[2023-03-18 08:31:56,276] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:31:56,276] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:31:56,276] [INFO] DQC Reference Directory: /var/lib/cwl/stg170f251b-f6ce-4900-a496-a7002f9a3e7d/dqc_reference
[2023-03-18 08:31:57,410] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:31:57,411] [INFO] Task started: Prodigal
[2023-03-18 08:31:57,411] [INFO] Running command: cat /var/lib/cwl/stgc1a68710-4234-41e3-87a2-cceabb0ea820/OceanDNA-b13390.fa | prodigal -d OceanDNA-b13390/cds.fna -a OceanDNA-b13390/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:32:05,222] [INFO] Task succeeded: Prodigal
[2023-03-18 08:32:05,222] [INFO] Task started: HMMsearch
[2023-03-18 08:32:05,222] [INFO] Running command: hmmsearch --tblout OceanDNA-b13390/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg170f251b-f6ce-4900-a496-a7002f9a3e7d/dqc_reference/reference_markers.hmm OceanDNA-b13390/protein.faa > /dev/null
[2023-03-18 08:32:05,379] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:32:05,379] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc1a68710-4234-41e3-87a2-cceabb0ea820/OceanDNA-b13390.fa]
[2023-03-18 08:32:05,396] [INFO] Query marker FASTA was written to OceanDNA-b13390/markers.fasta
[2023-03-18 08:32:05,396] [INFO] Task started: Blastn
[2023-03-18 08:32:05,396] [INFO] Running command: blastn -query OceanDNA-b13390/markers.fasta -db /var/lib/cwl/stg170f251b-f6ce-4900-a496-a7002f9a3e7d/dqc_reference/reference_markers.fasta -out OceanDNA-b13390/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:32:05,855] [INFO] Task succeeded: Blastn
[2023-03-18 08:32:05,855] [INFO] Selected 13 target genomes.
[2023-03-18 08:32:05,856] [INFO] Target genome list was writen to OceanDNA-b13390/target_genomes.txt
[2023-03-18 08:32:05,863] [INFO] Task started: fastANI
[2023-03-18 08:32:05,863] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1a68710-4234-41e3-87a2-cceabb0ea820/OceanDNA-b13390.fa --refList OceanDNA-b13390/target_genomes.txt --output OceanDNA-b13390/fastani_result.tsv --threads 1
[2023-03-18 08:32:11,336] [INFO] Task succeeded: fastANI
[2023-03-18 08:32:11,336] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg170f251b-f6ce-4900-a496-a7002f9a3e7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:32:11,336] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg170f251b-f6ce-4900-a496-a7002f9a3e7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:32:11,344] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:32:11,344] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:32:11,345] [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
Poseidonibacter lekithochrous	strain=DSM 100870	GCA_013283835.1	1904463	1904463	type	True	78.1027	207	484	95	below_threshold
Poseidonibacter lekithochrous	strain=LFT 1.7	GCA_001878855.1	1904463	1904463	type	True	78.0928	205	484	95	below_threshold
Arcobacter caeni	strain=RW17-10	GCA_003063245.1	1912877	1912877	type	True	77.8778	175	484	95	below_threshold
Arcobacter acticola	strain=KCTC 52212	GCA_013177675.1	1849015	1849015	type	True	77.7292	184	484	95	below_threshold
[Halarcobacter] arenosus	strain=CAU 1517	GCA_005771535.1	2576037	2576037	type	True	77.6652	168	484	95	below_threshold
Halarcobacter bivalviorum	strain=CECT 7835	GCA_004116675.1	663364	663364	type	True	77.5167	166	484	95	below_threshold
Halarcobacter bivalviorum	strain=LMG 26154	GCA_003346815.1	663364	663364	type	True	77.5043	168	484	95	below_threshold
Malaciobacter mytili	strain=LMG 24559	GCA_003346775.1	603050	603050	type	True	77.435	196	484	95	below_threshold
Malaciobacter pacificus	strain=LMG 26638	GCA_004214795.1	1080223	1080223	type	True	77.3267	163	484	95	below_threshold
Malaciobacter pacificus	strain=CGMCC 1.11011	GCA_014636355.1	1080223	1080223	type	True	77.3032	159	484	95	below_threshold
Arcobacter ellisii	strain=LMG 26155	GCA_003544915.1	913109	913109	type	True	77.239	180	484	95	below_threshold
Malaciobacter halophilus	strain=DSM 18005	GCA_002837275.1	197482	197482	type	True	77.1941	159	484	95	below_threshold
Arcobacter ellisii	strain=CECT 7837	GCA_004115815.1	913109	913109	type	True	77.1477	182	484	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:32:11,345] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13390/tc_result.tsv
[2023-03-18 08:32:11,345] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:32:11,345] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:32:11,345] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg170f251b-f6ce-4900-a496-a7002f9a3e7d/dqc_reference/checkm_data
[2023-03-18 08:32:11,346] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:32:11,349] [INFO] Task started: CheckM
[2023-03-18 08:32:11,350] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13390/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13390/checkm_input OceanDNA-b13390/checkm_result
[2023-03-18 08:32:35,891] [INFO] Task succeeded: CheckM
[2023-03-18 08:32:35,892] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.75%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 08:32:35,894] [INFO] ===== Completeness check finished =====
[2023-03-18 08:32:35,894] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:32:35,894] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13390/markers.fasta)
[2023-03-18 08:32:35,894] [INFO] Task started: Blastn
[2023-03-18 08:32:35,894] [INFO] Running command: blastn -query OceanDNA-b13390/markers.fasta -db /var/lib/cwl/stg170f251b-f6ce-4900-a496-a7002f9a3e7d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13390/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:32:36,391] [INFO] Task succeeded: Blastn
[2023-03-18 08:32:36,392] [INFO] Selected 8 target genomes.
[2023-03-18 08:32:36,392] [INFO] Target genome list was writen to OceanDNA-b13390/target_genomes_gtdb.txt
[2023-03-18 08:32:36,445] [INFO] Task started: fastANI
[2023-03-18 08:32:36,445] [INFO] Running command: fastANI --query /var/lib/cwl/stgc1a68710-4234-41e3-87a2-cceabb0ea820/OceanDNA-b13390.fa --refList OceanDNA-b13390/target_genomes_gtdb.txt --output OceanDNA-b13390/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:32:40,197] [INFO] Task succeeded: fastANI
[2023-03-18 08:32:40,202] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:32:40,202] [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_013215985.1	s__NORP36 sp013215985	81.7753	297	484	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	81.6413	299	484	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__NORP36	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215945.1	s__NORP36 sp004566295	79.375	272	484	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__NORP36	95.0	99.94	99.94	0.99	0.99	2	-
GCA_002733685.1	s__NORP36 sp002733685	79.307	252	484	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__NORP36	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479135.1	s__Poseidonibacter sp905479135	78.3996	133	484	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861145.1	s__Poseidonibacter lekithochrous_A	78.1884	197	484	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003667345.1	s__Poseidonibacter antarcticus	78.0162	189	484	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004214795.1	s__Aliarcobacter pacificus	77.3267	163	484	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-03-18 08:32:40,202] [INFO] GTDB search result was written to OceanDNA-b13390/result_gtdb.tsv
[2023-03-18 08:32:40,202] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:32:40,204] [INFO] DFAST_QC result json was written to OceanDNA-b13390/dqc_result.json
[2023-03-18 08:32:40,204] [INFO] DFAST_QC completed!
[2023-03-18 08:32:40,204] [INFO] Total running time: 0h0m44s