[2023-03-18 03:59:27,748] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:59:27,748] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:59:27,748] [INFO] DQC Reference Directory: /var/lib/cwl/stg80bd63e6-c2d7-469c-a708-284ee3816786/dqc_reference
[2023-03-18 03:59:29,371] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:59:29,371] [INFO] Task started: Prodigal
[2023-03-18 03:59:29,371] [INFO] Running command: cat /var/lib/cwl/stgb5b579d0-7518-4a5b-aea1-7352d1c32693/OceanDNA-b13378.fa | prodigal -d OceanDNA-b13378/cds.fna -a OceanDNA-b13378/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:59:39,296] [INFO] Task succeeded: Prodigal
[2023-03-18 03:59:39,296] [INFO] Task started: HMMsearch
[2023-03-18 03:59:39,296] [INFO] Running command: hmmsearch --tblout OceanDNA-b13378/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80bd63e6-c2d7-469c-a708-284ee3816786/dqc_reference/reference_markers.hmm OceanDNA-b13378/protein.faa > /dev/null
[2023-03-18 03:59:39,471] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:59:39,471] [INFO] Found 6/6 markers.
[2023-03-18 03:59:39,487] [INFO] Query marker FASTA was written to OceanDNA-b13378/markers.fasta
[2023-03-18 03:59:39,488] [INFO] Task started: Blastn
[2023-03-18 03:59:39,488] [INFO] Running command: blastn -query OceanDNA-b13378/markers.fasta -db /var/lib/cwl/stg80bd63e6-c2d7-469c-a708-284ee3816786/dqc_reference/reference_markers.fasta -out OceanDNA-b13378/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:59:40,022] [INFO] Task succeeded: Blastn
[2023-03-18 03:59:40,022] [INFO] Selected 19 target genomes.
[2023-03-18 03:59:40,023] [INFO] Target genome list was writen to OceanDNA-b13378/target_genomes.txt
[2023-03-18 03:59:40,033] [INFO] Task started: fastANI
[2023-03-18 03:59:40,033] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5b579d0-7518-4a5b-aea1-7352d1c32693/OceanDNA-b13378.fa --refList OceanDNA-b13378/target_genomes.txt --output OceanDNA-b13378/fastani_result.tsv --threads 1
[2023-03-18 03:59:48,388] [INFO] Task succeeded: fastANI
[2023-03-18 03:59:48,389] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80bd63e6-c2d7-469c-a708-284ee3816786/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:59:48,389] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80bd63e6-c2d7-469c-a708-284ee3816786/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:59:48,400] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:59:48,400] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:59:48,400] [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	78.9287	340	670	95	below_threshold
Poseidonibacter lekithochrous	strain=LFT 1.7	GCA_001878855.1	1904463	1904463	type	True	78.8605	340	670	95	below_threshold
Arcobacter acticola	strain=KCTC 52212	GCA_013177675.1	1849015	1849015	type	True	78.8048	270	670	95	below_threshold
Arcobacter caeni	strain=RW17-10	GCA_003063245.1	1912877	1912877	type	True	78.7936	258	670	95	below_threshold
Malaciobacter mytili	strain=LMG 24559	GCA_003346775.1	603050	603050	type	True	78.4867	286	670	95	below_threshold
Malaciobacter mytili	strain=CECT 7386	GCA_004116555.1	603050	603050	type	True	78.4074	282	670	95	below_threshold
Malaciobacter pacificus	strain=CGMCC 1.11011	GCA_014636355.1	1080223	1080223	type	True	78.3129	236	670	95	below_threshold
Malaciobacter pacificus	strain=LMG 26638	GCA_004214795.1	1080223	1080223	type	True	78.2809	241	670	95	below_threshold
Malaciobacter marinus	strain=JCM 15502	GCA_003544855.1	505249	505249	type	True	78.2436	267	670	95	below_threshold
Arcobacter aquimarinus	strain=CECT 8442	GCA_004115795.1	1315211	1315211	type	True	78.2379	253	670	95	below_threshold
Malaciobacter canalis	strain=F138-33	GCA_002723485.1	1912871	1912871	type	True	78.2324	265	670	95	below_threshold
Arcobacter aquimarinus	strain=W63	GCA_013177635.1	1315211	1315211	type	True	78.1979	258	670	95	below_threshold
Arcobacter defluvii	strain=LMG 25694	GCA_013201725.1	873191	873191	type	True	78.1711	254	670	95	below_threshold
Malaciobacter molluscorum	strain=F98-3	GCA_002701265.1	1032072	1032072	type	True	78.1661	273	670	95	below_threshold
Arcobacter defluvii	strain=CECT 7697	GCA_004115775.1	873191	873191	type	True	78.1596	259	670	95	below_threshold
Malaciobacter molluscorum	strain=CECT 7696	GCA_003544935.1	1032072	1032072	type	True	78.1026	280	670	95	below_threshold
Aliarcobacter lanthieri	strain=LMG 28516	GCA_013201625.1	1355374	1355374	type	True	77.5231	196	670	95	below_threshold
Aliarcobacter trophiarum	strain=LMG 25534	GCA_003355515.1	708186	708186	type	True	77.3797	146	670	95	below_threshold
Aliarcobacter trophiarum	strain=LMG 25534	GCA_024584015.1	708186	708186	type	True	77.2594	152	670	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:59:48,400] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13378/tc_result.tsv
[2023-03-18 03:59:48,400] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:59:48,400] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:59:48,400] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80bd63e6-c2d7-469c-a708-284ee3816786/dqc_reference/checkm_data
[2023-03-18 03:59:48,401] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:59:48,405] [INFO] Task started: CheckM
[2023-03-18 03:59:48,405] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13378/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13378/checkm_input OceanDNA-b13378/checkm_result
[2023-03-18 04:00:17,417] [INFO] Task succeeded: CheckM
[2023-03-18 04:00:17,417] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:00:17,419] [INFO] ===== Completeness check finished =====
[2023-03-18 04:00:17,419] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:00:17,420] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13378/markers.fasta)
[2023-03-18 04:00:17,420] [INFO] Task started: Blastn
[2023-03-18 04:00:17,420] [INFO] Running command: blastn -query OceanDNA-b13378/markers.fasta -db /var/lib/cwl/stg80bd63e6-c2d7-469c-a708-284ee3816786/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13378/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:00:18,165] [INFO] Task succeeded: Blastn
[2023-03-18 04:00:18,166] [INFO] Selected 13 target genomes.
[2023-03-18 04:00:18,166] [INFO] Target genome list was writen to OceanDNA-b13378/target_genomes_gtdb.txt
[2023-03-18 04:00:18,182] [INFO] Task started: fastANI
[2023-03-18 04:00:18,182] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5b579d0-7518-4a5b-aea1-7352d1c32693/OceanDNA-b13378.fa --refList OceanDNA-b13378/target_genomes_gtdb.txt --output OceanDNA-b13378/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:00:25,472] [INFO] Task succeeded: fastANI
[2023-03-18 04:00:25,480] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 04:00:25,481] [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_013215915.1	s__NORP36 sp013215915	99.8895	625	670	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__NORP36	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013215985.1	s__NORP36 sp013215985	94.4982	566	670	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	80.3617	389	670	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	80.2213	382	670	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	79.2304	323	670	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	79.0225	292	670	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013283835.1	s__Poseidonibacter lekithochrous	78.89	343	670	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	99.16	98.33	0.97	0.93	3	-
GCA_018816105.1	s__Aliarcobacter sp018816105	78.7141	249	670	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004116725.1	s__Malaciobacter sp004116725	78.5902	248	670	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004214795.1	s__Aliarcobacter pacificus	78.3119	239	670	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013177635.1	s__Aliarcobacter aquimarinus	78.2626	253	670	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003544855.1	s__Malaciobacter marinus	78.2573	266	670	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	98.03	95.41	0.91	0.86	14	-
GCF_013201725.1	s__Aliarcobacter defluvii	78.1552	255	670	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.85	98.15	0.93	0.88	4	-
--------------------------------------------------------------------------------
[2023-03-18 04:00:25,481] [INFO] GTDB search result was written to OceanDNA-b13378/result_gtdb.tsv
[2023-03-18 04:00:25,481] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:00:25,483] [INFO] DFAST_QC result json was written to OceanDNA-b13378/dqc_result.json
[2023-03-18 04:00:25,483] [INFO] DFAST_QC completed!
[2023-03-18 04:00:25,483] [INFO] Total running time: 0h0m58s