02:16,960] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:16,960] [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 lanthieri	strain=LMG 28516	GCA_024584095.1	1355374	1355374	type	True	100.0	730	731	95	conclusive
Aliarcobacter lanthieri	strain=LMG 28516	GCA_013201625.1	1355374	1355374	type	True	99.9998	730	731	95	conclusive
Aliarcobacter lanthieri	strain=AF1440	GCA_000585115.1	1355374	1355374	type	True	99.9966	726	731	95	conclusive
Aliarcobacter vitoriensis	strain=CECT 9230	GCA_003316695.1	2011099	2011099	type	True	88.104	597	731	95	below_threshold
Aliarcobacter vitoriensis	strain=LMG 30050	GCA_024583985.1	2011099	2011099	type	True	88.0884	598	731	95	below_threshold
Aliarcobacter faecis	strain=AF1078	GCA_000585155.1	1564138	1564138	type	True	83.1163	507	731	95	below_threshold
Aliarcobacter faecis	strain=CCUG 66484	GCA_013201705.1	1564138	1564138	type	True	83.1128	507	731	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:16,962] [INFO] DFAST Taxonomy check result was written to GCF_024584095.1_ASM2458409v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:16,963] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:16,963] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:16,963] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7cbbc2b0-87ff-4ddf-a0ab-43176e12f585/dqc_reference/checkm_data
[2024-01-24 13:02:16,965] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:16,996] [INFO] Task started: CheckM
[2024-01-24 13:02:16,996] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024584095.1_ASM2458409v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024584095.1_ASM2458409v1_genomic.fna/checkm_input GCF_024584095.1_ASM2458409v1_genomic.fna/checkm_result
[2024-01-24 13:02:36,041] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:36,042] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:36,061] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:36,061] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:36,062] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024584095.1_ASM2458409v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:36,062] [INFO] Task started: Blastn
[2024-01-24 13:02:36,062] [INFO] Running command: blastn -query GCF_024584095.1_ASM2458409v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cbbc2b0-87ff-4ddf-a0ab-43176e12f585/dqc_reference/reference_markers_gtdb.fasta -out GCF_024584095.1_ASM2458409v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:37,008] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:37,011] [INFO] Selected 14 target genomes.
[2024-01-24 13:02:37,011] [INFO] Target genome list was writen to GCF_024584095.1_ASM2458409v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:37,023] [INFO] Task started: fastANI
[2024-01-24 13:02:37,023] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf444bfe-82bb-4a6d-8963-369cb9f43de5/GCF_024584095.1_ASM2458409v1_genomic.fna.gz --refList GCF_024584095.1_ASM2458409v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024584095.1_ASM2458409v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:44,332] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:44,348] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:44,348] [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_013201625.1	s__Aliarcobacter lanthieri	99.9998	730	731	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.15	95.77	0.93	0.89	6	conclusive
GCA_003316695.1	s__Aliarcobacter sp003316695	88.104	597	731	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.67	97.67	0.88	0.88	2	-
GCF_013201705.1	s__Aliarcobacter faecis	83.1214	506	731	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.88	99.77	0.97	0.95	3	-
GCF_900187115.1	s__Aliarcobacter butzleri	82.5487	491	731	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.53	96.98	0.89	0.81	50	-
GCF_003063295.1	s__Aliarcobacter lacus	82.5401	482	731	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003660105.1	s__Aliarcobacter cryaerophilus	82.5384	469	731	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	82.4811	465	731	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.88	97.88	0.90	0.90	2	-
GCF_014352935.1	s__Aliarcobacter cryaerophilus_A	82.3906	472	731	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.54	96.41	0.86	0.82	23	-
GCF_016106035.1	s__Aliarcobacter sp016106035	82.1206	451	731	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003355515.1	s__Aliarcobacter trophiarum	81.9406	446	731	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.76	99.53	0.96	0.92	3	-
GCF_004214815.1	s__Aliarcobacter thereius	81.7067	417	731	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.14	98.62	0.93	0.89	8	-
GCF_013372265.1	s__Aliarcobacter cibarius	81.6826	445	731	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.17	98.67	0.91	0.84	6	-
GCF_004299785.2	s__Aliarcobacter porcinus	81.5442	422	731	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.76	98.06	0.91	0.88	6	-
GCF_003544915.1	s__Aliarcobacter ellisii	80.7607	429	731	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.73	97.46	0.92	0.84	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:44,350] [INFO] GTDB search result was written to GCF_024584095.1_ASM2458409v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:44,351] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:44,356] [INFO] DFAST_QC result json was written to GCF_024584095.1_ASM2458409v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:44,357] [INFO] DFAST_QC completed!
[2024-01-24 13:02:44,357] [INFO] Total running time: 0h0m38s