[2023-03-17 07:47:46,559] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:47:46,559] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:47:46,560] [INFO] DQC Reference Directory: /var/lib/cwl/stge3fc1858-0736-4bcf-b6e6-dee86508357c/dqc_reference
[2023-03-17 07:47:47,649] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:47:47,649] [INFO] Task started: Prodigal
[2023-03-17 07:47:47,649] [INFO] Running command: cat /var/lib/cwl/stg20b0bbf3-e4e2-4db9-bf3e-c952d3ad2562/OceanDNA-b13445.fa | prodigal -d OceanDNA-b13445/cds.fna -a OceanDNA-b13445/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:47:54,041] [INFO] Task succeeded: Prodigal
[2023-03-17 07:47:54,041] [INFO] Task started: HMMsearch
[2023-03-17 07:47:54,041] [INFO] Running command: hmmsearch --tblout OceanDNA-b13445/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3fc1858-0736-4bcf-b6e6-dee86508357c/dqc_reference/reference_markers.hmm OceanDNA-b13445/protein.faa > /dev/null
[2023-03-17 07:47:54,178] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:47:54,178] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg20b0bbf3-e4e2-4db9-bf3e-c952d3ad2562/OceanDNA-b13445.fa]
[2023-03-17 07:47:54,195] [INFO] Query marker FASTA was written to OceanDNA-b13445/markers.fasta
[2023-03-17 07:47:54,195] [INFO] Task started: Blastn
[2023-03-17 07:47:54,195] [INFO] Running command: blastn -query OceanDNA-b13445/markers.fasta -db /var/lib/cwl/stge3fc1858-0736-4bcf-b6e6-dee86508357c/dqc_reference/reference_markers.fasta -out OceanDNA-b13445/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:47:54,630] [INFO] Task succeeded: Blastn
[2023-03-17 07:47:54,631] [INFO] Selected 22 target genomes.
[2023-03-17 07:47:54,631] [INFO] Target genome list was writen to OceanDNA-b13445/target_genomes.txt
[2023-03-17 07:47:54,642] [INFO] Task started: fastANI
[2023-03-17 07:47:54,642] [INFO] Running command: fastANI --query /var/lib/cwl/stg20b0bbf3-e4e2-4db9-bf3e-c952d3ad2562/OceanDNA-b13445.fa --refList OceanDNA-b13445/target_genomes.txt --output OceanDNA-b13445/fastani_result.tsv --threads 1
[2023-03-17 07:48:02,881] [INFO] Task succeeded: fastANI
[2023-03-17 07:48:02,882] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3fc1858-0736-4bcf-b6e6-dee86508357c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:48:02,882] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3fc1858-0736-4bcf-b6e6-dee86508357c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:48:02,890] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:48:02,890] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 07:48:02,891] [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 ellisii	strain=LMG 26155	GCA_003544915.1	913109	913109	type	True	77.2001	56	281	95	below_threshold
Halarcobacter bivalviorum	strain=CECT 7835	GCA_004116675.1	663364	663364	type	True	77.1856	52	281	95	below_threshold
Arcobacter ellisii	strain=CECT 7837	GCA_004115815.1	913109	913109	type	True	77.1521	57	281	95	below_threshold
Halarcobacter bivalviorum	strain=LMG 26154	GCA_003346815.1	663364	663364	type	True	77.1343	53	281	95	below_threshold
[Halarcobacter] arenosus	strain=CAU 1517	GCA_005771535.1	2576037	2576037	type	True	77.0055	56	281	95	below_threshold
Poseidonibacter lekithochrous	strain=LFT 1.7	GCA_001878855.1	1904463	1904463	type	True	76.9631	65	281	95	below_threshold
Poseidonibacter lekithochrous	strain=DSM 100870	GCA_013283835.1	1904463	1904463	type	True	76.9631	65	281	95	below_threshold
Arcobacter suis	strain=CECT7833	GCA_004023465.1	1278212	1278212	type	True	76.8899	52	281	95	below_threshold
Arcobacter suis	strain=CECT 7833	GCA_003544815.1	1278212	1278212	type	True	76.8502	53	281	95	below_threshold
Arcobacter acticola	strain=KCTC 52212	GCA_013177675.1	1849015	1849015	type	True	76.6784	61	281	95	below_threshold
Arcobacter aquimarinus	strain=W63	GCA_013177635.1	1315211	1315211	type	True	76.4897	51	281	95	below_threshold
Arcobacter aquimarinus	strain=CECT 8442	GCA_004115795.1	1315211	1315211	type	True	76.4508	52	281	95	below_threshold
Malaciobacter canalis	strain=F138-33	GCA_002723485.1	1912871	1912871	type	True	76.2026	67	281	95	below_threshold
Malaciobacter canalis	strain=LMG 29148	GCA_008000835.1	1912871	1912871	type	True	76.1902	66	281	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 07:48:02,891] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13445/tc_result.tsv
[2023-03-17 07:48:02,891] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:48:02,891] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:48:02,891] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3fc1858-0736-4bcf-b6e6-dee86508357c/dqc_reference/checkm_data
[2023-03-17 07:48:02,892] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:48:02,895] [INFO] Task started: CheckM
[2023-03-17 07:48:02,895] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13445/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13445/checkm_input OceanDNA-b13445/checkm_result
[2023-03-17 07:48:24,936] [INFO] Task succeeded: CheckM
[2023-03-17 07:48:24,936] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.61%
Contamintation: 0.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:48:24,938] [INFO] ===== Completeness check finished =====
[2023-03-17 07:48:24,939] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:48:24,939] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13445/markers.fasta)
[2023-03-17 07:48:24,939] [INFO] Task started: Blastn
[2023-03-17 07:48:24,939] [INFO] Running command: blastn -query OceanDNA-b13445/markers.fasta -db /var/lib/cwl/stge3fc1858-0736-4bcf-b6e6-dee86508357c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13445/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:48:25,348] [INFO] Task succeeded: Blastn
[2023-03-17 07:48:25,349] [INFO] Selected 19 target genomes.
[2023-03-17 07:48:25,349] [INFO] Target genome list was writen to OceanDNA-b13445/target_genomes_gtdb.txt
[2023-03-17 07:48:25,492] [INFO] Task started: fastANI
[2023-03-17 07:48:25,492] [INFO] Running command: fastANI --query /var/lib/cwl/stg20b0bbf3-e4e2-4db9-bf3e-c952d3ad2562/OceanDNA-b13445.fa --refList OceanDNA-b13445/target_genomes_gtdb.txt --output OceanDNA-b13445/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:48:33,327] [INFO] Task succeeded: fastANI
[2023-03-17 07:48:33,334] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:48:33,334] [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_002163065.1	s__NORP36 sp002163065	85.8085	159	281	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	77.5822	61	281	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__NORP36	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002869565.1	s__Halarcobacter sp002869565	77.5427	62	281	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	77.2355	64	281	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956695.1	s__Poseidonibacter parvus	77.1943	66	281	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	98.33	98.33	0.91	0.91	2	-
GCF_003346815.1	s__Halarcobacter bivalviorum	77.1851	52	281	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	98.23	96.46	0.96	0.92	3	-
GCF_009208075.1	s__Poseidonibacter sp009208075	77.0235	59	281	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	99.63	99.63	0.93	0.93	3	-
GCF_003667345.1	s__Poseidonibacter antarcticus	77.0171	64	281	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771535.1	s__Halarcobacter arenosus	77.0055	56	281	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003544815.1	s__Aliarcobacter suis	76.8502	53	281	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018861145.1	s__Poseidonibacter lekithochrous_A	76.7762	68	281	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001655195.1	s__Arcobacter_A sp001655195	76.4786	58	281	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Arcobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:48:33,335] [INFO] GTDB search result was written to OceanDNA-b13445/result_gtdb.tsv
[2023-03-17 07:48:33,335] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:48:33,336] [INFO] DFAST_QC result json was written to OceanDNA-b13445/dqc_result.json
[2023-03-17 07:48:33,336] [INFO] DFAST_QC completed!
[2023-03-17 07:48:33,336] [INFO] Total running time: 0h0m47s