[2023-03-18 20:40:39,454] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:40:39,455] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:40:39,455] [INFO] DQC Reference Directory: /var/lib/cwl/stgcbb84ae1-0dfb-4f05-85d6-af718cd6523a/dqc_reference
[2023-03-18 20:40:41,208] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:40:41,208] [INFO] Task started: Prodigal
[2023-03-18 20:40:41,209] [INFO] Running command: cat /var/lib/cwl/stga36e0ed3-7935-45ac-aea8-efe53373fae6/OceanDNA-b13342.fa | prodigal -d OceanDNA-b13342/cds.fna -a OceanDNA-b13342/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:40:55,718] [INFO] Task succeeded: Prodigal
[2023-03-18 20:40:55,718] [INFO] Task started: HMMsearch
[2023-03-18 20:40:55,718] [INFO] Running command: hmmsearch --tblout OceanDNA-b13342/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcbb84ae1-0dfb-4f05-85d6-af718cd6523a/dqc_reference/reference_markers.hmm OceanDNA-b13342/protein.faa > /dev/null
[2023-03-18 20:40:55,956] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:40:55,957] [INFO] Found 6/6 markers.
[2023-03-18 20:40:55,976] [INFO] Query marker FASTA was written to OceanDNA-b13342/markers.fasta
[2023-03-18 20:40:55,977] [INFO] Task started: Blastn
[2023-03-18 20:40:55,977] [INFO] Running command: blastn -query OceanDNA-b13342/markers.fasta -db /var/lib/cwl/stgcbb84ae1-0dfb-4f05-85d6-af718cd6523a/dqc_reference/reference_markers.fasta -out OceanDNA-b13342/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:40:56,523] [INFO] Task succeeded: Blastn
[2023-03-18 20:40:56,524] [INFO] Selected 23 target genomes.
[2023-03-18 20:40:56,524] [INFO] Target genome list was writen to OceanDNA-b13342/target_genomes.txt
[2023-03-18 20:40:56,532] [INFO] Task started: fastANI
[2023-03-18 20:40:56,532] [INFO] Running command: fastANI --query /var/lib/cwl/stga36e0ed3-7935-45ac-aea8-efe53373fae6/OceanDNA-b13342.fa --refList OceanDNA-b13342/target_genomes.txt --output OceanDNA-b13342/fastani_result.tsv --threads 1
[2023-03-18 20:41:08,428] [INFO] Task succeeded: fastANI
[2023-03-18 20:41:08,428] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcbb84ae1-0dfb-4f05-85d6-af718cd6523a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:41:08,429] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcbb84ae1-0dfb-4f05-85d6-af718cd6523a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:41:08,442] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:41:08,442] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 20:41:08,442] [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 nitrofigilis	strain=DSM 7299	GCA_000092245.1	28199	28199	type	True	92.4678	814	956	95	below_threshold
Arcobacter venerupis	strain=LMG 26156	GCA_013201665.1	1054033	1054033	type	True	79.725	430	956	95	below_threshold
Arcobacter venerupis	strain=CECT7836	GCA_004023405.1	1054033	1054033	type	True	79.6645	439	956	95	below_threshold
Arcobacter suis	strain=CECT7833	GCA_004023465.1	1278212	1278212	type	True	79.2941	388	956	95	below_threshold
Arcobacter ellisii	strain=LMG 26155	GCA_003544915.1	913109	913109	type	True	79.258	409	956	95	below_threshold
Arcobacter suis	strain=CECT 7833	GCA_003544815.1	1278212	1278212	type	True	79.2467	398	956	95	below_threshold
[Halarcobacter] arenosus	strain=CAU 1517	GCA_005771535.1	2576037	2576037	type	True	79.2383	396	956	95	below_threshold
Arcobacter defluvii	strain=CECT 7697	GCA_004115775.1	873191	873191	type	True	79.2347	371	956	95	below_threshold
Malaciobacter pacificus	strain=CGMCC 1.11011	GCA_014636355.1	1080223	1080223	type	True	79.1261	355	956	95	below_threshold
Arcobacter defluvii	strain=LMG 25694	GCA_013201725.1	873191	873191	type	True	79.1254	373	956	95	below_threshold
Halarcobacter bivalviorum	strain=LMG 26154	GCA_003346815.1	663364	663364	type	True	79.0952	374	956	95	below_threshold
Halarcobacter bivalviorum	strain=CECT 7835	GCA_004116675.1	663364	663364	type	True	79.0924	377	956	95	below_threshold
Malaciobacter pacificus	strain=LMG 26638	GCA_004214795.1	1080223	1080223	type	True	79.0499	368	956	95	below_threshold
Malaciobacter canalis	strain=F138-33	GCA_002723485.1	1912871	1912871	type	True	78.9991	390	956	95	below_threshold
Aliarcobacter butzleri	strain=NCTC 12481	GCA_900187115.1	28197	28197	type	True	78.9944	329	956	95	below_threshold
Aliarcobacter butzleri	strain=RM4018	GCA_000014025.1	28197	28197	type	True	78.9704	330	956	95	below_threshold
Halarcobacter ebronensis	strain=CECT 8441	GCA_004116565.1	1462615	1462615	type	True	78.9557	373	956	95	below_threshold
Malaciobacter mytili	strain=LMG 24559	GCA_003346775.1	603050	603050	type	True	78.9495	398	956	95	below_threshold
Malaciobacter mytili	strain=CECT 7386	GCA_004116555.1	603050	603050	type	True	78.93	392	956	95	below_threshold
Malaciobacter marinus	strain=JCM 15502	GCA_003544855.1	505249	505249	type	True	78.8997	377	956	95	below_threshold
Halarcobacter ebronensis	strain=LMG 27922	GCA_013201825.1	1462615	1462615	type	True	78.8718	372	956	95	below_threshold
[Arcobacter] porcinus	strain=CCUG 56899	GCA_004299785.2	1935204	1935204	type	True	77.9355	256	956	95	below_threshold
[Arcobacter] porcinus	strain=LMG 24487	GCA_024584075.1	1935204	1935204	type	True	77.8761	261	956	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 20:41:08,442] [INFO] DFAST Taxonomy check result was written to OceanDNA-b13342/tc_result.tsv
[2023-03-18 20:41:08,442] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:41:08,442] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:41:08,442] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcbb84ae1-0dfb-4f05-85d6-af718cd6523a/dqc_reference/checkm_data
[2023-03-18 20:41:08,443] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:41:08,447] [INFO] Task started: CheckM
[2023-03-18 20:41:08,448] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b13342/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b13342/checkm_input OceanDNA-b13342/checkm_result
[2023-03-18 20:41:47,134] [INFO] Task succeeded: CheckM
[2023-03-18 20:41:47,134] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:41:47,136] [INFO] ===== Completeness check finished =====
[2023-03-18 20:41:47,136] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:41:47,137] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b13342/markers.fasta)
[2023-03-18 20:41:47,137] [INFO] Task started: Blastn
[2023-03-18 20:41:47,137] [INFO] Running command: blastn -query OceanDNA-b13342/markers.fasta -db /var/lib/cwl/stgcbb84ae1-0dfb-4f05-85d6-af718cd6523a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b13342/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:41:47,851] [INFO] Task succeeded: Blastn
[2023-03-18 20:41:47,852] [INFO] Selected 14 target genomes.
[2023-03-18 20:41:47,852] [INFO] Target genome list was writen to OceanDNA-b13342/target_genomes_gtdb.txt
[2023-03-18 20:41:47,886] [INFO] Task started: fastANI
[2023-03-18 20:41:47,886] [INFO] Running command: fastANI --query /var/lib/cwl/stga36e0ed3-7935-45ac-aea8-efe53373fae6/OceanDNA-b13342.fa --refList OceanDNA-b13342/target_genomes_gtdb.txt --output OceanDNA-b13342/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:41:56,614] [INFO] Task succeeded: fastANI
[2023-03-18 20:41:56,623] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 20:41:56,623] [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_004116465.1	s__Arcobacter sp004116465	93.7812	837	956	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Arcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092245.1	s__Arcobacter nitrofigilis	92.4593	814	956	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Arcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002869535.1	s__Arcobacter sp002869535	85.083	632	956	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Arcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002869565.1	s__Halarcobacter sp002869565	80.0594	465	956	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013201665.1	s__Aliarcobacter venerupis	79.7065	432	956	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	0.99	0.99	2	-
GCA_004116495.1	s__Malaciobacter sp004116495	79.2083	386	956	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004116725.1	s__Malaciobacter sp004116725	79.131	383	956	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009208075.1	s__Poseidonibacter sp009208075	79.1158	367	956	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	99.63	99.63	0.93	0.93	3	-
GCF_001956695.1	s__Poseidonibacter parvus	79.0908	353	956	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	79.0814	376	956	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	98.23	96.46	0.96	0.92	3	-
GCF_004214795.1	s__Aliarcobacter pacificus	79.05	368	956	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900187115.1	s__Aliarcobacter butzleri	79.0004	328	956	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.53	96.98	0.89	0.81	50	-
GCF_013201825.1	s__Halarcobacter ebronensis	78.8668	373	956	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	98.25	96.51	0.95	0.90	3	-
GCF_004299785.2	s__Aliarcobacter porcinus	77.9253	254	956	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.76	98.06	0.91	0.88	6	-
--------------------------------------------------------------------------------
[2023-03-18 20:41:56,623] [INFO] GTDB search result was written to OceanDNA-b13342/result_gtdb.tsv
[2023-03-18 20:41:56,623] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:41:56,625] [INFO] DFAST_QC result json was written to OceanDNA-b13342/dqc_result.json
[2023-03-18 20:41:56,626] [INFO] DFAST_QC completed!
[2023-03-18 20:41:56,626] [INFO] Total running time: 0h1m17s