[2023-03-17 11:08:00,501] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:08:00,501] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:08:00,501] [INFO] DQC Reference Directory: /var/lib/cwl/stg02021541-e4bd-46b9-85b9-1bde571075d2/dqc_reference
[2023-03-17 11:08:01,579] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:08:01,579] [INFO] Task started: Prodigal
[2023-03-17 11:08:01,579] [INFO] Running command: cat /var/lib/cwl/stg180cac0d-9be8-47f7-83ca-8c86b239e7f8/OceanDNA-b13341.fa | prodigal -d OceanDNA-b13341/cds.fna -a OceanDNA-b13341/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:08:05,803] [INFO] Task succeeded: Prodigal
[2023-03-17 11:08:05,804] [INFO] Task started: HMMsearch
[2023-03-17 11:08:05,804] [INFO] Running command: hmmsearch --tblout OceanDNA-b13341/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02021541-e4bd-46b9-85b9-1bde571075d2/dqc_reference/reference_markers.hmm OceanDNA-b13341/protein.faa > /dev/null
[2023-03-17 11:08:05,955] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:08:05,956] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg180cac0d-9be8-47f7-83ca-8c86b239e7f8/OceanDNA-b13341.fa]
[2023-03-17 11:08:05,964] [INFO] Query marker FASTA was written to OceanDNA-b13341/markers.fasta
[2023-03-17 11:08:05,964] [INFO] Task started: Blastn
[2023-03-17 11:08:05,964] [INFO] Running command: blastn -query OceanDNA-b13341/markers.fasta -db /var/lib/cwl/stg02021541-e4bd-46b9-85b9-1bde571075d2/dqc_reference/reference_markers.fasta -out OceanDNA-b13341/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:08:06,480] [INFO] Task succeeded: Blastn
[2023-03-17 11:08:06,480] [INFO] Selected 18 target genomes.
[2023-03-17 11:08:06,481] [INFO] Target genome list was writen to OceanDNA-b13341/target_genomes.txt
[2023-03-17 11:08:06,490] [INFO] Task started: fastANI
[2023-03-17 11:08:06,490] [INFO] Running command: fastANI --query /var/lib/cwl/stg180cac0d-9be8-47f7-83ca-8c86b239e7f8/OceanDNA-b13341.fa --refList OceanDNA-b13341/target_genomes.txt --output OceanDNA-b13341/fastani_result.tsv --threads 1
[2023-03-17 11:08:12,990] [INFO] Task succeeded: fastANI
[2023-03-17 11:08:12,990] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02021541-e4bd-46b9-85b9-1bde571075d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:08:12,990] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02021541-e4bd-46b9-85b9-1bde571075d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:08:13,001] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:08:13,001] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:08:13,001] [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
Arcobacter venerupis	strain=LMG 26156	GCA_013201665.1	1054033	1054033	type	True	77.4498	67	266	95	below_threshold
Arcobacter venerupis	strain=CECT7836	GCA_004023405.1	1054033	1054033	type	True	77.3345	69	266	95	below_threshold
Arcobacter defluvii	strain=CECT 7697	GCA_004115775.1	873191	873191	type	True	77.1206	70	266	95	below_threshold
Aliarcobacter cryaerophilus	strain=LMG 24291	GCA_002992955.1	28198	28198	suspected-type	True	77.0413	63	266	95	below_threshold
Arcobacter ellisii	strain=CECT 7837	GCA_004115815.1	913109	913109	type	True	76.9586	75	266	95	below_threshold
Aliarcobacter thereius	strain=LMG 24486	GCA_001695395.1	544718	544718	type	True	76.9394	54	266	95	below_threshold
Aliarcobacter thereius	strain=LMG 24486	GCA_024584025.1	544718	544718	type	True	76.9394	54	266	95	below_threshold
Arcobacter ellisii	strain=LMG 26155	GCA_003544915.1	913109	913109	type	True	76.8932	74	266	95	below_threshold
Malaciobacter molluscorum	strain=F98-3	GCA_002701265.1	1032072	1032072	type	True	76.777	86	266	95	below_threshold
Malaciobacter molluscorum	strain=CECT 7696	GCA_003544935.1	1032072	1032072	type	True	76.7437	83	266	95	below_threshold
Halarcobacter ebronensis	strain=CECT 8441	GCA_004116565.1	1462615	1462615	type	True	76.735	69	266	95	below_threshold
Halarcobacter ebronensis	strain=LMG 27922	GCA_013201825.1	1462615	1462615	type	True	76.706	72	266	95	below_threshold
Aliarcobacter faecis	strain=LMG 28519	GCA_024584135.1	1564138	1564138	type	True	76.6966	69	266	95	below_threshold
Aliarcobacter faecis	strain=AF1078	GCA_000585155.1	1564138	1564138	type	True	76.6621	69	266	95	below_threshold
Aliarcobacter faecis	strain=CCUG 66484	GCA_013201705.1	1564138	1564138	type	True	76.5983	71	266	95	below_threshold
Aliarcobacter trophiarum	strain=LMG 25534	GCA_024584015.1	708186	708186	type	True	76.5349	59	266	95	below_threshold
Poseidonibacter lekithochrous	strain=DSM 100870	GCA_013283835.1	1904463	1904463	type	True	76.3094	72	266	95	below_threshold
Poseidonibacter lekithochrous	strain=LFT 1.7	GCA_001878855.1	1904463	1904463	type	True	76.2998	71	266	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:08:13,002] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13341/tc_result.tsv
[2023-03-17 11:08:13,002] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:08:13,002] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:08:13,002] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02021541-e4bd-46b9-85b9-1bde571075d2/dqc_reference/checkm_data
[2023-03-17 11:08:13,003] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:08:13,009] [INFO] Task started: CheckM
[2023-03-17 11:08:13,010] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13341/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13341/checkm_input OceanDNA-b13341/checkm_result
[2023-03-17 11:08:29,629] [INFO] Task succeeded: CheckM
[2023-03-17 11:08:29,629] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.72%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:08:29,631] [INFO] ===== Completeness check finished =====
[2023-03-17 11:08:29,631] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:08:29,631] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13341/markers.fasta)
[2023-03-17 11:08:29,631] [INFO] Task started: Blastn
[2023-03-17 11:08:29,631] [INFO] Running command: blastn -query OceanDNA-b13341/markers.fasta -db /var/lib/cwl/stg02021541-e4bd-46b9-85b9-1bde571075d2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13341/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:08:30,336] [INFO] Task succeeded: Blastn
[2023-03-17 11:08:30,337] [INFO] Selected 19 target genomes.
[2023-03-17 11:08:30,337] [INFO] Target genome list was writen to OceanDNA-b13341/target_genomes_gtdb.txt
[2023-03-17 11:08:30,549] [INFO] Task started: fastANI
[2023-03-17 11:08:30,549] [INFO] Running command: fastANI --query /var/lib/cwl/stg180cac0d-9be8-47f7-83ca-8c86b239e7f8/OceanDNA-b13341.fa --refList OceanDNA-b13341/target_genomes_gtdb.txt --output OceanDNA-b13341/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:08:37,376] [INFO] Task succeeded: fastANI
[2023-03-17 11:08:37,385] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:08:37,385] [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
GCA_015663165.1	s__CAIJNA01 sp015663165	77.5608	82	266	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__CAIJNA01	95.0	99.59	99.59	0.85	0.85	2	-
GCF_013201665.1	s__Aliarcobacter venerupis	77.4498	67	266	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	0.99	0.99	2	-
GCA_018662405.1	s__JADHTT01 sp018662405	77.4352	77	266	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__JADHTT01	95.0	99.77	99.69	0.93	0.90	13	-
GCF_004116625.1	s__Halarcobacter mediterraneus	77.1848	78	266	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013201725.1	s__Aliarcobacter defluvii	77.1155	71	266	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.85	98.15	0.93	0.88	4	-
GCF_003346815.1	s__Halarcobacter bivalviorum	77.0981	61	266	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	98.23	96.46	0.96	0.92	3	-
GCF_003346775.1	s__Malaciobacter mytili	77.0447	73	266	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	99.45	98.91	0.96	0.92	3	-
GCA_004116725.1	s__Malaciobacter sp004116725	77.0113	79	266	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373175.1	s__Halarcobacter sp013373175	76.9941	62	266	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004214815.1	s__Aliarcobacter thereius	76.9044	53	266	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.14	98.62	0.93	0.89	8	-
GCF_003544915.1	s__Aliarcobacter ellisii	76.8611	75	266	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.73	97.46	0.92	0.84	3	-
GCF_003544935.1	s__Malaciobacter molluscorum	76.8017	81	266	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	99.44	98.88	0.96	0.91	3	-
GCF_013201825.1	s__Halarcobacter ebronensis	76.706	72	266	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	98.25	96.51	0.95	0.90	3	-
GCF_013201705.1	s__Aliarcobacter faecis	76.572	72	266	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.88	99.77	0.97	0.95	3	-
GCF_013283835.1	s__Poseidonibacter lekithochrous	76.3094	72	266	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	99.16	98.33	0.97	0.93	3	-
--------------------------------------------------------------------------------
[2023-03-17 11:08:37,386] [INFO] GTDB search result was written to OceanDNA-b13341/result_gtdb.tsv
[2023-03-17 11:08:37,386] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:08:37,388] [INFO] DFAST_QC result json was written to OceanDNA-b13341/dqc_result.json
[2023-03-17 11:08:37,388] [INFO] DFAST_QC completed!
[2023-03-17 11:08:37,388] [INFO] Total running time: 0h0m37s