[2024-01-25 18:07:35,527] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:07:35,528] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:07:35,528] [INFO] DQC Reference Directory: /var/lib/cwl/stg7521f05f-5829-4a4e-bd4b-111cf78e67a1/dqc_reference
[2024-01-25 18:07:36,684] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:07:36,685] [INFO] Task started: Prodigal
[2024-01-25 18:07:36,685] [INFO] Running command: gunzip -c /var/lib/cwl/stg6479c19d-194f-4152-93c6-ba9b720b0a41/GCF_013201825.1_ASM1320182v1_genomic.fna.gz | prodigal -d GCF_013201825.1_ASM1320182v1_genomic.fna/cds.fna -a GCF_013201825.1_ASM1320182v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:07:41,439] [INFO] Task succeeded: Prodigal
[2024-01-25 18:07:41,439] [INFO] Task started: HMMsearch
[2024-01-25 18:07:41,439] [INFO] Running command: hmmsearch --tblout GCF_013201825.1_ASM1320182v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7521f05f-5829-4a4e-bd4b-111cf78e67a1/dqc_reference/reference_markers.hmm GCF_013201825.1_ASM1320182v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:07:41,671] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:07:41,672] [INFO] Found 6/6 markers.
[2024-01-25 18:07:41,699] [INFO] Query marker FASTA was written to GCF_013201825.1_ASM1320182v1_genomic.fna/markers.fasta
[2024-01-25 18:07:41,700] [INFO] Task started: Blastn
[2024-01-25 18:07:41,700] [INFO] Running command: blastn -query GCF_013201825.1_ASM1320182v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7521f05f-5829-4a4e-bd4b-111cf78e67a1/dqc_reference/reference_markers.fasta -out GCF_013201825.1_ASM1320182v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:42,251] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:42,256] [INFO] Selected 13 target genomes.
[2024-01-25 18:07:42,256] [INFO] Target genome list was writen to GCF_013201825.1_ASM1320182v1_genomic.fna/target_genomes.txt
[2024-01-25 18:07:42,279] [INFO] Task started: fastANI
[2024-01-25 18:07:42,279] [INFO] Running command: fastANI --query /var/lib/cwl/stg6479c19d-194f-4152-93c6-ba9b720b0a41/GCF_013201825.1_ASM1320182v1_genomic.fna.gz --refList GCF_013201825.1_ASM1320182v1_genomic.fna/target_genomes.txt --output GCF_013201825.1_ASM1320182v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:07:50,008] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:50,008] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7521f05f-5829-4a4e-bd4b-111cf78e67a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:07:50,009] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7521f05f-5829-4a4e-bd4b-111cf78e67a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:07:50,020] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:07:50,020] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:07:50,020] [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
Halarcobacter ebronensis	strain=LMG 27922	GCA_013201825.1	1462615	1462615	type	True	100.0	1050	1056	95	conclusive
Halarcobacter ebronensis	strain=CECT 8441	GCA_004116565.1	1462615	1462615	type	True	99.9744	1016	1056	95	conclusive
Halarcobacter anaerophilus	strain=DSM 24636	GCA_006459125.1	877500	877500	type	True	80.3471	610	1056	95	below_threshold
[Halarcobacter] arenosus	strain=CAU 1517	GCA_005771535.1	2576037	2576037	type	True	80.1985	503	1056	95	below_threshold
Halarcobacter anaerophilus	strain=DSM 24636	GCA_004116345.1	877500	877500	type	True	80.1938	607	1056	95	below_threshold
Halarcobacter bivalviorum	strain=LMG 26154	GCA_003346815.1	663364	663364	type	True	80.1161	490	1056	95	below_threshold
Malaciobacter molluscorum	strain=CECT 7696	GCA_003544935.1	1032072	1032072	type	True	79.4058	435	1056	95	below_threshold
Malaciobacter molluscorum	strain=F98-3	GCA_002701265.1	1032072	1032072	type	True	79.2764	426	1056	95	below_threshold
Arcobacter nitrofigilis	strain=DSM 7299	GCA_000092245.1	28199	28199	type	True	78.9529	433	1056	95	below_threshold
Aliarcobacter butzleri	strain=RM4018	GCA_000014025.1	28197	28197	type	True	78.9075	363	1056	95	below_threshold
Arcobacter cloacae	strain=LMG 26153	GCA_013201935.1	1054034	1054034	type	True	78.777	408	1056	95	below_threshold
Arcobacter cloacae	strain=CECT 7834	GCA_004115805.1	1054034	1054034	type	True	78.6074	389	1056	95	below_threshold
Aliarcobacter skirrowii	strain=LMG 6621	GCA_024584055.1	28200	28200	type	True	78.5957	294	1056	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:07:50,023] [INFO] DFAST Taxonomy check result was written to GCF_013201825.1_ASM1320182v1_genomic.fna/tc_result.tsv
[2024-01-25 18:07:50,023] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:07:50,024] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:07:50,024] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7521f05f-5829-4a4e-bd4b-111cf78e67a1/dqc_reference/checkm_data
[2024-01-25 18:07:50,025] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:07:50,062] [INFO] Task started: CheckM
[2024-01-25 18:07:50,063] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013201825.1_ASM1320182v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013201825.1_ASM1320182v1_genomic.fna/checkm_input GCF_013201825.1_ASM1320182v1_genomic.fna/checkm_result
[2024-01-25 18:08:09,923] [INFO] Task succeeded: CheckM
[2024-01-25 18:08:09,924] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:08:09,945] [INFO] ===== Completeness check finished =====
[2024-01-25 18:08:09,946] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:08:09,946] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013201825.1_ASM1320182v1_genomic.fna/markers.fasta)
[2024-01-25 18:08:09,946] [INFO] Task started: Blastn
[2024-01-25 18:08:09,946] [INFO] Running command: blastn -query GCF_013201825.1_ASM1320182v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7521f05f-5829-4a4e-bd4b-111cf78e67a1/dqc_reference/reference_markers_gtdb.fasta -out GCF_013201825.1_ASM1320182v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:10,709] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:10,711] [INFO] Selected 16 target genomes.
[2024-01-25 18:08:10,712] [INFO] Target genome list was writen to GCF_013201825.1_ASM1320182v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:08:10,726] [INFO] Task started: fastANI
[2024-01-25 18:08:10,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg6479c19d-194f-4152-93c6-ba9b720b0a41/GCF_013201825.1_ASM1320182v1_genomic.fna.gz --refList GCF_013201825.1_ASM1320182v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013201825.1_ASM1320182v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:08:20,477] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:20,487] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:08:20,487] [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_013201825.1	s__Halarcobacter ebronensis	100.0	1050	1056	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	98.25	96.51	0.95	0.90	3	conclusive
GCF_006459125.1	s__Halarcobacter anaerophilus	80.3464	613	1056	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	98.86	97.73	0.95	0.89	3	-
GCA_003252105.1	s__Halarcobacter sp003252105	80.2667	484	1056	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771535.1	s__Halarcobacter arenosus	80.1904	503	1056	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003346815.1	s__Halarcobacter bivalviorum	80.0986	491	1056	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	98.23	96.46	0.96	0.92	3	-
GCA_004118855.1	s__Halarcobacter sp004118855	79.8949	485	1056	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004116455.1	s__Halarcobacter sp004116455	79.5427	455	1056	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	96.86	96.86	0.84	0.84	2	-
GCA_013373175.1	s__Halarcobacter sp013373175	79.5131	461	1056	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001895145.1	s__Halarcobacter sp001895145	79.4254	485	1056	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003544935.1	s__Malaciobacter molluscorum	79.3959	436	1056	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	99.44	98.88	0.96	0.91	3	-
GCF_003063295.1	s__Aliarcobacter lacus	79.0009	331	1056	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002869535.1	s__Arcobacter sp002869535	78.9778	363	1056	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Arcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092245.1	s__Arcobacter nitrofigilis	78.9476	429	1056	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Arcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900187115.1	s__Aliarcobacter butzleri	78.894	359	1056	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.53	96.98	0.89	0.81	50	-
GCF_013201935.1	s__Aliarcobacter cloacae	78.7977	406	1056	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.96	95.91	0.93	0.87	3	-
GCF_003660105.1	s__Aliarcobacter cryaerophilus	78.5454	278	1056	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.99	99.99	1.00	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:08:20,489] [INFO] GTDB search result was written to GCF_013201825.1_ASM1320182v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:08:20,489] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:08:20,493] [INFO] DFAST_QC result json was written to GCF_013201825.1_ASM1320182v1_genomic.fna/dqc_result.json
[2024-01-25 18:08:20,493] [INFO] DFAST_QC completed!
[2024-01-25 18:08:20,493] [INFO] Total running time: 0h0m45s