[2023-03-16 18:40:20,525] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:40:20,526] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:40:20,526] [INFO] DQC Reference Directory: /var/lib/cwl/stged748832-3a21-4a32-a77a-f94269165452/dqc_reference
[2023-03-16 18:40:22,807] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:40:22,807] [INFO] Task started: Prodigal
[2023-03-16 18:40:22,807] [INFO] Running command: cat /var/lib/cwl/stgea57eb7d-c60c-41b2-8fc1-c1d420944748/OceanDNA-b13439.fa | prodigal -d OceanDNA-b13439/cds.fna -a OceanDNA-b13439/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:40:41,322] [INFO] Task succeeded: Prodigal
[2023-03-16 18:40:41,323] [INFO] Task started: HMMsearch
[2023-03-16 18:40:41,323] [INFO] Running command: hmmsearch --tblout OceanDNA-b13439/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged748832-3a21-4a32-a77a-f94269165452/dqc_reference/reference_markers.hmm OceanDNA-b13439/protein.faa > /dev/null
[2023-03-16 18:40:41,583] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:40:41,583] [INFO] Found 6/6 markers.
[2023-03-16 18:40:41,623] [INFO] Query marker FASTA was written to OceanDNA-b13439/markers.fasta
[2023-03-16 18:40:41,625] [INFO] Task started: Blastn
[2023-03-16 18:40:41,626] [INFO] Running command: blastn -query OceanDNA-b13439/markers.fasta -db /var/lib/cwl/stged748832-3a21-4a32-a77a-f94269165452/dqc_reference/reference_markers.fasta -out OceanDNA-b13439/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:40:42,216] [INFO] Task succeeded: Blastn
[2023-03-16 18:40:42,217] [INFO] Selected 17 target genomes.
[2023-03-16 18:40:42,217] [INFO] Target genome list was writen to OceanDNA-b13439/target_genomes.txt
[2023-03-16 18:40:42,250] [INFO] Task started: fastANI
[2023-03-16 18:40:42,250] [INFO] Running command: fastANI --query /var/lib/cwl/stgea57eb7d-c60c-41b2-8fc1-c1d420944748/OceanDNA-b13439.fa --refList OceanDNA-b13439/target_genomes.txt --output OceanDNA-b13439/fastani_result.tsv --threads 1
[2023-03-16 18:40:57,018] [INFO] Task succeeded: fastANI
[2023-03-16 18:40:57,019] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged748832-3a21-4a32-a77a-f94269165452/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:40:57,019] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged748832-3a21-4a32-a77a-f94269165452/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:40:57,029] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:40:57,029] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 18:40:57,029] [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 suis	strain=CECT 7833	GCA_003544815.1	1278212	1278212	type	True	77.7191	216	1027	95	below_threshold
Poseidonibacter lekithochrous	strain=LFT 1.7	GCA_001878855.1	1904463	1904463	type	True	77.7152	295	1027	95	below_threshold
Arcobacter suis	strain=CECT7833	GCA_004023465.1	1278212	1278212	type	True	77.6688	220	1027	95	below_threshold
Poseidonibacter lekithochrous	strain=DSM 100870	GCA_013283835.1	1904463	1904463	type	True	77.6391	301	1027	95	below_threshold
Arcobacter caeni	strain=RW17-10	GCA_003063245.1	1912877	1912877	type	True	77.5493	240	1027	95	below_threshold
Arcobacter nitrofigilis	strain=DSM 7299	GCA_000092245.1	28199	28199	type	True	77.4745	233	1027	95	below_threshold
Arcobacter aquimarinus	strain=CECT 8442	GCA_004115795.1	1315211	1315211	type	True	77.4053	226	1027	95	below_threshold
Malaciobacter halophilus	strain=DSM 18005	GCA_002837275.1	197482	197482	type	True	77.2849	214	1027	95	below_threshold
Malaciobacter molluscorum	strain=F98-3	GCA_002701265.1	1032072	1032072	type	True	77.2568	247	1027	95	below_threshold
Malaciobacter molluscorum	strain=CECT 7696	GCA_003544935.1	1032072	1032072	type	True	77.2402	253	1027	95	below_threshold
Malaciobacter marinus	strain=JCM 15502	GCA_003544855.1	505249	505249	type	True	77.1168	245	1027	95	below_threshold
Malaciobacter canalis	strain=F138-33	GCA_002723485.1	1912871	1912871	type	True	77.0776	228	1027	95	below_threshold
Malaciobacter canalis	strain=LMG 29148	GCA_008000835.1	1912871	1912871	type	True	77.0217	232	1027	95	below_threshold
Aliarcobacter butzleri	strain=RM4018	GCA_000014025.1	28197	28197	type	True	76.9514	200	1027	95	below_threshold
Aliarcobacter butzleri	strain=NCTC 12481	GCA_900187115.1	28197	28197	type	True	76.9267	202	1027	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 18:40:57,029] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13439/tc_result.tsv
[2023-03-16 18:40:57,029] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:40:57,030] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:40:57,030] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged748832-3a21-4a32-a77a-f94269165452/dqc_reference/checkm_data
[2023-03-16 18:40:57,030] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:40:57,036] [INFO] Task started: CheckM
[2023-03-16 18:40:57,036] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13439/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13439/checkm_input OceanDNA-b13439/checkm_result
[2023-03-16 18:41:39,185] [INFO] Task succeeded: CheckM
[2023-03-16 18:41:39,185] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:41:39,188] [INFO] ===== Completeness check finished =====
[2023-03-16 18:41:39,188] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:41:39,188] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13439/markers.fasta)
[2023-03-16 18:41:39,189] [INFO] Task started: Blastn
[2023-03-16 18:41:39,189] [INFO] Running command: blastn -query OceanDNA-b13439/markers.fasta -db /var/lib/cwl/stged748832-3a21-4a32-a77a-f94269165452/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13439/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:41:40,010] [INFO] Task succeeded: Blastn
[2023-03-16 18:41:40,010] [INFO] Selected 10 target genomes.
[2023-03-16 18:41:40,011] [INFO] Target genome list was writen to OceanDNA-b13439/target_genomes_gtdb.txt
[2023-03-16 18:41:40,092] [INFO] Task started: fastANI
[2023-03-16 18:41:40,093] [INFO] Running command: fastANI --query /var/lib/cwl/stgea57eb7d-c60c-41b2-8fc1-c1d420944748/OceanDNA-b13439.fa --refList OceanDNA-b13439/target_genomes_gtdb.txt --output OceanDNA-b13439/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:41:46,034] [INFO] Task succeeded: fastANI
[2023-03-16 18:41:46,041] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 18:41:46,041] [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_013215945.1	s__NORP36 sp004566295	98.503	952	1027	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__NORP36	95.0	99.94	99.94	0.99	0.99	2	conclusive
GCA_002733685.1	s__NORP36 sp002733685	94.0444	884	1027	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__NORP36	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215915.1	s__NORP36 sp013215915	80.5531	396	1027	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__NORP36	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215985.1	s__NORP36 sp013215985	80.0704	433	1027	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__NORP36	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956695.1	s__Poseidonibacter parvus	78.1407	286	1027	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	98.33	98.33	0.91	0.91	2	-
GCF_003667345.1	s__Poseidonibacter antarcticus	78.1	293	1027	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003063245.1	s__Aliarcobacter caeni	77.5629	239	1027	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001895145.1	s__Halarcobacter sp001895145	77.4406	290	1027	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002837275.1	s__Malaciobacter halophilus	77.3258	211	1027	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002869535.1	s__Arcobacter sp002869535	77.018	215	1027	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Arcobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:41:46,041] [INFO] GTDB search result was written to OceanDNA-b13439/result_gtdb.tsv
[2023-03-16 18:41:46,041] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:41:46,042] [INFO] DFAST_QC result json was written to OceanDNA-b13439/dqc_result.json
[2023-03-16 18:41:46,043] [INFO] DFAST_QC completed!
[2023-03-16 18:41:46,043] [INFO] Total running time: 0h1m26s