[2023-03-15 05:51:32,067] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:51:32,068] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:51:32,068] [INFO] DQC Reference Directory: /var/lib/cwl/stg144d979e-3473-4042-9b2e-d20754fa1fae/dqc_reference
[2023-03-15 05:51:33,647] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:51:33,648] [INFO] Task started: Prodigal
[2023-03-15 05:51:33,648] [INFO] Running command: cat /var/lib/cwl/stg3bf84cf1-bdab-4cbf-ba0d-1fc9a53d2e97/OceanDNA-b7188.fa | prodigal -d OceanDNA-b7188/cds.fna -a OceanDNA-b7188/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:51:49,726] [INFO] Task succeeded: Prodigal
[2023-03-15 05:51:49,726] [INFO] Task started: HMMsearch
[2023-03-15 05:51:49,726] [INFO] Running command: hmmsearch --tblout OceanDNA-b7188/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg144d979e-3473-4042-9b2e-d20754fa1fae/dqc_reference/reference_markers.hmm OceanDNA-b7188/protein.faa > /dev/null
[2023-03-15 05:51:49,926] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:51:49,927] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3bf84cf1-bdab-4cbf-ba0d-1fc9a53d2e97/OceanDNA-b7188.fa]
[2023-03-15 05:51:49,946] [INFO] Query marker FASTA was written to OceanDNA-b7188/markers.fasta
[2023-03-15 05:51:49,947] [INFO] Task started: Blastn
[2023-03-15 05:51:49,947] [INFO] Running command: blastn -query OceanDNA-b7188/markers.fasta -db /var/lib/cwl/stg144d979e-3473-4042-9b2e-d20754fa1fae/dqc_reference/reference_markers.fasta -out OceanDNA-b7188/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:51:50,540] [INFO] Task succeeded: Blastn
[2023-03-15 05:51:50,543] [INFO] Selected 15 target genomes.
[2023-03-15 05:51:50,543] [INFO] Target genome list was writen to OceanDNA-b7188/target_genomes.txt
[2023-03-15 05:51:50,553] [INFO] Task started: fastANI
[2023-03-15 05:51:50,553] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bf84cf1-bdab-4cbf-ba0d-1fc9a53d2e97/OceanDNA-b7188.fa --refList OceanDNA-b7188/target_genomes.txt --output OceanDNA-b7188/fastani_result.tsv --threads 1
[2023-03-15 05:51:59,481] [INFO] Task succeeded: fastANI
[2023-03-15 05:51:59,481] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg144d979e-3473-4042-9b2e-d20754fa1fae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:51:59,481] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg144d979e-3473-4042-9b2e-d20754fa1fae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:51:59,491] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:51:59,491] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:51:59,491] [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
Gillisia marina	strain=CBA3202	GCA_000258765.1	1167637	1167637	type	True	78.0829	273	851	95	below_threshold
Gillisia mitskevichiae	strain=DSM 19839	GCA_003634585.1	270921	270921	type	True	78.0534	352	851	95	below_threshold
Gillisia hiemivivida	strain=IC154	GCA_007997295.1	291190	291190	type	True	77.9829	337	851	95	below_threshold
Gillisia limnaea	strain=DSM 15749	GCA_000243235.1	195907	195907	type	True	77.1312	230	851	95	below_threshold
Antarcticibacterium flavum	strain=KCTC 52984	GCA_006159205.1	2058175	2058175	type	True	76.8996	169	851	95	below_threshold
Salegentibacter holothuriorum	strain=DSM 23405	GCA_900168045.1	241145	241145	type	True	76.5698	186	851	95	below_threshold
Salegentibacter agarivorans	strain=DSM 23515	GCA_900113135.1	345907	345907	type	True	76.4616	179	851	95	below_threshold
Zunongwangia atlantica	strain=22II14-10F7	GCA_002094855.1	1502297	1502297	type	True	76.3735	177	851	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	76.3394	159	851	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	76.3064	68	851	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	75.9465	68	851	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	75.6647	75	851	95	below_threshold
Aquimarina muelleri	strain=KCTC 12285	GCA_014651355.1	279356	279356	type	True	75.5879	92	851	95	below_threshold
Aquimarina muelleri	strain=DSM 19832	GCA_000430665.1	279356	279356	type	True	75.5432	96	851	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	75.4201	61	851	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:51:59,492] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7188/tc_result.tsv
[2023-03-15 05:51:59,494] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:51:59,494] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:51:59,494] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg144d979e-3473-4042-9b2e-d20754fa1fae/dqc_reference/checkm_data
[2023-03-15 05:51:59,495] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:51:59,501] [INFO] Task started: CheckM
[2023-03-15 05:51:59,501] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7188/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7188/checkm_input OceanDNA-b7188/checkm_result
[2023-03-15 05:52:42,659] [INFO] Task succeeded: CheckM
[2023-03-15 05:52:42,660] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:52:42,681] [INFO] ===== Completeness check finished =====
[2023-03-15 05:52:42,682] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:52:42,682] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7188/markers.fasta)
[2023-03-15 05:52:42,683] [INFO] Task started: Blastn
[2023-03-15 05:52:42,683] [INFO] Running command: blastn -query OceanDNA-b7188/markers.fasta -db /var/lib/cwl/stg144d979e-3473-4042-9b2e-d20754fa1fae/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7188/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:52:43,615] [INFO] Task succeeded: Blastn
[2023-03-15 05:52:43,618] [INFO] Selected 10 target genomes.
[2023-03-15 05:52:43,618] [INFO] Target genome list was writen to OceanDNA-b7188/target_genomes_gtdb.txt
[2023-03-15 05:52:43,627] [INFO] Task started: fastANI
[2023-03-15 05:52:43,627] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bf84cf1-bdab-4cbf-ba0d-1fc9a53d2e97/OceanDNA-b7188.fa --refList OceanDNA-b7188/target_genomes_gtdb.txt --output OceanDNA-b7188/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:52:50,691] [INFO] Task succeeded: fastANI
[2023-03-15 05:52:50,698] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:52:50,698] [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
GCF_900104765.1	s__Gillisia sp900104765	84.949	625	851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	98.23	98.23	0.92	0.92	2	-
GCF_000403785.1	s__Gillisia sp000403785	78.5237	351	851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000258765.1	s__Gillisia marina	78.0829	273	851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634585.1	s__Gillisia mitskevichiae	78.0562	351	851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364325.1	s__Gillisia sp002364325	78.0495	264	851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997295.1	s__Gillisia hiemivivida	77.9782	338	851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	95.35	95.35	0.83	0.83	2	-
GCF_000243235.1	s__Gillisia limnaea	77.121	231	851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gillisia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900168045.1	s__Salegentibacter holothuriorum	76.5622	188	851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113135.1	s__Salegentibacter agarivorans	76.4733	178	851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Salegentibacter	95.0	97.64	95.65	0.87	0.86	4	-
GCF_002094855.1	s__Zunongwangia atlantica	76.3699	176	851	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zunongwangia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:52:50,700] [INFO] GTDB search result was written to OceanDNA-b7188/result_gtdb.tsv
[2023-03-15 05:52:50,701] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:52:50,704] [INFO] DFAST_QC result json was written to OceanDNA-b7188/dqc_result.json
[2023-03-15 05:52:50,704] [INFO] DFAST_QC completed!
[2023-03-15 05:52:50,704] [INFO] Total running time: 0h1m19s