[2023-03-15 08:55:06,627] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:55:06,627] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:55:06,627] [INFO] DQC Reference Directory: /var/lib/cwl/stgf93bbbe3-5a90-4f0e-8311-aa0e17654883/dqc_reference
[2023-03-15 08:55:08,348] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:55:08,348] [INFO] Task started: Prodigal
[2023-03-15 08:55:08,348] [INFO] Running command: cat /var/lib/cwl/stg21cebf2d-ce35-48eb-a43b-8fdac776e6ff/OceanDNA-b13329.fa | prodigal -d OceanDNA-b13329/cds.fna -a OceanDNA-b13329/protein.faa -g 11 -q > /dev/null
[2023-03-15 08:55:13,787] [INFO] Task succeeded: Prodigal
[2023-03-15 08:55:13,787] [INFO] Task started: HMMsearch
[2023-03-15 08:55:13,787] [INFO] Running command: hmmsearch --tblout OceanDNA-b13329/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf93bbbe3-5a90-4f0e-8311-aa0e17654883/dqc_reference/reference_markers.hmm OceanDNA-b13329/protein.faa > /dev/null
[2023-03-15 08:55:13,971] [INFO] Task succeeded: HMMsearch
[2023-03-15 08:55:13,972] [INFO] Found 6/6 markers.
[2023-03-15 08:55:13,981] [INFO] Query marker FASTA was written to OceanDNA-b13329/markers.fasta
[2023-03-15 08:55:13,982] [INFO] Task started: Blastn
[2023-03-15 08:55:13,982] [INFO] Running command: blastn -query OceanDNA-b13329/markers.fasta -db /var/lib/cwl/stgf93bbbe3-5a90-4f0e-8311-aa0e17654883/dqc_reference/reference_markers.fasta -out OceanDNA-b13329/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:55:14,515] [INFO] Task succeeded: Blastn
[2023-03-15 08:55:14,515] [INFO] Selected 22 target genomes.
[2023-03-15 08:55:14,516] [INFO] Target genome list was writen to OceanDNA-b13329/target_genomes.txt
[2023-03-15 08:55:14,526] [INFO] Task started: fastANI
[2023-03-15 08:55:14,526] [INFO] Running command: fastANI --query /var/lib/cwl/stg21cebf2d-ce35-48eb-a43b-8fdac776e6ff/OceanDNA-b13329.fa --refList OceanDNA-b13329/target_genomes.txt --output OceanDNA-b13329/fastani_result.tsv --threads 1
[2023-03-15 08:55:22,589] [INFO] Task succeeded: fastANI
[2023-03-15 08:55:22,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf93bbbe3-5a90-4f0e-8311-aa0e17654883/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 08:55:22,590] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf93bbbe3-5a90-4f0e-8311-aa0e17654883/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 08:55:22,602] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 08:55:22,602] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 08:55:22,602] [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
Malaciobacter pacificus	strain=LMG 26638	GCA_004214795.1	1080223	1080223	type	True	77.8987	118	356	95	below_threshold
Arcobacter ellisii	strain=LMG 26155	GCA_003544915.1	913109	913109	type	True	77.7983	124	356	95	below_threshold
Halarcobacter bivalviorum	strain=LMG 26154	GCA_003346815.1	663364	663364	type	True	77.6884	121	356	95	below_threshold
Halarcobacter bivalviorum	strain=CECT 7835	GCA_004116675.1	663364	663364	type	True	77.684	119	356	95	below_threshold
Arcobacter ellisii	strain=CECT 7837	GCA_004115815.1	913109	913109	type	True	77.6378	128	356	95	below_threshold
Arcobacter venerupis	strain=LMG 26156	GCA_013201665.1	1054033	1054033	type	True	77.5633	121	356	95	below_threshold
Arcobacter aquimarinus	strain=CECT 8442	GCA_004115795.1	1315211	1315211	type	True	77.5621	113	356	95	below_threshold
Arcobacter venerupis	strain=CECT7836	GCA_004023405.1	1054033	1054033	type	True	77.5364	126	356	95	below_threshold
Malaciobacter marinus	strain=JCM 15502	GCA_003544855.1	505249	505249	type	True	77.5149	124	356	95	below_threshold
Arcobacter suis	strain=CECT 7833	GCA_003544815.1	1278212	1278212	type	True	77.4177	132	356	95	below_threshold
Arcobacter suis	strain=CECT7833	GCA_004023465.1	1278212	1278212	type	True	77.3746	130	356	95	below_threshold
Arcobacter defluvii	strain=LMG 25694	GCA_013201725.1	873191	873191	type	True	77.361	135	356	95	below_threshold
Arcobacter defluvii	strain=CECT 7697	GCA_004115775.1	873191	873191	type	True	77.3515	136	356	95	below_threshold
Aliarcobacter cryaerophilus	strain=LMG 9904	GCA_006165035.1	28198	28198	suspected-type	True	77.2412	90	356	95	below_threshold
Aliarcobacter cryaerophilus	strain=ATCC 43158	GCA_003660105.1	28198	28198	suspected-type	True	77.2274	91	356	95	below_threshold
Aliarcobacter cryaerophilus	strain=LMG 24291	GCA_002992955.1	28198	28198	suspected-type	True	77.2258	88	356	95	below_threshold
Aliarcobacter thereius	strain=LMG 24486	GCA_024584025.1	544718	544718	type	True	77.1713	98	356	95	below_threshold
Malaciobacter molluscorum	strain=F98-3	GCA_002701265.1	1032072	1032072	type	True	77.1591	148	356	95	below_threshold
Malaciobacter molluscorum	strain=CECT 7696	GCA_003544935.1	1032072	1032072	type	True	77.1355	148	356	95	below_threshold
Aliarcobacter faecis	strain=CCUG 66484	GCA_013201705.1	1564138	1564138	type	True	76.9727	94	356	95	below_threshold
Aliarcobacter skirrowii	strain=LMG 6621	GCA_024584055.1	28200	28200	type	True	76.9128	104	356	95	below_threshold
Aliarcobacter skirrowii	strain=LMG 6621	GCA_004115735.1	28200	28200	type	True	76.8681	107	356	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 08:55:22,602] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13329/tc_result.tsv
[2023-03-15 08:55:22,602] [INFO] ===== Taxonomy check completed =====
[2023-03-15 08:55:22,603] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 08:55:22,603] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf93bbbe3-5a90-4f0e-8311-aa0e17654883/dqc_reference/checkm_data
[2023-03-15 08:55:22,603] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 08:55:22,624] [INFO] Task started: CheckM
[2023-03-15 08:55:22,624] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13329/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13329/checkm_input OceanDNA-b13329/checkm_result
[2023-03-15 08:55:42,191] [INFO] Task succeeded: CheckM
[2023-03-15 08:55:42,192] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 08:55:42,193] [INFO] ===== Completeness check finished =====
[2023-03-15 08:55:42,193] [INFO] ===== Start GTDB Search =====
[2023-03-15 08:55:42,194] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13329/markers.fasta)
[2023-03-15 08:55:42,194] [INFO] Task started: Blastn
[2023-03-15 08:55:42,194] [INFO] Running command: blastn -query OceanDNA-b13329/markers.fasta -db /var/lib/cwl/stgf93bbbe3-5a90-4f0e-8311-aa0e17654883/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13329/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 08:55:42,949] [INFO] Task succeeded: Blastn
[2023-03-15 08:55:42,950] [INFO] Selected 19 target genomes.
[2023-03-15 08:55:42,950] [INFO] Target genome list was writen to OceanDNA-b13329/target_genomes_gtdb.txt
[2023-03-15 08:55:43,004] [INFO] Task started: fastANI
[2023-03-15 08:55:43,004] [INFO] Running command: fastANI --query /var/lib/cwl/stg21cebf2d-ce35-48eb-a43b-8fdac776e6ff/OceanDNA-b13329.fa --refList OceanDNA-b13329/target_genomes_gtdb.txt --output OceanDNA-b13329/fastani_result_gtdb.tsv --threads 1
[2023-03-15 08:55:51,116] [INFO] Task succeeded: fastANI
[2023-03-15 08:55:51,127] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 08:55:51,128] [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_018662405.1	s__JADHTT01 sp018662405	99.6451	325	356	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__JADHTT01	95.0	99.77	99.69	0.93	0.90	13	conclusive
GCA_016784825.1	s__JADHTT01 sp016784825	82.4235	115	356	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__JADHTT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003544915.1	s__Aliarcobacter ellisii	77.7727	125	356	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.73	97.46	0.92	0.84	3	-
GCF_003667345.1	s__Poseidonibacter antarcticus	77.754	138	356	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009208075.1	s__Poseidonibacter sp009208075	77.7473	150	356	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	99.63	99.63	0.93	0.93	3	-
GCF_003346815.1	s__Halarcobacter bivalviorum	77.6884	121	356	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	98.23	96.46	0.96	0.92	3	-
GCF_004116625.1	s__Halarcobacter mediterraneus	77.6357	116	356	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177635.1	s__Aliarcobacter aquimarinus	77.5881	112	356	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013201665.1	s__Aliarcobacter venerupis	77.5633	121	356	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	0.99	0.99	2	-
GCA_004116465.1	s__Arcobacter sp004116465	77.5219	128	356	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Arcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003544855.1	s__Malaciobacter marinus	77.4903	125	356	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	98.03	95.41	0.91	0.86	14	-
GCF_003063295.1	s__Aliarcobacter lacus	77.4451	116	356	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003544815.1	s__Aliarcobacter suis	77.3955	133	356	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013201725.1	s__Aliarcobacter defluvii	77.3832	134	356	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.85	98.15	0.93	0.88	4	-
GCF_004214815.1	s__Aliarcobacter thereius	77.2573	92	356	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.14	98.62	0.93	0.89	8	-
GCA_003252105.1	s__Halarcobacter sp003252105	77.2348	125	356	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003660105.1	s__Aliarcobacter cryaerophilus	77.2274	91	356	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.99	99.99	1.00	0.99	3	-
GCF_003544935.1	s__Malaciobacter molluscorum	77.1509	147	356	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	99.44	98.88	0.96	0.91	3	-
GCF_013201705.1	s__Aliarcobacter faecis	76.9727	94	356	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.88	99.77	0.97	0.95	3	-
--------------------------------------------------------------------------------
[2023-03-15 08:55:51,128] [INFO] GTDB search result was written to OceanDNA-b13329/result_gtdb.tsv
[2023-03-15 08:55:51,128] [INFO] ===== GTDB Search completed =====
[2023-03-15 08:55:51,130] [INFO] DFAST_QC result json was written to OceanDNA-b13329/dqc_result.json
[2023-03-15 08:55:51,130] [INFO] DFAST_QC completed!
[2023-03-15 08:55:51,130] [INFO] Total running time: 0h0m45s