[2023-03-19 01:13:44,419] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:13:44,419] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:13:44,419] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0a415c0-7b46-410f-a731-6c2472b014da/dqc_reference
[2023-03-19 01:13:45,544] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:13:45,544] [INFO] Task started: Prodigal
[2023-03-19 01:13:45,544] [INFO] Running command: cat /var/lib/cwl/stgef7e42a2-cd02-49b0-85b1-613382f60036/OceanDNA-b11392.fa | prodigal -d OceanDNA-b11392/cds.fna -a OceanDNA-b11392/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:14:01,256] [INFO] Task succeeded: Prodigal
[2023-03-19 01:14:01,256] [INFO] Task started: HMMsearch
[2023-03-19 01:14:01,256] [INFO] Running command: hmmsearch --tblout OceanDNA-b11392/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0a415c0-7b46-410f-a731-6c2472b014da/dqc_reference/reference_markers.hmm OceanDNA-b11392/protein.faa > /dev/null
[2023-03-19 01:14:01,442] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:14:01,442] [INFO] Found 6/6 markers.
[2023-03-19 01:14:01,461] [INFO] Query marker FASTA was written to OceanDNA-b11392/markers.fasta
[2023-03-19 01:14:01,462] [INFO] Task started: Blastn
[2023-03-19 01:14:01,462] [INFO] Running command: blastn -query OceanDNA-b11392/markers.fasta -db /var/lib/cwl/stgf0a415c0-7b46-410f-a731-6c2472b014da/dqc_reference/reference_markers.fasta -out OceanDNA-b11392/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:14:02,118] [INFO] Task succeeded: Blastn
[2023-03-19 01:14:02,119] [INFO] Selected 19 target genomes.
[2023-03-19 01:14:02,119] [INFO] Target genome list was writen to OceanDNA-b11392/target_genomes.txt
[2023-03-19 01:14:02,128] [INFO] Task started: fastANI
[2023-03-19 01:14:02,129] [INFO] Running command: fastANI --query /var/lib/cwl/stgef7e42a2-cd02-49b0-85b1-613382f60036/OceanDNA-b11392.fa --refList OceanDNA-b11392/target_genomes.txt --output OceanDNA-b11392/fastani_result.tsv --threads 1
[2023-03-19 01:14:15,209] [INFO] Task succeeded: fastANI
[2023-03-19 01:14:15,209] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0a415c0-7b46-410f-a731-6c2472b014da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:14:15,209] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0a415c0-7b46-410f-a731-6c2472b014da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:14:15,225] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:14:15,226] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 01:14:15,226] [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
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	80.1175	521	857	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	80.0957	523	857	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	79.5878	447	857	95	below_threshold
Winogradskyella ludwigii	strain=HL116	GCA_013403985.1	2686076	2686076	type	True	79.4242	464	857	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	79.3175	443	857	95	below_threshold
Winogradskyella marina	strain=F6397	GCA_015645385.1	2785530	2785530	type	True	79.2595	417	857	95	below_threshold
Winogradskyella helgolandensis	strain=Z963	GCA_013404085.1	2697010	2697010	type	True	79.2294	430	857	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	78.8797	417	857	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	78.8046	397	857	95	below_threshold
Winogradskyella schleiferi	strain=Z215	GCA_013394655.1	2686078	2686078	type	True	78.729	394	857	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	78.6728	390	857	95	below_threshold
Winogradskyella eckloniae	strain=EC29	GCA_013249045.1	1089306	1089306	type	True	78.658	406	857	95	below_threshold
Winogradskyella aurantia	strain=WNB302	GCA_002266855.1	1915063	1915063	type	True	77.0561	195	857	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	76.9563	159	857	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.8827	172	857	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	76.6344	154	857	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.6021	138	857	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.5736	165	857	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.5152	133	857	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:14:15,226] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11392/tc_result.tsv
[2023-03-19 01:14:15,226] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:14:15,227] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:14:15,227] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0a415c0-7b46-410f-a731-6c2472b014da/dqc_reference/checkm_data
[2023-03-19 01:14:15,228] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:14:15,252] [INFO] Task started: CheckM
[2023-03-19 01:14:15,252] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11392/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11392/checkm_input OceanDNA-b11392/checkm_result
[2023-03-19 01:14:56,632] [INFO] Task succeeded: CheckM
[2023-03-19 01:14:56,632] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.42%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 01:14:56,635] [INFO] ===== Completeness check finished =====
[2023-03-19 01:14:56,635] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:14:56,635] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11392/markers.fasta)
[2023-03-19 01:14:56,636] [INFO] Task started: Blastn
[2023-03-19 01:14:56,636] [INFO] Running command: blastn -query OceanDNA-b11392/markers.fasta -db /var/lib/cwl/stgf0a415c0-7b46-410f-a731-6c2472b014da/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11392/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:14:57,561] [INFO] Task succeeded: Blastn
[2023-03-19 01:14:57,562] [INFO] Selected 13 target genomes.
[2023-03-19 01:14:57,562] [INFO] Target genome list was writen to OceanDNA-b11392/target_genomes_gtdb.txt
[2023-03-19 01:14:57,573] [INFO] Task started: fastANI
[2023-03-19 01:14:57,573] [INFO] Running command: fastANI --query /var/lib/cwl/stgef7e42a2-cd02-49b0-85b1-613382f60036/OceanDNA-b11392.fa --refList OceanDNA-b11392/target_genomes_gtdb.txt --output OceanDNA-b11392/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:15:07,324] [INFO] Task succeeded: fastANI
[2023-03-19 01:15:07,332] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:15:07,332] [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_016744625.1	s__Winogradskyella sp016744625	82.6447	621	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828715.1	s__Winogradskyella sp000828715	80.161	524	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297365.1	s__Winogradskyella echinorum	80.109	521	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000171875.1	s__Winogradskyella sp000171875	80.0768	529	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364335.1	s__Winogradskyella sp002364335	79.8924	482	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386165.1	s__Winogradskyella eximia	79.6867	490	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860565.1	s__Winogradskyella psychrotolerans_B	79.6397	461	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403985.1	s__Winogradskyella ludwigii	79.4135	465	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249065.1	s__Winogradskyella litoriviva	79.3188	443	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015645385.1	s__Winogradskyella sp015645385	79.2494	419	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002682935.1	s__Winogradskyella sp002682935	78.713	377	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013249045.1	s__Winogradskyella eckloniae	78.6586	406	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019203985.1	s__Winogradskyella sp019203985	78.5901	401	857	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:15:07,332] [INFO] GTDB search result was written to OceanDNA-b11392/result_gtdb.tsv
[2023-03-19 01:15:07,332] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:15:07,334] [INFO] DFAST_QC result json was written to OceanDNA-b11392/dqc_result.json
[2023-03-19 01:15:07,334] [INFO] DFAST_QC completed!
[2023-03-19 01:15:07,334] [INFO] Total running time: 0h1m23s