[2024-01-24 13:55:19,893] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:19,901] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:19,902] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e4ac5f6-8575-4980-a1fd-310b373ba27f/dqc_reference
[2024-01-24 13:55:21,250] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:21,251] [INFO] Task started: Prodigal
[2024-01-24 13:55:21,251] [INFO] Running command: gunzip -c /var/lib/cwl/stg83de0210-f6e4-4c19-84ef-804c500adbcc/GCF_013201705.1_ASM1320170v1_genomic.fna.gz | prodigal -d GCF_013201705.1_ASM1320170v1_genomic.fna/cds.fna -a GCF_013201705.1_ASM1320170v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:25,173] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:25,173] [INFO] Task started: HMMsearch
[2024-01-24 13:55:25,173] [INFO] Running command: hmmsearch --tblout GCF_013201705.1_ASM1320170v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e4ac5f6-8575-4980-a1fd-310b373ba27f/dqc_reference/reference_markers.hmm GCF_013201705.1_ASM1320170v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:25,435] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:25,436] [INFO] Found 6/6 markers.
[2024-01-24 13:55:25,459] [INFO] Query marker FASTA was written to GCF_013201705.1_ASM1320170v1_genomic.fna/markers.fasta
[2024-01-24 13:55:25,460] [INFO] Task started: Blastn
[2024-01-24 13:55:25,460] [INFO] Running command: blastn -query GCF_013201705.1_ASM1320170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e4ac5f6-8575-4980-a1fd-310b373ba27f/dqc_reference/reference_markers.fasta -out GCF_013201705.1_ASM1320170v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:26,134] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:26,137] [INFO] Selected 10 target genomes.
[2024-01-24 13:55:26,137] [INFO] Target genome list was writen to GCF_013201705.1_ASM1320170v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:26,154] [INFO] Task started: fastANI
[2024-01-24 13:55:26,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg83de0210-f6e4-4c19-84ef-804c500adbcc/GCF_013201705.1_ASM1320170v1_genomic.fna.gz --refList GCF_013201705.1_ASM1320170v1_genomic.fna/target_genomes.txt --output GCF_013201705.1_ASM1320170v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:32,318] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:32,318] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e4ac5f6-8575-4980-a1fd-310b373ba27f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:32,319] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e4ac5f6-8575-4980-a1fd-310b373ba27f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:32,332] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:55:32,332] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:32,332] [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 faecis	strain=CCUG 66484	GCA_013201705.1	1564138	1564138	type	True	100.0	809	815	95	conclusive
Aliarcobacter faecis	strain=AF1078	GCA_000585155.1	1564138	1564138	type	True	99.9729	793	815	95	conclusive
Aliarcobacter faecis	strain=LMG 28519	GCA_024584135.1	1564138	1564138	type	True	99.9527	764	815	95	conclusive
Arcobacter vandammei	strain=R-73987	GCA_016106035.1	2782243	2782243	type	True	86.0598	540	815	95	below_threshold
Arcobacter vandammei	strain=LMG 31429	GCA_024583975.1	2782243	2782243	type	True	86.0502	539	815	95	below_threshold
Aliarcobacter cibarius	strain=DSM 17680	GCA_005818875.1	255507	255507	type	True	85.353	521	815	95	below_threshold
Aliarcobacter cibarius	strain=LMG 21996	GCA_000522465.1	255507	255507	type	True	85.2949	538	815	95	below_threshold
Aliarcobacter cibarius	strain=LMG 21996	GCA_013372265.1	255507	255507	type	True	85.1959	559	815	95	below_threshold
Aliarcobacter vitoriensis	strain=CECT 9230	GCA_003316695.1	2011099	2011099	type	True	83.1549	509	815	95	below_threshold
Aliarcobacter vitoriensis	strain=LMG 30050	GCA_024583985.1	2011099	2011099	type	True	83.1522	511	815	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:32,337] [INFO] DFAST Taxonomy check result was written to GCF_013201705.1_ASM1320170v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:32,338] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:32,338] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:32,338] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e4ac5f6-8575-4980-a1fd-310b373ba27f/dqc_reference/checkm_data
[2024-01-24 13:55:32,339] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:32,371] [INFO] Task started: CheckM
[2024-01-24 13:55:32,372] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013201705.1_ASM1320170v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013201705.1_ASM1320170v1_genomic.fna/checkm_input GCF_013201705.1_ASM1320170v1_genomic.fna/checkm_result
[2024-01-24 13:55:52,062] [INFO] Task succeeded: CheckM
[2024-01-24 13:55:52,063] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:55:52,081] [INFO] ===== Completeness check finished =====
[2024-01-24 13:55:52,081] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:55:52,082] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013201705.1_ASM1320170v1_genomic.fna/markers.fasta)
[2024-01-24 13:55:52,082] [INFO] Task started: Blastn
[2024-01-24 13:55:52,083] [INFO] Running command: blastn -query GCF_013201705.1_ASM1320170v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e4ac5f6-8575-4980-a1fd-310b373ba27f/dqc_reference/reference_markers_gtdb.fasta -out GCF_013201705.1_ASM1320170v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:52,898] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:52,902] [INFO] Selected 14 target genomes.
[2024-01-24 13:55:52,902] [INFO] Target genome list was writen to GCF_013201705.1_ASM1320170v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:55:52,914] [INFO] Task started: fastANI
[2024-01-24 13:55:52,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg83de0210-f6e4-4c19-84ef-804c500adbcc/GCF_013201705.1_ASM1320170v1_genomic.fna.gz --refList GCF_013201705.1_ASM1320170v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013201705.1_ASM1320170v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:00,789] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:00,801] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:00,802] [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_013201705.1	s__Aliarcobacter faecis	100.0	810	815	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.88	99.77	0.97	0.95	3	conclusive
GCF_016106035.1	s__Aliarcobacter sp016106035	86.0805	539	815	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013372265.1	s__Aliarcobacter cibarius	85.2233	557	815	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.17	98.67	0.91	0.84	6	-
GCF_003660105.1	s__Aliarcobacter cryaerophilus	83.8648	498	815	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.99	99.99	1.00	0.99	3	-
GCA_017996075.1	s__Aliarcobacter sp017996075	83.7377	224	815	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	83.4671	455	815	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.76	99.53	0.96	0.92	3	-
GCF_013201625.1	s__Aliarcobacter lanthieri	83.3095	521	815	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.15	95.77	0.93	0.89	6	-
GCF_002993025.1	s__Aliarcobacter cryaerophilus_B	83.274	475	815	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.88	97.88	0.90	0.90	2	-
GCA_003316695.1	s__Aliarcobacter sp003316695	83.1539	509	815	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.67	97.67	0.88	0.88	2	-
GCF_900187115.1	s__Aliarcobacter butzleri	82.3055	488	815	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.53	96.98	0.89	0.81	50	-
GCF_004299785.2	s__Aliarcobacter porcinus	82.237	448	815	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	82.1729	440	815	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	82.0746	452	815	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	80.2577	374	815	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.13	99.13	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:00,804] [INFO] GTDB search result was written to GCF_013201705.1_ASM1320170v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:00,804] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:00,808] [INFO] DFAST_QC result json was written to GCF_013201705.1_ASM1320170v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:00,809] [INFO] DFAST_QC completed!
[2024-01-24 13:56:00,809] [INFO] Total running time: 0h0m41s